|  | 
This page contains an alphabetical listing of the annotation tracks available
on various Genome Browser assemblies. This page was last updated on 
3 March 2005 and is no longer maintained. For more current information on 
a specific annotation track, see the description page associated with the
track in the Genome Browser.  
To learn more about configuring and using the tracks displayed in the 
Genome Browser track window, see the section
Interpreting and fine-tuning the Genome 
Browser display in the Genome Browser User's Guide. 
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	      [Z] 2X Reg PotentialThis track displays the 2-way regulatory potential (RP) score computed from 
alignments of the human and mouse assemblies. RP scores compare frequencies of 
short alignment patterns between regulatory elements and neutral DNA.
 
		| -- | Display conventions: 
	This track uses the display conventions for wiggle tracks. |  | -- | Table details: 
	To view a text version of the data set, select the 
	regPotential2X positional table in the Table Browser. To view the table
	definition, click 
	here. |  3X Reg PotentialThis track displays the 3-way regulatory potential (RP) score computed from 
alignments of the human, mouse, and rat assemblies. RP scores compare frequencies of 
short alignment patterns between regulatory elements and neutral DNA.
 
		| -- | Display conventions: 
	This track uses the display conventions for wiggle tracks. |  | -- | Table details: 
	To view a text version of the data set, select the 
	regPotential3X positional table in the Table Browser. To view the table
	definition, click 
	here. |  Acembly GenesThis track shows gene models reconstructed solely from mRNA and EST evidence 
by Danielle and Jean Thierry-Mieg and Vahan Simonyan using the Acembly program. 
Acembly attempts to find the best alignment of each mRNA against the genome, 
and considers alternative splice models. If more than one gene model is 
produced that has statistical significance, all of these models are
displayed.
 
		| -- | Display conventions: 
	This track uses the display conventions for gene prediction
	tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show 
	position information, links to translated protein, predicted mRNA, and genomic
	sequence, and a link to an extensive text and graphical annotation of 
	supporting data at NCBI's AceView. |  | -- | Table details: 
	To view a text version of the data set, select the 
	acembly positional table in the Table Browser. To view the table
	definition, click 
	here. |  Affy GNF1HThis track shows the location of the sequences used for the selection of probes 
on Affymetrix GNF1H chips.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	In dense or packed display mode, the track shows averages of related
	tissues. In full display mode, all tissues are displayed. Click on an 
	individual tissue entry to show a gene expression map for all tissues in 
	the experiment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyGnf1h positional table in the Table Browser. To view the table
	definition, click here. |  Affy GNF1MThis track shows the location of the sequences used for the selection of probes 
on Affymetrix GNF1M chips.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	In dense or packed display mode, the track shows averages of related
	tissues. In full display mode, all tissues are displayed. Click on an 
	individual tissue entry to show a gene expression map for all tissues in 
	the experiment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyGnf1m positional table in the Table Browser. To view the table
	definition, click here. |  Affy GNF1HThis track shows the location of the sequences used for the selection of probes 
on Affymetrix GNF1M chips.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	In dense or packed display mode, the track shows averages of related
	tissues. In full display mode, all tissues are displayed. Click on an 
	individual tissue entry to show a gene expression map for all tissues in 
	the experiment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyGnf1m positional table in the Table Browser. To view the table
	definition, click here. |  Affy MOE430This track shows the location of the sequences used for 
the selection of probes on the Affymetrix Mouse MOE430 set of chips (A and B).
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	Clicking on an item in one of the fuller modes displays positional
	and % identity information. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyMOE430 positional table in the Table Browser. To view the table
	definition, click here. |  Affy RAE230This track shows the location of the sequences used for the selection of probes 
on Affymetrix RAE230 chips.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	In dense or packed display mode, the track shows averages of related
	tissues. In full display mode, all tissues are displayed. Click on an 
	individual tissue entry to show a gene expression map for all tissues in 
	the experiment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyRAE230 positional table in the Table Browser. To view the table
	definition, click here. |  Affy RG-U34AThis track shows the location of the sequences used for the selection of probes 
on Affymetrix RG-U34A chips.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	In dense or packed display mode, the track shows averages of related
	tissues. In full display mode, all tissues are displayed. Click on an 
	individual tissue entry to show a gene expression map for all tissues in 
	the experiment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyU34A positional table in the Table Browser. To view the table
	definition, click here. |  Affy U74This track shows the location of sequences used for 
the selection of probes on the Affymetrix MG-U74v2 set of chips (A, B, and C).
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	Clicking on an item in one of the fuller modes displays positional
	and % identity information. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyU74 positional table in the Table Browser. To view the table
	definition, click here. |  Affy U95This track shows the location of the consensus and exemplar sequences used for 
the selection of probes on the Affymetrix HG-U95Av2 chip.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	Clicking on an item in one of the fuller modes displays positional
	and % identity information. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyU95 positional table in the Table Browser. To view the table
	definition, click here. |  Affy U133This track shows the location of the consensus and exemplar sequences used for 
the selection of probes on the Affymetrix HG-U133A and HG-U133B chips.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	Clicking on an item in one of the fuller modes displays positional
	and % identity information. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyU133 positional table in the Table Browser. To view the table
	definition, click here. |  Affy U133Plus2This track shows the location of the consensus and exemplar sequences used for 
the selection of probes on the Affymetrix HG-U133 Plus 2.0 chip.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	Clicking on an item in one of the fuller modes displays positional
	and % identity information. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyU133Plus2 positional table in the Table Browser. To view the table
	definition, click here. |  Affy Zebrafish (Zebrafish)This track shows the location of the sequences used for the selection of probes 
on the Affymetrix Zebrafish chip.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	In dense or packed display mode, the track shows averages of related
	tissues. In full display mode, all tissues are displayed. Click on an 
	individual tissue entry to show a gene expression map for all tissues in 
	the experiment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyZebrafish positional table in the Table Browser. To view the table
	definition, click here. |  All Ciona ESTsSee the description for Human ESTs.
 Alt-SplicingThis track summarizes the alternative splicing shown in the mRNA and EST tracks.
 
		| -- | Display conventions: 
	Exons are represented by blocks; possible splice junctions by lines. 
	In full mode with the resolution set to approximately gene-level, 
	alternative exons are laid out with minimal overlap and are therefore
	easier to view. The level of shading of exons and splice junctions 
	reflects the quantity of ESTs and mRNAs that contain that exon or splice 
	junction. |  | -- | Track details: 
	Clicking on an item in one of the fuller modes displays positional 
	information and alt-splicing plots, as well as a link to a zoomed-in
	browser view of that feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	altGraphX positional table in the Table Browser. To view the table
	definition, click here. |  A. gambiae Chain This track shows A. gambiae genomic alignments to the selected genome using 
blastz and axtChain. See the Human Chain track description for more information.
 A. gambiae ESTsSee the description for Human ESTs.
 A. gambiae mRNAsSee the description for Human mRNAs.
 A. gambiae Net This track shows the best A. gambiae chain for every part of the selected genome.
See the Human Net track description for more information.
 A. mellifera Chain This track shows A. mellifera genomic alignments to the selected genome using 
blastz and axtChain. See the Human Chain track description for more information.
 A. mel. ESTsA. mellifera ESTs. See the description for Human ESTs.
 A. mel. mRNAsA. mellifera mRNAs. See the description for Human mRNAs.
 A. mellifera Net This track shows the best A. mellifera chain for every part of the selected 
genome.  See the Human Net track description for more information.
 Anopheles EcoresThis track shows Anopheles evolutionary conserved regions (ecores) computed 
against the selected assembly genome by the Exofish program at Genoscope. For 
information on this track, see the Human Ecores track description.
 AssemblyThis track shows the draft assembly of the human genome. This assembly merges
contigs from overlapping draft and finished clones into longer sequence 
contigs. The sequence contigs are ordered and oriented when possible by mRNA, 
EST, paired plasmid reads (from the SNP Consortium) and BAC end sequence pairs.
 
		| -- | Display conventions:
	In dense display mode, this track depicts in alternating gold and brown the 
	path through the draft and finished clones (aka the golden path) used to 
	create the assembled sequence. Individual boxes show the assembly extractable 
	from a single clone fragment. Where gaps exist in the path, spaces are shown 
	between the gold and brown blocks. If the relative order and orientation of 
	the contigs between the two blocks is known, a line is drawn to bridge the 
	blocks. The display must be sufficiently zoomed in to view the gap and bridge 
	features. |  | -- | Track details: 
	Clicking on an item in full display mode will show information about the
	clone fragment and bases, position information, and the DNA sequence
	corresponding to the fragment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	gold positional table in the Table Browser. To view the table
	definition, click here. |  BAC End PairsThis track shows the genome sequence of bacterial artificial chromosomes 
(BACs) in which a small amount of the both ends have been sequenced to place 
the full insert on the assembly. A valid pair of BAC end sequences must be 
separated by at least 50Kb but no more than 600Kb, and must have opposite 
orientations.  Strand assignment follows 
Clone Registry 
storage conventions.  The BAC end sequences are placed on the assembled 
sequence using BLAT.
 
		| -- | Display conventions: 
	The sequenced BAC ends are represented by black boxes connected by a
	line with hatch marks indicating the direction of transcription. |  | -- | Track details: 
	Clicking on an entry in full display mode will show hyperlinks to the
	NCBI clone registry and GenBank, position information, and genomic
	alignments. |  | -- | Table details: 
	To view a text version of the data set, select the 
	bacEndPairs positional table in the Table Browser. To view the table
	definition, click here. |  BactigsThe rat genome assembly is pieced together from bactig assemblies rather than clone-by-clone assemblies. Bactigs are reassemblies of the reads
from sets of overlapping skimmed BAC clones, including mapped whole shotgun
reads. The assembly process reworks the contigs (splitting some) and
selects them under more stringent criteria than is used for the BAC submissions.
 
		| -- | Display conventions:
	Bactig positions are indicated by rectangular blocks. Bactig names are 
	of the form gaab_gnmm, the internal names of the two bracketing 
	projects. |  | -- | Track details: 
	Clicking on an entry in full display mode will show position information
	and the first and last contig in the bactig. |  | -- | Table details: 
	To view a text version of the data set, select the 
	bactigPos positional table in the Table Browser. To view the table
	definition, click here. |  Base PositionShows the chromosomal coordinates as numbered starting from the telomere of 
the short p arm. The coordinates differ between assemblies.
 
		| -- | Display conventions:
	Clicking on a position in this track will zoom in the display by 3x,
	centered around the click. This track has only on and off modes, and no 
	dense mode. |  | -- | Track details: 
	None. |  | -- | Table details: 
	None. |  BDGP Genes (D. melanogaster)This track shows protein-coding genes annotated by the Berkeley Drosophila 
Genome Project (BDGP). 
For a description of the methods used to generate the 
data, see the BDGP Methods web page.
 
		| -- | Display conventions:
	This track uses the display conventions for known genes and gene 
	predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display provides links to the 
	corresponding protein, mRNA, and genomic sequences, and related links to 
	outside databases. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn
	on codon coloring for the track. Click the "Codon coloring 
	help" link on the page for more information about this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	bdgpGene positional table in the Table Browser. To view the table
	definition, click here. |  BDGP Insertions (D. melanogaster)This track shows the locations of P transposable element insertions from 
P-Screen, the online database of the 
BDGP 
Gene Disruption Project. When a stock order number is available 
for the strain, a link is provided to the Bloomington stock center. The 
project's strain library contains more than 7140 strains disrupting at least 
5362 different genes, corresponding to 39% of the 13,666 currently annotated 
Drosophila genes.
 
		| -- | Display conventions:
	Triangular arrows on the reference sequence indicate the 
	approximate locations where P elements have inserted themselves
	in the mutant strain. Left-pointing arrows indicate insertions
	that are oriented in a backwards direction; right-pointing arrows 
	indicated forwards-oriented insertions.
	The item name indicates the strain having a P element disruption
	at that location. |  | -- | Track details: 
	Clicking on an entry in full display mode provides position and strand
	information, strain name, a link to the Bloomington stock center (when
	applicable), and a link to the underlying DNA for the feature. |  | -- | Track configuration: 
	The track description page allows the user to set the minimum 
	unnormalized score of the data displayed in the track. |  | -- | Table details: 
	To view a text version of the data set, select the 
	pscreen positional table in the Table Browser. To view the table
	definition, click here. |  BDGP Non-Coding Genes (D. melanogaster)This track shows non-coding genes annotated by the Berkeley Drosophila 
Genome Project (BDGP). 
For a description of the methods used to generate the 
data, see the BDGP Methods web page.
 
		| -- | Display conventions:
	This track uses the display conventions for known genes and gene 
	predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display provides links to the 
	corresponding protein, mRNA, and genomic sequences, and related links to 
	outside databases. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn
	on codon coloring for the track. Click the "Codon coloring 
	help" link on the page for more information about this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	bdgpNonCoding positional table in the Table Browser. To view 
	the table definition, click here. |  Best HumanThis track displays Blastz alignments of the Nov. 2002 human draft
assembly to the mouse genome filtered to display only the best alignment for any
given region of the mouse genome.  See the track's description page for more 
details.
 
		| -- | Display conventions:
	This track uses the display conventions for cross-species synteny 
	tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show mouse and 
	human position information, alignment details, and a link to a detailed
	view of parts of the alignment. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn 
	on the chromosome color track or to filter the display output by 
	chromosome. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blastzBestHuman positional table in the Table Browser. To view the table
	definition, click here. |  Best MouseThis track displays Blastz alignments of the specified mouse draft
assembly to the human genome filtered to display only the best alignment for any
given region of the human genome.  See the track's description page for more 
details.
 
		| -- | Display conventions:
	This track uses the display conventions for cross-species synteny 
	tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show human and 
	mouse position information, alignment details, and a link to a detailed
	view of parts of the alignment. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn 
	on the chromosome color track or to filter the display output by 
	chromosome. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blastzBestMouse positional table in the Table Browser. To view the table
	definition, click here. |  Best RatThis track displays Blastz alignments of the Nov. 2002 rat draft
assembly to the mouse genome filtered to display only the best alignment for any
given region of the mouse genome.  See the track's description page for more 
details.
 
		| -- | Display conventions:
	This track uses the display conventions for cross-species synteny 
	tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show rat and 
	mouse position information, alignment details, and a link to a detailed
	view of parts of the alignment. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn 
	on the chromosome color track or to filter the display output by 
	chromosome. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blastzBestRat positional table in the Table Browser. To view the table
	definition, click here. |  BGI CoverageThis track shows areas of coverage for genomic regions of 3 alternate strains of 
chicken sequenced by the Beijing Genomics Institute (BGI): Broiler, Layer, and Silkie. 
Single reads from those three strains were mapped to the reference assembly for the Red 
Jungle Fowl (RJF).
 
		| -- | Display conventions:
	Coverage regions are represented by solid blocks. |  | -- | Track details: 
	Clicking on an entry in full display mode shows position information and a link 
	to the DNA underlying this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	bgiCov positional table in the Table Browser. To view the table
	definition, click here. |  BGI GenesThis track shows protein-coding genes annotated by the Beijing Genomics Institute (BGI). 
If Single Nucleotide Polymorphisms (SNPs) and/or insertions/deletions from BGI have been 
associated with a gene, those SNPs are listed with links to their details pages.
 
		| -- | Display conventions:
	This track uses the display conventions for known genes and gene 
	predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode shows position information, GO and 
	InterPro terms from BGI, BGI SNPs associated with the gene, and links to the
	predicted protein, mRNA, and genomic sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	bgiGene positional table in the Table Browser. To view the table
	definition, click here. |  BGI SNPsThis track shows the single nucleotide polymorphisms (SNPs) and/or insertions/deletions 
(indels) determined by the Beijing Genomics Institute (BGI). Genomic sequence reads from 
3 alternate strains of chicken (Broiler, Layer and Silkie) were used to determine the SNPs 
relative to the reference assembly for the Red Jungle Fowl (RJF). SNPs and indels are 
associated with genes (annotations by BGI until Ensembl annotations are ready). 
Information on the association can be displayed along with a link to the details page 
for the gene.
 
		| -- | Display conventions: 
	SNP locations are indicated by thin vertical lines. SNP names are of the format
	[supercontig].[contig].[position].[type].[strain]. See the track description
	page for more information. |  |  | -- | Track details: 
	Clicking in full display mode shows information position and SNP information, 
	primer sequences, and a link to the DNA underlying the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	bgiSnp positional table in the Table Browser. To view the table
	definition, click here. |  Binomial ConsThis track displays the conservation scores resulting from an analysis of Zoo 
blastz alignments. Conservation scores were generated by weighing the relative 
contribution of each species sequence to the overall conservation score, based 
on how diverged each species was from the reference sequence. This weighting 
scheme was determined by calculating the neutral substitution
rates at 4-fold degenerate positions.
 
		| -- | Display conventions:
	This track uses the display conventions for wiggle tracks. |  | -- | Track configuration: 
	The track description page contains options to configure 
	several of the graph characteristics. To read more information
	about each option, click the "Graph configuration help" link. |  | -- | Track details: 
	Clicking on one of the peaks in the track when in full display mode will 
	show genome position information for the window and a link to the
	underlying DNA sequence. In full mode in 
	a zoomed-out display, detailed information may not be accessible for an 
	individual feature. In this case, zoom in and try again. |  | -- | Table details: 
	To view a text version of the data set, select the 
	binomialCons2 positional table in the Table Browser. To view the table
	definition, click here. |  Blastz MouseThis track displays blastz alignments of the specified mouse draft
assembly to the selected genome.
 
		| -- | Display conventions:
	This track uses the display conventions for cross-species synteny 
	tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will position information 
	for the mouse and the selected genome, alignment details, and a link 
	to a detailed
	view of parts of the alignment. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn 
	on the chromosome color track or to filter the display output by 
	chromosome. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blastzX positional table in the Table Browser, where X represents
	the assembly version in which you are interested, e.g. Mm4). To view the
	table definition, click here. |  Briggsae Aligns This track shows best-in-genome C. elegans/C. briggsae alignments 
based on the C. elegans/C. briggsae alignment net, i.e. the best 
chain for every part of the C. elegans genome. See the D. pseud Aligns 
track description for more information.
 Briggsae Blastz This track displays Blastz alignments of the C. briggsae assembly to 
selected assembly. See the Blastz Mouse track description for more information.
 Briggsae Chain This track shows C. briggsae genomic alignment to the selected genome 
using blastz and axtChain. See the Human Chain track description for more 
information.
 Briggsae Net This track shows the best C. briggsae chain for every part of the 
selected genome. 
See the Human Net track description for more information.
 Briggsae Waba This track shows alignments of C. briggsae to C. elegans 
using the Wobble Aware Bulk Aligner (WABA), an alignment tool developed by 
Jim Kent for doing large-scale alignments between genomic DNA of different 
species.
 
		| -- | Display conventions: 
	Aligning regions are represented by blocks. The shading indicates the
	hidden Markov model (HMM) states of the bases. |  | -- | Track details: 
	Clicking on an item in full display mode will show alignment details
	and the HMM state for each alignment pair`. Markov model . |  | -- | Table details: 
	To view a text version of the data set, select the 
	wabaCbr positional table in the Table Browser. To view the table
	definition, click here. |  C. briggsae ESTsSee the description for Human ESTs.
 C. briggsae mRNAsSee the description for Human mRNAs.
 C. elegans ESTsSee the description for Human ESTs.
 C. elegans mRNAsSee the description for Human mRNAs.
 Chicken Chain This track shows chicken genomic alignment to the selected genome using blastz 
and axtChain. See the Human Chain track description for more information.
 Chicken ESTsSee the description for Human ESTs.
 Chicken mRNAsSee the description for Human mRNAs.
 Chicken Net This track shows the best chicken chain for every part of the selected genome. 
See the Human Net track description for more information.
 Chimp BAC Ends This track displays BAC alignments of the chimp genome (Pan troglodytes) to human, based on BLAT alignments from Ingo Ebersberger, Joshua Bacher, and Svante Pääbo at the MPI for Evolutionary Anthropology.
 
		| -- | Display conventions: 
	This track follows the display conventions for BLAT tracks. |  | -- | Track details: 
	Clicking on an item will show details on the chimp sequence fragment and 
	alignment details, as well as a link to more information on the track data. |  | -- | Table details: 
	To view a text version of the data set, select the 
	chimpBac positional table in the Table Browser. To view the table
	definition, click here. |  Chimp Blat This track displays alignments of the chimp genome (Pan troglodytes) to human, based on Blat alignments from Ingo Ebersberger, Joshua Bacher, and Svante Pääbo at the MPI for Evolutionary Anthropology.
 
		| -- | Display conventions: 
	This track follows the display conventions for BLAT tracks. |  | -- | Track details: 
	Clicking on an item will show details on the chimp sequence fragment and 
	alignment details, as well as a link to more information on the track data. |  | -- | Table details: 
	To view a text version of the data set, select the 
	chimpBlat positional table in the Table Browser. To view the table
	definition, click here. |  Chimp Chain This track shows chimp genomic alignment to the selected genome using blastz and
axtChain. See the Human Chain track description for more information.
 Chimp DeletionsThis track displays regions of the human assembly that are deleted in the 
chimp assembly. Only regions of between 80 and 12000 bases are included. 
The name of each deletion is a unique pointer to that deletion followed by an 
underscore and then its length. A similar track, showing human deletions in the 
chimp assembly, appears in the chimp Genome Browser.
 
		| -- | Display conventions:
	Deletions are indicated by thin vertical lines. |  | -- | Track details: 
	Clicking on a deletion in full display mode provides the item name,
	position, genomic size, and a link to the DNA underlying the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	chimpDels positional table in the Table Browser. To view the table
	definition, click here. |  Chimp DiffThis track shows simple differences between chimp alignments and the human 
assembly within regions of high quality chimp sequence. For a difference to be 
included in this track, it had to meet the following criteria:
 
Only reciprocal best chimp alignments were considered for this track (see the 
Chimp Net track description page for more information about this alignment 
strategy).the difference must occur at a base of quality 30 or better 
all bases within an 11-base window around this base must have a quality of 
25 or better 
the 11-base window must contain no more than two base differences 
no insertions or deletions may be present within the window 
 
		| -- | Display conventions:
	Differences are indicated by thin vertical lines. |  | -- | Track details: 
	Clicking on a deletion in full display mode provides the item name,
	position, genomic size, and a link to the DNA underlying the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	chimpSimpleDiff positional table in the Table Browser. To view 
	the table definition, click here. |  Chimp ESTsSee the description for Human ESTs.
 Chimp mRNAsSee the description for Human mRNAs.
 Chimp Recip Chain This track displays "reciprocal best" human/chimpanzee genomic 
alignment chains.
 
		Track details: 
	In full display mode, clicking on a box shows details information about 
	the chain as a whole, while clicking on a line shows information
	about the gap. The detailed information is useful in determining the 
	cause of the gap or, for lower level chains, the genomic 
	rearrangement.| -- | Display conventions:
	This track uses the display conventions for chain tracks. |  | -- | Table details: 
	To view a text version of the data set, select the 
	rBestChainPanTro1 positional table in the Table Browser. 
	To view the table definition, click here. |  Chimp Recip Net This track shows the reciprocal best alignment net between the chimpanzee and the
selected genome assembly. Due to the draft nature of the
initial chimp assembly, this track uses a "reciprocal best" strategy that
attempts to minimize paralog fill-in for missing orthologous chimp sequence by
filtering out of the human net all sequences not in the chimp side of the net.
See the track description page for more information about the methods used to
generate this track.
 
		| -- | Display conventions:
	This track uses the display conventions for net tracks. |  | -- | Track details: 
	In full display mode, clicking on a box shows details information about 
	the chain as a whole, while clicking on a line shows information
	about the gap. The detailed information is useful in determining the 
	cause of the gap or, for lower level chains, the genomic 
	rearrangement. |  | -- | Table details: 
	To view a text version of the data set, select the 
	rBestNetPanTro1 positional table in the Table Browser, where X
	is the assembly version in which you're interested. To view the table
	definition, click here. |  Chromosome BandThe light and dark blocks indicate the approximate location of
traditional cytological bands seen on Giemsa-stained chromosomes at an 850
band resolution. The bands were mapped
by fluorescent in situ hybridization (FISH) of large-insert clones
with sequence tags, STS markers, and BAC end sequence locations.  
resolution of 862 bands genome-wide. The uncertainty of 
mapping to band staining is still a megabase or more.
 
		| -- | Display conventions:
	The light and dark blocks indicate the approximate location of the bands on the
	assembly sequence. |  | -- | Track details: 
	Clicking on a band in full display mode will show more details about
	the track, a discussion of mapping methods used, and lab
	credits. |  | -- | Table details: 
	To view a text version of the data set, select the 
	cytoBand positional table in the Table Browser. To view the table
	definition, click here. |  C. intestinalis ESTsSee the description for Human mRNAs.
 C. intestinalis mRNAsSee the description for Human mRNAs.
 Ciona mRNAsSee the description for Human mRNAs.
 ConservationThis track shows a measure of evolutionary conservation among several species, 
based on a phylogenetic hidden Markov model (phylo-HMM). The multiz 
alignments of the various assemblies were used to construct the annotation.
The raw conservation scores used to generate this track can be downloaded
from the [assembly_name]/phastCons directory on the Genome Browser 
FTP 
server.
 
		| -- | Display conventions:
	In full display mode, the track displays pairwise alignments of several
	species aligned to the human genome. The pairwise alignments 
	are displayed in standard UCSC browser "dense" mode using a grey-scale 
	density gradient.  When zoomed-in to the base-display level, the track 
	shows the base composition of each alignment. The numbers and symbols on 
	the "human gap" line indicate the lengths of gaps in the human sequence 
	at those alignment positions. If the gap size is greater than 9, the 
	"+" symbol is displayed. The track must be zoomed-in to 30,000
	or fewer bases to access detailed information about the 
	alignments at a specific position. |  | -- | Track details: 
	Clicking on an entry in full display mode will show detailed alignment 
	information for each of the organisms. |  | -- | Table details: 
 
		| -- | To view an index of the multiz multiple alignment data used to 
	generate
 	this track, select one of the following positional tables from the 
	Table Browser: multiNway (most recent assemblies), 
 	mz*_pHMM (hg16), mz*_phast (canFam1, dm1), 
        c_briggsae_pwMaf (C. elegans). 
 |  | -- | To view the wiggle track data used to generate the conservation 
	display, select onf of the following positional tables: phastCons
	(most assemblies), mz*_wig (hg16), mz*phast_wig 
	(canFam1, dm1). 
 |  | -- | To download the raw conservation scores displayed in the 
	Conservation track, download the data files from the 
	[assembly_name]/phastCons directory on the Genome Browser 
	FTP 
	server. 
 |  | -- | To view the table definition for the multiz multiple alignment
	tables, click here. 
 |  | -- | To view the table definition for the phastCons tables, click here. 
 |  |  Contamination (Chicken)This track shows locations of likely contamination in the chicken (galGal2) assembly, i.e. 
high-scoring alignments of E.coli, vector and maize mitochondrion sequence. The 
name of each feature indicates the type of contamination found there.
 
		| -- | Display conventions:
	Area of contamination are represented by solid blocks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show the type of contamination,
	position and size information, and a link to display the DNA for the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	contamination positional table in the Table Browser. 
	To view the table definition, click here. |  Contigs (Zebrafish)This track shows the whole genome shotgun (WGS) contigs of the zebrafish assembly from 
The Wellcome Trust Sanger Institute.
 
		| -- | Display conventions: 
	Contigs are represented by blocks that indicate their location
	on the assembly sequence. |  | -- | Track details: 
	Clicking on an item in full display mode will show contig and positional 
	information. |  | -- | Table details: 
	To view a text version of the data set, select the 
	ctgPos2 positional table in the Table Browser. To view the table
	definition, click here. |  CoverageShows the coverage level and positions of all clones in the genome.
 
		| -- | Display conventions:
	In dense display mode, this track shows the coverage level of the
	genome. Finished regions are shown in black. Draft regions are
	shown in various shades of gray that correspond to the level of
	coverage: 
 
		o White: no coverage (gap) o Light Gray: predraft (less than 4x shotgun)
 o Medium Gray: draft (at least 4x shotgun)
 o Dark Gray: covered by multiple draft clones
 o Black: covered by a finished clone
 |  |  | In full display mode, this track shows the position of each clone that
	aligns to the genome sequence. Finished clones are shown in black and
	unfinished clones are shown in gray. In assemblies prior to the April 
	2003 human release,
	coverage for each unfinished clone is represented as a 
	two-tiered gray box.  The fragments inside the clone are shown as numbered 
	black boxes. Their positions correspond to their relative assembly placement, 
	including strand assignment. For some assemblies, clones in the sequencing 
	center tiling path are shown with blue rather than gray backgrounds. |  | -- | Track details: 
	Clicking on an item in full display mode will show the clone hyperlink to 
	GenBank record and the fasta format sequence (one per fragment). |  | -- | Table details: 
	To view a text version of the data set, select the 
	clonePos positional table in the Table Browser. To view the table
	definition, click here. |  Cow Chain This track shows cow genomic alignments to the selected genome using 
blastz and axtChain. See the Human Chain track description for more information.
 Cow ESTsSee the description for Human ESTs.
 Cow mRNAsthe description for Human mRNAs.
 Cow Net This track shows the best cow chain for every part of the selected 
genome.  See the Human Net track description for more information.
 CpG Islands  This track shows CpG islands, areas rich in the dinucleotide CG. A CpG island
is a region where C's followed by G's (CpGs) are present at significantly 
higher levels than is typical for the genome as a whole. The CpG islands 
displayed in this browser are all at least 200 bases long, and have a GC 
content of at least 50%.
 
CpG islands are associated with genes, particularly housekeeping genes, in 
vertebrates. They are particularly common near transcription start sites, and 
may be associated with promoter regions. Normally a CpG is rare in vertebrate 
DNA because the C's in such an arrangement tend to be methylated. This 
methylation helps distinguish the newly synthesized DNA strand from the parent 
strand, which aids in the final stages of DNA proofreading after duplication. 
However, over evolutionary time, methylated C's tend to turn into T's due to 
spontaneous deamination. The result is that CpGs are relatively rare unless 
there is selective pressure to keep them or a region is not methylated for 
some reason, perhaps having to do with the regulation of gene expression. 
 
		| -- | Display conventions:
	CpG islands are represented by green boxes. Darker green items indicate CpG 
	islands that contain  300 or more bases. |  | -- | Display conventions:
	Clicking on a CpG entry in full display mode will show basic track information, 
	detailed information about the CpG island, and sequence information. |  | -- | Table details: 
	To view a text version of the data set, select the 
	cpgIsland positional table in the Table Browser. To view the table
	definition, click here. |  C. savignyi BlatThis track displays translated BLAT alignments of the C. savignyi genome 
against the C. intestinalis genome assembly. The alignments 
were done with Blat in translated protein mode
requiring 2 nearby 4-mer matches to trigger a detailed alignment. The 
C. intestinalis genome was masked with RepeatMasker and Tandem Repeats Finder 
before running Blat.
 
		| -- | Display conventions:
	This track uses the display conventions for BLAT tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode displays links to the DNA
	sequence and the alignment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blatCioSav1 positional table in the Table Browser. To view the table
	definition, click here. |  Cytokine Genes (Tetraodon)This track shows cytokine genes annotated by human experts using 
sequence similarity information between Tetraodon and human, mouse and 
zebrafish cytokine protein and nucleotide sequences. These annotations 
are available only on the following chromosomes: 1, 2, 3, 4, 7, 8, 10, 12, 13, 
15, 16, 1_random, 3_random, and Un_random.
 
		| -- | Display conventions: 
	This track uses the display conventions for gene prediction tracks. |  | -- | Track configuration: 
	The track description page contains a control that can be used to turn 
	on codon coloring. |  | -- | Track details: 
	Clicking on a track feature in full display mode shows position 
	information and provides links to the translated protein, predicted mRNA,
	and genome sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	cytokines positional table in the Table Browser. To view the table
	definition, click here. |  DBTSS mRNAThis track shows RefSeq mRNA sequences extended to the 5' end, based on sequence
information in the DataBase of 
Transcriptional Start Sites (DBTSS). For more information on the process used
to construct this track, refer to the track's description page.
 
		| -- | Display conventions:
	This track uses the display conventions for PSL alignment tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show PSL output information
	about the item. |  | -- | Table details: 
	To view a text version of the data set, select the 
	dbtssAli positional table in the Table Browser. To view the table
	definition, click here. |  D. mel. ChainThis track shows D. melanogaster genomic alignment to the selected genome using 
blastz and axtChain. See the Human Chain track description for more information.
 D. mel. NetThis track shows the best D. melanogaster chain for every part of the selected 
genome. See the Human Net track description for more information.
 D. mel. Proteins (A. gambiae, A. melliferaThis track contains tBLASTn alignments of the peptides from the predicted and 
known genes identified in the specified version of FlyBase.
 
		| -- | Display conventions:
	This track uses the display conventions for PSL alignment tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will provide positional
	information, a link to the related FlyBase record, protein length, and
	links to the alignment and peptide sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blastDm1FB positional table in the Table Browser. To view the table
	definition, click here. |  D. melanogaster ESTsSee the description for Human ESTs.
 D. melanogaster mRNAsSee the description for Human mRNAs.
 DNAse HyperSens (Zoo)This track depicts DNAse I hypersensitive sites (DHS) mapped to the human genome 
sequence. Each track element represents the surrounding 500 bp from the position 
of the estimated DHS, as determined from Smith et al. (2000) "Multiple 
Potential Intragenic Regulatory Elements in the CFTR Gene", Genomics
64(1):90-6.
 
		| -- | Display conventions:
	Each DHS is depicted by a block representing the 500 bp surrounding the
	position of the estimated DHS. |  | -- | Track details: 
	Clicking on an entry in full display mode will show position information
	and a link to the underlying DNA sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	dhs positional table in the Table Browser. To view the table
	definition, click here. |  Dog Chain This track shows dog genomic alignment to the selected genome using blastz 
and axtChain. See the Human Chain track description for more information.
 Dog ESTsSee the description for Human ESTs.
 Dog mRNAsSee the description for Human mRNAs.
 Dog Net This track shows the best dog chain for every part of the selected genome. 
See the Human Net track description for more information.
 D. ananassae Chain This track shows D. ananassae genomic alignments to the selected genome using 
blastz and axtChain. See the Human Chain track description for more information.
 D. anan. mRNAsD. ananassae mRNAs. See the description for Human mRNAs.
 D. ananassae Net This track shows the best D. ananassae chain for every part of the selected 
genome.  See the Human Net track description for more information.
 D. mojavensis Chain This track shows D. mojavensis genomic alignments to the selected genome using 
blastz and axtChain. See the Human Chain track description for more information.
 D. moj. mRNAsD. mojavensis mRNAs. See the description for Human mRNAs.
 D. mojavensis Net This track shows the best D. mojavensis chain for every part of the selected 
genome.  See the Human Net track description for more information.
 D. pseudo. Aligns  (D. melanogaster)This track shows blastz scores from the 
D. pseudoobscura/D. melanogaster alignment Net track, i.e. the best 
D. pseudoobscura/D. melanogaster chain for every part of the 
D. melanogaster genome.
 
		| -- | Display conventions:
	In dense display mode, darker shading indicates those best chained and
	netted alignments that have the higher scores. In full display mode, 
	the height of the vertical line corresponds to the score. |  | -- | Track details: 
	Clicking on an entry in full display mode will show position information
	and -- when zoomed in to the base level -- the base composition of the 
	alignments. |  | -- | Table details: 
	To view a text version of the data set, select the 
	axtNetX positional table in the Table Browser, where X
	represents the assembly that is being aligned, e.g. Dp1. To view the 
	table definition, click here. |  D. pseudo. Chain  (D. melanogaster)This track shows D. pseudoobscura genomic alignment to the selected 
genome using blastz and axtChain. See the Human Chain track description for 
more information.
 D. pseudo. ESTsD. pseudoobscura ESTs. See the description for Human ESTs.
 D. pseudo. mRNAsD. pseudoobscura mRNAs. See the description for Human mRNAs.
 D. pseudo. Net  (D. melanogaster)This track shows the best D. pseudoobscura chain for every part of 
the selected genome. See the Human Net track description for more information.
 D. virilis Chain This track shows D. virilis genomic alignments to the selected genome using 
blastz and axtChain. See the Human Chain track description for more information.
 D. vir. mRNAsD. virilis mRNAs. See the description for Human mRNAs.
 D. virilis Net This track shows the best D. virilis chain for every part of the selected 
genome.  See the Human Net track description for more information.
 D. yakuba Chain This track shows D. yakuba genomic alignments to the selected genome using 
blastz and axtChain. See the Human Chain track description for more information.
 D. yakuba ESTsD. yakuba ESTs. See the description for Human ESTs.
 D. yakuba mRNAsD. yakuba mRNAs. See the description for Human mRNAs.
 D. yakuba Net This track shows the best D. yakuba chain for every part of the selected 
genome.  See the Human Net track description for more information.
 Duplications This track shows genomic 
duplications greater than 1,000 bp if not overly repeat-masked. Duplications are 
more common in unordered and unassigned contigs (i.e., difficult to assign to their 
proper position).
 
		| -- | Display conventions:
	Duplications are show as red if 99%+ identity (likely unmerged assembly 
	overlap artifact), as yellow for 98-99% identity (origin uncertain), and as 
	gray for 90-98% identity (below draft sequencing error, often genuine 
	pericentromeric or subtelomeric duplication). |  | -- | Track details: 
	In the left panel of the browser, duplications are named by the chromosome 
	and start of the other member of the duplication pair. Clicking on an 
	individual duplication gives details of both locations and match quality 
	parameters. |  D. yakuba ESTsSee the description for Human ESTs.
 D. yakuba mRNAsSee the description for Human mRNAs.
 ECgene GenesThis track shows gene predictions generated by combining genome-based EST 
clustering and transcript assembly methods. The EST clustering is based on 
genomic alignment of mRNA and ESTs similar to that of NCBI's UniGene for the 
human genome. The transcript assembly procedure yields gene models for each 
cluster that include alternative splicing variants. This algorithm was developed 
by Prof. Sanghyuk Lee's Lab of Bioinformatics at Ewha Womans University in 
Seoul, Korea. For more information, see the 
ECgene web site.
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode brings up basic track
	information, links to the predicted mRNA, genomic sequence, and 
	comparative sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	ECgene positional table in the Table Browser. To view the table
	definition, click here. |  Elegans BlastzThis track displays Blastz alignments of the C. elegans assembly
to the C. briggsae assembly
 
		| -- | Display conventions:
	This track uses the display conventions for cross-species synteny 
	tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show human and 
	mouse position information, alignment details, and a link to a detailed
	view of parts of the alignment. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn 
	on the chromosome color track or to filter the display output by 
	chromosome. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blastzX positional table in the Table Browser, where X
	represents the C. elegans assembly, e.g. Ce2. To view the table
	definition, click here. |  Elegans ChainThis track shows C. elegans genomic alignment to the selected 
genome using blastz and axtChain. See the Human Chain track description for 
more information.
 ENCODE RegionsThis track depicts target regions for the NHGRI ENCODE project, which is 
described in The 
ENCODE Project: ENCyclopedia of DNA Elements. The long-term goal of this 
project is to identify all functional elements in the human genome sequence to 
facilitate a better understanding of human biology and disease. 
During the pilot phase, 44 regions comprising 30 Mb -- approximately 1% of 
the human genome -- have been selected for intensive study to identify, locate 
and analyze functional elements within the regions. These targets are being 
studied by a diverse public research consortium to test and evaluate the 
efficacy of various methods, technologies, and strategies for locating genomic 
features. The outcome of this initial phase will form the basis for a 
larger-scale effort to analyze the entire human genome. 
See the track description page for more information.
 
		| -- | Display conventions:
	ENCODE regions are represented by blocks. |  | -- | Track details: 
	Clicking on an item in full display mode shows position information
	 and provides a link to the DNA sequence associated with this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	encodeRegions positional table in the Table Browser, where X
	is the assembly version in which you're interested. To view the table
	definition, click here. |  Ensembl ESTsThis track shows gene predictions from Project Ensembl based on ESTs. For a description of
the methods used in Ensembl gene prediction, refer to
The Ensembl genome database project, Nucleic Acids Research, 2002, 30(1) 38-41.
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode brings up basic track
	information, links to the translated protein, predicted mRNA, and
	genomic sequences, plus a link to detailed supporting evidence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	ensEst positional table in the Table Browser. To view the table
	definition, click here. |  Ensembl GenesThis track shows gene predictions from Project Ensembl. For a description of
the methods used in Ensembl gene prediction, refer to
The Ensembl genome database project, Nucleic Acids Research, 2002, 30(1) 38-41.
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode brings up basic track
	information, links to the translated protein, predicted mRNA, and
	genomic sequences, plus a link to detailed supporting evidence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	ensGene positional table in the Table Browser. To view the table
	definition, click here. |  Exofish ecoresThe track displays conserved regions, generally protein-coding homologs, 
from a genomics project of long random reads in the 
pufferfish, Tetraodon 
nigroviridis.  Ecore is an acronym for evolutionary conserved 
region. The data was 
used to estimate the number of human genes.
 
		| -- | Display conventions:
	Regions of greater homology are displayed in a darker blue. |  | -- | Track details: 
	Clicking on an entry in full mode brings up information on a particular 
	ecore, access the relevant Genoscope page, and the relevant DNA. |  | -- | Table details: 
	To view a text version of the data set, select the 
	exoFish positional table in the Table Browser. To view the table
	definition, click here. |  ExoniphyThe exoniphy program identifies evolutionarily conserved protein-coding exons in multiple
sequences aligned with multiz using a phylogenetic hidden Markov model (phylo-HMM), a 
statistical model that simultaneously describes exon structure and exon evolution.
 
		| -- | Display conventions:
	Evoluntionarily-conserved protein-coding exons are represented by blocks.
	Arrows indicated the direction of transcription. |  | -- | Track details: 
	Clicking on an entry in full mode displays positional information and related 
	sequence links. |  | -- | Table details: 
	To view a text version of the data set, select the 
	exoniphy positional table in the Table Browser. To view the table
	definition, click here. |  Fgenesh++ GenesThis tracks shows Fgenesh++ gene predictions based on Softberry Inc.'s gene-finding
software. Fgenesh++ uses both hidden Markov models (HMMs) and protein 
similarity to find genes in a completely automated manner, with less
emphasis on cDNA/EST data. See the paper 
"Ab 
initio gene finding in Drosophila genomic DNA", Genome Research 10(4) 516-522 
for more information.
 
NOTE: The data in the softberryGene.txt and 
softberryPep.txt tables is free for academic and nonprofit use. Commercial users 
should contact Softberry Inc..
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode brings up basic track
	information, links to the translated protein, predicted mRNA, and
	genomic sequences, plus a link to the best matching protein at GenBank. |  | -- | Table details: 
	To view a text version data set, select the 
	softberryGene positional table in the Table Browser. 
	To view the table definition, click here. |  First EFThis track displays predictions from First Exon Finder (FirstEF), a 5' terminal 
exon and promoter prediction program.
Three types of predictions are shown: exon, promoter and CpG window. If two 
consecutive predictions are separated by less than 1000 bp, FirstEF treats them 
as one cluster of alternative first exons that may belong to same gene. 
Each predicted exon is either CpG-related or non-CpG-related, based on a score 
of the frequency of CpG dinucleotides. An exon is classified as CpG-related if 
the CpG score is greater than a threshhold value and non-CpG-related if 
less than the threshold. If an exon is CpG-related, its associated CpG-window is displayed.
 
		| -- | Display conventions:
	This track uses the display conventions for BLAT tracks. Higher CpG 
	scores are shown in darker shades of gray/black. The cluster 
	number is displayed in parentheses in the item label. For example, 
	"exon(405-)" represents the exon prediction in cluster number 
	405 on the minus strand. The exon, promoter and CpG-window are 
	interconnected by this cluster number. Alternative predictions within 
	the same cluster are denoted by "#N" where "N" is the 
	serial number of an alternative prediction in the cluster. |  | -- | Track details: 
	Clicking on an entry in full display mode displays probability, size, 
	and position information, and a link to the DNA sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	firstEF positional table in the Table Browser. To view the table
	definition, click here. |  Fish Blat This track displays translated alignments of 728 million bases
of Tetraodon nigroviridis whole genome shotgun reads vs. the
draft human genome. Areas painted by this track are quite likely to be coding
regions. The alignments were done with BLAT in translated protein mode
requiring 2 nearby 4-mer matches to trigger a detailed alignment. The human 
genome was masked with RepeatMasker and Tandem Repeats Finder before running 
BLAT. The Tetraodon sequence was provided by Genoscope.
 
		| -- | Display conventions:
	This track uses the display conventions for BLAT tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode brings up links to the DNA
	sequence and the alignment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blatFish positional table in the Table Browser. To view the table
	definition, click here. |  FISH ClonesShows the location of fluorescent in situ hybridization (FISH) mapped clones along 
the draft assembly sequence.
 
		| -- | Display conventions:
	The green blocks depict the clone placements on the assembly sequence. |  | -- | Track details:
	Clicking on a specific marker in full display mode will show information on 
	clone placement, clone registry, its STS markers, and BAC end sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	fishClones positional table in the Table Browser. To view the table
	definition, click here. |  FlyBase Genes (D. melanogaster)This track shows protein-coding genes annotated by FlyBase (version 3.2).
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display provides links to the 
	corresponding protein, mRNA, and genomic sequences, microarray expression data, 
	protein structure information, homology information and related links to 
	several tools and databases, including FlyBase. |  | -- | Table details: 
	To view a text version of the data set, select the 
	bdgpGene positional table in the Table Browser. To view the table
	definition, click here. |  FlyBase Non-coding (D. melanogaster)This track shows non-coding genes annotated by FlyBase (version 3.2).
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display provides links to FlyBase and BDGP,
	basic track information, and links to the corresponding predicted genomic and
	predicted mRNA sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	bdgpGene positional table in the Table Browser. To view the table
	definition, click here. |  FlyReg (D. melanogaster)This track shows DNase I Footprint data from the
FlyReg version 2.0 
database. FlyReg provides access to results of the systematic curation and 
genome annotation of 1,350 DNase I footprints for the fruitfly 
D. melanogaster reported in Bergman, C.M. et al., 
Drosophila DNase I footprint database: a systematic genome 
annotation of transcription factor binding sites in the fruitfly, D. 
melanogaster, Bioinformatics 2004 Nov. 30 [Epub ahead of 
print].
 
		| -- | Display conventions:
	Footprint regions are represented by blocks. |  | -- | Track details: 
	Clicking on an entry in full display provides footprint information,
	links to external databases, and a link to view the related genomic
	DNA. When available, a footprint motif is also displayed, based on a 
	MEME matrix computed by Dan Pollard on the set of footprints for 
	the factor. |  | -- | Table details: 
	To view a text version of the data set, select the 
	flyreg2 positional table in the Table Browser. To view the table
	definition, click here. |  Fosmid End PairsA valid pair of fosmid end sequences must be at least 32Kb but no more than 47Kb 
away from each other. The orientation of the first fosmid end sequence must be 
"+" and the orientation of the second fosmid end sequence must be "-". End 
sequences were trimmed at the NCBI using ssahaCLIP written by Jim Mullikan. 
The trimmed end sequences were placed on the assembled sequence using Jim 
Kent's BLAT program.
 
		| -- | Display conventions:
	This track uses the display conventions for PSL alignment tracks. |  | -- | Track details:
	Clicking on an entry in full display mode will show position information 
	and provide links to genomic alignments of the Fosmid ends. |  | -- | Table details: 
	To view a text version of the data set, select the 
	fosEndPairs positional table in the Table Browser. To view the table
	definition, click here. |  Fugu Blat This track displays translated BLAT alignments of Takifugu rubripes whole genome 
shotgun reads against the currently selected genome assembly. The alignments 
were done with BLAT in translated protein mode
requiring 2 nearby 4-mer matches to trigger a detailed alignment. The human 
genome was masked with RepeatMasker and Tandem Repeats Finder before running 
BLAT. The fugu sequence used in this track is version 3.0, provided by the
DOE Joint Genome Institute (JGI).
 
		| -- | Display conventions:
	This track uses the display conventions for BLAT tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode brings up links to the DNA
	sequence and the alignment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blatFugu positional table in the Table Browser. To view the table
	definition, click here. |  Fugu Chain This track shows Fugu genomic alignment to the selected genome using blastz and
axtChain.
 
		| -- | Display conventions:
	This track uses the display conventions for chain tracks. |  | -- | Track details: 
	Clicking on an item in full display mode shows position information
	in the Fugu and the selected genome, the chain ID and score, and provides 
	links to view details of parts of the chain or to open the Fugu browser 
	to the corresponding position. |  | -- | Table details: 
	To view a text version of the data set, select the 
	chainFrX positional table in the Table Browser, where X
	is the assembly version in which you're interested. To view the table
	definition, click here. |  Fugu EcoresThis track shows Fugu evolutionary conserved regions (ecores) computed against 
the selected assembly genome by the Exofish program at Genoscope. For 
information on this track, see the Human Ecores track description.
 Fugu ESTsSee the description for Human ESTs.
 Fugu mRNAsSee the description for Human mRNAs.
 Fugu Net This track shows the best Fugu chain for every part of the selected genome.
See the Human Net track description for more information.
 GapThis track depicts gaps in the assembly. These gaps - with the
exception of intractable heterochromatic gaps - are closed
during the finishing process.
 
		| -- | Display conventions:
	Gaps are represented as black boxes. If the relative order and 
	orientation of the contigs on either side of the gap is known from mRNA, 
	ESTs, or paired BAC end reads, it is a "bridged" gap and a white line is 
	drawn through the black box representing the gap. The display must be 
	sufficiently zoomed in to view these features: at a coarser scale, the 
	gaps can appear to coalesce in the the graphic. In full display mode, 
	the gap label indicates the type
	of gap (see below) and whether the gap is bridged. |  |  | Strand misorientation errors can occur adjacent to unbridged gaps.
	Unbridged gaps are assigned somewhat arbitrary sequence sizes (runs of 
	N's in genomic DNA); uncertainty is less with bridged gaps. A gap within 
	contig fragments of a clone is typically smaller than a gap between 
	draft clones. |  | -- | Track details: 
	Clicking on an item in full display mode will show the gap type,
	bridging information and position information about the gap. Unfinished 
	clones may have gaps of uncertain size between fragments. |  | -- | Table details: 
	To view a text version of the data set, select the 
	gap positional table in the Table Browser. To view the table
	definition, click here. |  GC PercentThis shows the percentage of bases that are G or C in a 5-base window. High GC 
content is associated with gene rich areas.
 
		| -- | Display conventions: 
	This track uses the display conventions for wiggle tracks. |  | -- | Track configuration: 
	The track description page contains options to configure 
	several of the graph characteristics. To read more information
	about each option, click the "Graph configuration help" link. |  | -- | Track details: 
	Clicking on one of the peaks in the track when in full display mode will 
	show position information and provide a link to the underlying DNA
	sequence.  In full mode in a zoomed-out display, detailed information 
	may not be accessible for an individual feature. In this case, zoom in 
	and try again. |  | -- | Table details: 
	To view a text version of the data set, select the 
	gc5Base positional table in the Table Browser. To view the table
	definition, click here. |  GC Samples (Zoo)This track shows the percentage of bases that are G or C in small regions across 
the genome. Windows with high GC content are plotted at higher vertical 
positions than windows with low GC content. High GC content is associated with 
gene-rich areas.
 
		| -- | Display conventions: 
	This track uses the display conventions for wiggle tracks. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn 
	on the chromosome color track or to filter the display output by 
	chromosome. |  | -- | Track details: 
	Clicking on one of the peaks in the track when in full display mode will 
	show position information and provide a link to the underlying DNA
	sequence.  In full mode in 
	a zoomed-out display, detailed information may not be accessible for an 
	individual feature. In this case, zoom in and try again. |  | -- | Table details: 
	To view a text version of the data set, select the 
	pGC positional table in the Table Browser. To view the table
	definition, click here. |  Gene Annotations (Zoo)This track displays NISC-generated, curated gene annotations for each of the 
zoo species and human. Exon locations of known genes were determined by aligning 
human and/or mouse reference cDNA sequences with each species' assembled genomic 
sequence. Any splice-site consensus, exon structure, or protein translation 
errors encountered were manually inspected and corrected.
 
		| -- | Display conventions: 
	This track uses the display conventions for gene prediction tracks. As with other
	tracks in this category, it may be necessary to zoom in to 
	display entries in full display mode due to the 300 line display 
	limit. |  | -- | Track details: 
	Clicking on an item in full mode provides position, size, and score 
	information, and a link to dsplay the DNA sequence associated with this 
	feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	pjt_gene positional table in the Table Browser. To view the table
	definition, click here. |  Gene BoundsThis track shows the boundaries of genes and the direction of transcription as 
deduced from clustering spliced ESTs and mRNAs against the genome. When there 
are many spliced variants of the same gene, this track shows the variant that 
spans the greatest distance in the genome.
 
		| -- | Display conventions: 
	This track uses the display conventions for EST tracks. As with other
	tracks in this category, it may be necessary to zoom in to 
	display entries in full display mode due to the 300 line display 
	limit. |  | -- | Track details: 
	Clicking on an item in full mode provides position, size, and score 
	information, and a link to dsplay the DNA sequence associated with this 
	feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	rnaCluster positional table in the Table Browser. To view the table
	definition, click here. |  Geneid Gene PredictionsThis track shows gene predictions from the geneid program, which is
being developed at the Grup de Recerca en Informatica Biomedica at IMIM
in Barcelona. Geneid uses information from sequence signals involved in
genes specification, as well as coding coding statistics, to define exons
and genes.
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode brings up basic track
	information, plus links to the translated protein, predicted mRNA, and
	genomic sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	geneid positional table in the Table Browser. To view the table
	definition, click here. |  GenMapDB ClonesThis track shows BAC clones from the 
GenMapDB 
database placed on the draft sequence using BAC end sequence information and 
confirmed using STS markers by Vivian Cheung's lab at the Department of 
Pediatrics, University of Pennsylvania.
 
		| -- | Display conventions:
	The clone positions are shown in black. |  | -- | Track details: 
	Clicking on an entry in full display mode brings up basic position
	information and additional information about the clones and STS markers. |  | -- | Table details: 
	To view a text version of the data set, select the 
	genMapDb positional table in the Table Browser. To view the table
	definition, click here. |  Genoscope GAZE (Tetraodon)This track shows Genoscope gene model annotations from the GAZE program 
written by Kevin Howe. These annotaions were computed using GAZE with a i
custom-designed gene model. GAZE integrates information from Geneid, 
Genscan, Exofish (Human, Mouse and Fugu), Genewise (Human and Mouse) and 
Tetraodon cDNAs.
 
		| -- | Display conventions: 
	This track uses the display conventions for gene prediction tracks. |  | -- | Track configuration: 
	The track description page contains a control that can be used to turn 
	on codon coloring. |  | -- | Track details: 
	Clicking on a track feature in full display mode shows position 
	information and provides links to the translated protein, predicted mRNA,
	and genome sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	gaze positional table in the Table Browser. To view the table
	definition, click here. |  Genscan GenesThis track shows gene predictions from 
GenScan. These predictions are based on transcriptional, translational, 
and donor and acceptor splicing signals, plus length and compositional 
distributions of exons, introns and intergenic regions. The program does not 
use similarity to known proteins like 
GenomeScan.  For a description of the Genscan program and the model that
underlies it, refer to Burge, C. and Karlin, S. (1997) 
Prediction of complete gene structures in human genomic
DNA. J. Mol. Biol. 268(1):78-94.
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show basic track
	information, plus links to the translated protein, predicted mRNA, and
	genomic sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	genscan positional table in the Table Browser. To view the table
	definition, click here. |  Genscan Genes (Zoo)This track shows gene predictions from the 
GenScan program written by Chris Burge.
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode shows basic track
	information and provides a link to view the underlying genomic sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	pjt_genscan positional table in the Table Browser. To view the table
	definition, click here. |  GNF Atlas 2This track shows expression data from the GNF (The Genomics Institute of the
Novartis Research Foundation) Gene Expression Atlas 2. The data contains 2 
replicates each of 61 mouse tissues and 79 human tissues run over Affymetrix 
microarrays. For more
information about the experiments, refer to the description page for this track.
 
		| -- | Display conventions:
	This track uses display conventions similar to those for PSL alignment tracks. |  | -- | Track details: 
	In dense or packed display mode, the track shows averages of related
	tissues. In full display mode, all tissues are displayed. Click on an 
	individual tissue entry to show a gene expression map for all tissues in 
	the experiment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	gnfAtlas2 positional table in the Table Browser. To view the table
	definition, click here. |  GNF RatioThis track shows expression data from GNF (The Genomics Institute of the
Novartis Research Foundation) using Affymetrix GeneChips. For more
information about the experiments, refer to the description page for this track.
 
		| -- | Display conventions:
	In dense display mode, the track color denotes the average signal over
	all experiments on a log base 2 scale. Lighter colors correspond
	to lower signals and darker colors correspond to higher signals. 
	In full display mode, the color of each item represents the log base 2 ratio 
	of the signal of that particular experiment to the median signal of all 
	experiments for that probe. |  | -- | Track configuration: 
	The track description page contains options to change the display mode,
	group the displayed results, and change the display colors. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyRatio positional table in the Table Browser. To view the table
	definition, click here. |  GNF U74AThis track shows expression data from GNF using the Affymetrix U74A chip.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	In dense or packed display mode, the track shows averages of related
	tissues. In full display mode, all tissues are displayed. Click on an 
	individual tissue entry to show a gene expression map for all tissues in 
	the experiment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyGnfU74A positional table in the Table Browser. To view the table
	definition, click here. |  GNF U74BThis track shows expression data from GNF using the Affymetrix U74B chip.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	In dense or packed display mode, the track shows averages of related
	tissues. In full display mode, all tissues are displayed. Click on an 
	individual tissue entry to show a gene expression map for all tissues in 
	the experiment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyGnfU74B positional table in the Table Browser. To view the table
	definition, click here. |  GNF U74CThis track shows expression data from GNF using the Affymetrix U74C chip.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	In dense or packed display mode, the track shows averages of related
	tissues. In full display mode, all tissues are displayed. Click on an 
	individual tissue entry to show a gene expression map for all tissues in 
	the experiment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyGnfU74C positional table in the Table Browser. To view the table
	definition, click here. |  Haplotype Blocks  (chr21)See the description for Perlegen.
 Haplotype Blocks (chr22)This track shows haplotype blocks on Chromosome 22 from The University of 
Oxford and The Wellcome Trust Sanger Institute, as described in
Dawson E. et. al. (2002), 
"A first-generation linkage disequilibrium map of human 
chromosome 22", Nature 418:544-8.
 
		| -- | Display conventions:
	The location of each haplotype block is represented by a blue horizontal 
	line with tall vertical blue bars at the first and last SNPs of
	the block. Blocks are displayed as starting at the first SNP and ending 
	at the last SNP of the block. Individual SNPs are denoted
	by smaller black vertical bars. At multi-megabase resolution in dense 
	display mode, clusters of tall blue bars may indicate hotspots
	for recombination. |  | -- | Track details: 
	Clicking on an entry in full display mode will show basic position
	information, SNP information for the block, and a link to sequence 
	information for the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	haplotype positional table in the Table Browser. To view the table
	definition, click here. |  H-Inv This track shows alignments of full-length cDNAs used as the basis of the 
H-Invitational Gene Database (HInv-DB). Entries in this track include 
gene structures, functions, functional domains, metabolic pathways, and many
other entities.
 
		| -- | Display conventions:
	This track uses the display conventions for PSL alignment tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode provides gene ID, cluster
	ID, and cDNA accession information and a link to sequence 
	information for the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	HInvGeneMrna positional table in the Table Browser. To view the table
	definition, click here. |  HOX Genes (Tetraodon chr2, 8, 9, 17, 21, and un_random only)This track shows HOX genes annotated using information on 
sequence similarity between Tetraodon vs. human, mouse and zebrafish HOX 
protein and nucleotide sequences.
 
		| -- | Display conventions:
	This track uses the display conventions for gene prediction tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode provides position, size, and
	CDS information, and links to the related translated protein, predicted
	mRNA, and genomic sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	hoxGenes positional table in the Table Browser. To view the table
	definition, click here. |  Human Best This track displays best-in-genome alignments of the specified human draft
assembly to the selected genome baed on the associated alignment net, i.e. the
best chain for every part of the human genome. See the track description page
for the Human Net track for more information about the methods used to generate
this track.
 
		| -- | Display conventions:
	This track uses the display conventions for cross-species synteny 
	tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show position information
	for the human alignment and the selected genome, alignment details, and 
	a link to a detailed view of parts of the alignment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	axtNetHgX positional table in the Table Browser, where 
	X is the assembly version in which you're interested. 
	To view the table definition, click here. |  Human Blat This track displays translated BLAT alignments of the human genome
vs. the mouse genome. 
The alignments were done with BLAT in translated protein mode using the
parameters -q=dnax -t=dnax and otherwise the default settings. Both
genomes were masked with RepeatMasker and Tandem Repeats Finder before
running BLAT. Places where more than 250 alignments occurred
over the same place were filtered out. Beware of alignments of greater
than 97% identity: these may reflect mouse contamination in the human
genome or human contamination in the mouse genome.
 
		| -- | Display conventions:
	This track uses the display conventions for a BLAT alignment track. |  | -- | Track details: 
	Clicking on an entry in full display mode will show basic track
	information and a link to sequence information for the alignment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blatHuman positional table in the Table Browser. To view the table
	definition, click here. |  Human Chain This track shows human genomic alignment to the selected genome using blastz and
axtChain.
 
		| -- | Display conventions:
	This track uses the display conventions for chain tracks. |  | -- | Track details: 
	Clicking on an item in full display mode shows position information
	in the mouse and the selected genome, the chain ID and score, and 
	provides links to view details of parts of the chain or to open the 
	mouse browser to the corresponding position. |  | -- | Table details: 
	To view a text version of the data set, select the 
	chainX positional table in the Table Browser, where X
	is the assembly version in which you're interested, e.g. Hg16. To view 
	the table definition, click here. |  Human Cons This track displays the conservation between the mouse and human genomes for 
50bp windows in the mouse genome that have at least 15bp aligned to human. The 
score for a window reflects the probability that the level of observed 
conservation in that 50bp region would occur by chance under neutral evolution. 
It is given on a logarithmic scale, and thus it is called the "L-score". An 
L-score of 1 means there is a 1/10 probability that the observed conservation 
level would occur by chance, an L-score of 2 means a 1/100 probability, an 
L-score of 3 means a 1/1000 probability, etc. The L-scores display as 
"mountain ranges".
 
		| -- | Display conventions:
	This track uses the display conventions for wiggle tracks. |  | -- | Track configuration: 
	The track description page contains options to configure 
	several of the graph characteristics. To read more information
	about each option, click the "Graph configuration help" link. |  | -- | Track details: 
	Clicking on one of the peaks in the track when in full display mode will 
	show human genome 
	position information for the window, as well as position information for 
	the corresponding region in the human genome. The details page provides 
	links to the underlying sequence for the alignment and to the sequence 
	underlying the individual alignment windows. In full mode in 
	a zoomed-out display, detailed information may not be accessible for an 
	individual feature. In this case, zoom in and try again. |  | -- | Table details: 
	To view a text version of the data set, select the 
	musHumL positional table in the Table Browser. To view the table
	definition, click here. |  Human DeletionsThis track displays regions of the chimp assembly that are deleted in the 
human assembly. Only regions of between 80 and 12000 bases are included. 
The name of each deletion is a unique pointer to that deletion followed by an 
underscore and then its length. A similar track, showing chimp deletions in the 
human assembly, appears in the human Genome Browser.
 
		| -- | Display conventions:
	Deletions are indicated by thin vertical lines. |  | -- | Track details: 
	Clicking on a deletion in full display mode provides the item name,
	position, genomic size, and a link to the DNA underlying the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	humanDels positional table in the Table Browser. To view the table
	definition, click here. |  Human EcoresThis track shows human evolutionary conserved regions (ecores) computed against 
the selected assembly by the Exofish program at Genoscope.
 
		| -- | Display conventions:
	This track uses display conventions similar to PSL alignment tracks. Each 
	singleton block corresponds to an ecore. Blocks connected by a 
	line correspond to an "ecotig", a set of colinear ecores in a 
	syntenic region. |  | -- | Track details: 
	Clicking on an entry in full display mode will show positional 
	information, 
	a link to the Exofish browser, and a link to display the DNA sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	ecores positional table in the Table Browser, where 
	X is the assembly version in which you're interested (e.g. 
	hg16). 
	To view the table definition, click here. |  Human ESTs This track shows alignments between Expressed Sequence Tags (ESTs) -
spliced and unspliced - in GenBank and the genome. ESTs are single read 
(typically approximately 500 base) sequences 
that usually represent fragments of transcribed genes. 
To view only spliced ESTs, see the Spliced EST track.
This track was generated by aligning human ESTs from GenBank against the
genome using the BLAT program. Note that the maximum intron length
allowed by BLAT is 500,000 bases, which may eliminate some ESTs with
very long introns that might otherwise align. When a single EST aligns
in multiple places, the alignment having the highest base identity is
found. Only alignments that have a base identity level within 1% of the
best are kept. Alignments must also have at least 93% base identity to be 
kept.
 
		| -- | Display conventions:
	This track uses the display conventions for EST tracks.  Hatch marks on the 
	introns indicate the direction of transcription. In the December 2001 
	assembly and later, this direction is taken by looking at the splice sites. 
	In previous assemblies, the direction of transcription was taken from the
	GenBank annotations, which frequently were inaccurate; these should be 
	verified in the details page alignment on the basis of the GT-AG splice 
	donor/acceptor rule.  As with otherEST tracks, it may be necessary to zoom 
	in to display entries in full display mode due to the 300 line display 
	limit. |  | -- | Track configuration: 
	The track description page contains a filter to restrict the display to 
	only those entries that match certain keywords and to change the color 
	of the selected entries. |  | -- | Track details: 
	Clicking on an individual EST entry will show basic track information,
	the accession number, GenBank highlights, and links to EST/Genomic
	Alignments. |  | -- | Table details: 
	To view a text version of the data set, select the 
	all_est positional table in the Table Browser. To view the table
	definition, click here. |  Human mRNAsThis track shows alignments between mRNAs from the current assembly in GenBank 
and the genome.  The mRNAs are aligned against the genome using the BLAT 
program. When a single mRNA aligns 
in multiple places, the alignment having the highest base identity is found. 
Only alignments that have a base identity level within 1% of the best
are kept. Alignments must also have at least 95% base identity
to be kept.
 
		| -- | Display conventions:
	This track follows the display conventions for PSL alignment tracks. |  | -- | Track configuration: 
	The track description page contains a filter to restrict the display to 
	only those entries that match certain keywords and to change the color 
	of the selected entries. |  | -- | Track details: 
	Clicking on an entry in full display mode will show a summary of the GenBank 
	entry on that mRNA, convenient hyperlinks to major databases, and base-by-base 
	mRNA/genomic alignments. |  | -- | Table details: 
	To view a text version of the data set, select the 
	all_mrna positional table in the Table Browser. To view the table
	definition, click here. |  Human NetThis track shows the best human chain for every part of the selected genome.
 
		| -- | Display conventions:
	This track uses the display conventions for net tracks. |  | -- | Track details: 
	In full display mode, clicking on a box shows details information about 
	the chain as a whole, while clicking on a line shows information
	about the gap. The detailed information is useful in determining the 
	cause of the gap or, for lower level chains, the genomic 
	rearrangement. |  | -- | Table details: 
	To view a text version of the data set, select the 
	netX positional table in the Table Browser, where X
	is the assembly version in which you're interested, e.g. Hg16. To view 
	the table definition, click here. |  Human ProteinsThis track shows tBLASTn alignments of the peptides from the predicted and 
known genes indentified in the specified Known Genes track.
 
		| -- | Display conventions:
	This track follows the display conventions for PSL alignment tracks. |  | -- | Track configuration: 
	The track description page contains options to configure the information shown
	in the track element labels. |  | -- | Track details: 
	Clicking on an entry in full display mode will show position information, 
	external links to human mRNA and UniProtKB information, and links to the alignment
	and peptide sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blastHg16KG positional table in the Table Browser. To view the table
	definition, click here. |  Human SyntenyThis track shows syntenous (corresponding) regions between mouse and human 
chromosomes. The track was created by passing a 100k non-overlapping window over 
the genome and using the blastz best in human genome alignments to look for
high-scoring regions where at least 40% of the bases aligned with the same 
region in mouse. 100k segments were joined together if they agreed in direction 
and were within 500kb of each other in the mouse genome and within 4mb of each 
other in the human. Gaps were joined between syntenic anchors if the bases 
between two flanking regions agreed with synteny (direction and human location). 
The syntenic block was extended to include these areas.
 
		| -- | Display conventions:
	This track uses the display conventions for synteny tracks. |  | -- | Track details: 
	Clicking on an item in full display mode shows details of the
	mouse-human correspondence and provides a link to the genomic sequence 
	for this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	syntenyHuman positional table in the Table Browser. To view the table
	definition, click here. |  Human TightThis track displays Blastz alignments of the human
assembly to the current genome, filtered by axtBest and
subsetAxt with very stringent constraints. See the track's description
page for more details.
 
		| -- | Display conventions:
	This track uses the display conventions for cross-species synteny 
	tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show position information
	for the human and the current genome, alignment details, and a link to 
	a detailed view of parts of the alignment. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn 
	on the chromosome color track or to filter the display output by 
	chromosome. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blastzTightHg positional table in the Table Browser, where
	X is the number of the assembly. To view the table
	definition, click here. |  JGI Genes (C. intestinalis)This track contains alignments of predicted transcripts from the DOE Joint Genome Institute 
(JGI) to the C. intestinalis genome.
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode brings up basic track
	information, plus links to the translated protein, predicted mRNA, and
	genomic sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	jgiGene positional table in the Table Browser. To view the table
	definition, click here. |  Known Genes The Known Genes track shows known protein coding genes based on proteins from 
UniProtKB the corresponding mRNAs from GenBank. 
Features are colored according to origin and review status:
 
All mRNAs of a species are aligned against the genome using the BLAT program. 
When a single mRNA aligns in multiple places, only the best alignments with at
least 98% sequence identity are kept. The set of alignments is further reduced 
by keeping only those mRNAs that are referenced by a protein in UniProtKB. 
When a single protein references multiple mRNAs, the best 
mRNA is chosen based on a quality score that depends on its length, how good its 
translation matches the protein sequence, and its release date. The resulting 
list of mRNA and protein pairs is trimmed by removing short invalid entries and 
consolidating entries with identical CDS regions. Finally, RefSeq entries 
derived from DNA sequences instead of mRNA sequences are added.
Black: Feature has a corresponding entry in the Protein Data Bank (PDB).
Dark blue: Feature has a corresponding protein in UniProtKB or a corresponding 
NCBI Reference Sequence mRNA with a "Reviewed" status. 
Lighter blue: Feature has a corresponding NCBI Reference 
Sequence mRNA with "Provisional" status. 
Lightest blue: All other features.
 
		| -- | Display conventions:
	This track uses the display conventions for known genes and gene 
	predictions tracks. See above description of color coding conventions. |  | -- | Track details: 
	Clicking on an entry in full display provides links to the 
	corresponding protein, mRNA, and genomic sequences, microarray expression data, 
	protein structure information, homology information and related links to 
	several tools and databases. |  | -- | Table details: 
	To view a text version of the data set, select the 
	knownGene positional table in the Table Browser. To view the table
	definition, click here. |  Map ContigsThis track shows the locations of contigs of clones on the physical map. 
In assembly versions prior to the August 6 2001 assembly, this track was
based on the Washington University accession map, which in turn was
based on a fingerprint contig (FPC) map described in 
'A physical map of the human genome' in Nature volume 409 pages 934-941.
Starting with the August 6 2001 assembly, this track is based on tiling path 
fingerprint (TPF) maps curated by the sequencing centers responsible for each 
chromosome.  The TPF maps are merged with the FPC map,
favoring the TPF map where conflicts occur. This step increases the
clone coverage substantially over that in the TPF maps. The clone contigs in
this merged map are shown in this track.
 
		| -- | Display conventions: 
	The clone contigs are represented by blocks that indicate their location
	on the assembly sequence. |  | -- | Track details: 
	Clicking on an item in full display mode will show a brief description of the 
	extent and number of clones in contig, and the DNA sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	ctgPos positional table in the Table Browser. To view the table
	definition, click here. |  Mapped Human (X. tropicalis)This track contains tBLASTn alignments of the peptides from the predicted 
and known genes identified in the specified version of the Known Genes track.
 
		| -- | Display conventions:
	This track follows the display conventions for BLAT tracks. |  | -- | Track details: 
	Clicking on an item in full display mode shows positional information,
	related mRNA and UniProtKB links, the protein length, and links to the
	alignment an peptide sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blastHg17KG positional table in the Table Browser. To view the 
	table definition, click here. |  MCS Binomial (Zoo)This track shows Multi-Species Conserved Sequences (MCSs) defined using a 
conservation score threshold from the binomial-based method
that selects the top 5% most conserved sequence.
 
		| -- | Display conventions:
	Sequence positions are depicted by blocks. |  | -- | Track details: 
	Clicking on an item in full display mode shows position and size 
	information, and provides a link to the underlying DNA sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	mcs_b positional table in the Table Browser. To view the 
	table definition, click here. |  MCS Inter (Zoo)This track shows Multi-Species Conserved Sequences (MCSs) found by intersecting 
the sequences generated using the binomial-based and parsimony p-value-based 
methods (see the MCS Binomial and MCS ParsPVal track descriptions).
 
		| -- | Display conventions:
	Sequence positions are depicted by blocks. |  | -- | Track details: 
	Clicking on an item in full display mode shows position and size 
	information, and provides a link to the underlying DNA sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	intersectingMCS positional table in the Table Browser. To view the 
	table definition, click here. |  MCS InterMerged (Zoo)Same as MCS Inter, but regions less than 10 bp apart have been merged into one 
region.
 
		| -- | Display conventions:
	Sequence positions are depicted by blocks. |  | -- | Track details: 
	Clicking on an item in full display mode shows position and size 
	information, and provides a link to the underlying DNA sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	intersectingMergedMCS positional table in the Table Browser. To 
	view the table definition, click here. |  MCS ParsPVal (Zoo)This track shows Multi-Species Conserved Sequences (MCSs) defined using a 
conservation score threshold from the parsimony p-value method
that selects the top 5% most conserved sequence.
 
		| -- | Display conventions:
	Sequence positions are depicted by blocks. |  | -- | Track details: 
	Clicking on an item in full display mode shows position and size 
	information, and provides a link to the underlying DNA sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	mcs_p positional table in the Table Browser. To view the 
	table definition, click here. |  MGC GenesThis track displays alignments between Mammalian Gene Collection (MGC) human mRNAs with full-length ORFs and the human genome.
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show basic track
	information and links to the mRNA, genomic, and comparative sequences. |  | -- | Track configuration: 
	The track description page offers configuration options that can be used to turn
	on codon coloring for the track. Click the "Codon coloring 
	help" link on the page for more information about this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	mgcGenes positional table in the Table Browser. To view the table
	definition, click here. |  MicrosatellitesThis track contains all perfect microsatellite repeats with between 2 and 10 bp 
repeat units and 10 or more perfect copies. Over 90% of the items will be 
multi-allelic polymorphisms. This track was created by using three programs: 
Tandyman, display_VNTR and Primeleftright. See the track description page for
more information.
 
		| -- | Display conventions: 
	Microsatellite locations are indicated by thin grey vertical lines. |  | -- | Track details: 
 	Clicking on an item in full display mode shows position information, 
	details about the repeat, and a link to the DNA sequence associated with
	the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	vntr positional table in the Table Browser. To view the table
	definition, click here. |  miRNA This track shows microRNAs from the 
miRNA Registry 
at the Wellcome Trust Sanger Institute.
 
		| -- | Display conventions: 
	Mature miRNAs (miRs) are represented by thick lines; the predicted 
	stem-loop portions of the primary transcripts are indicated by thinner 
	lines. miRNAs in the sense orientation are shown in black; those in the 
	reverse orientation are colored grey. When a single precursor produces 
	two mature miRs from its 5' and 3' parts, it is displayed twice with the 
	two different positions of the mature miR. |  | -- | Track details: 
	Clicking in full mode displays positional information and 
	a link to item's entry in the miRNA registry. |  | -- | Table details: 
	To view a text version of the data set, select the 
	miRNA positional table in the Table Browser. To view the table
	definition, click here. |  Most ConservedThis track shows predictions of conserved elements produced by the phastCons program. 
Predictions are based on a phylogenetic hidden Markov model (phylo-HMM), a type of 
probabilistic model that describes both the process of DNA substitution at each site in 
a genome and the way this process changes from one site to the next. For more 
information on the methods used to produce this track, see the track's description
page.
 
		| -- | Display conventions:
	Rectangular blocks indicate the positions of conserved elements. |  | -- | Track details: 
	Clicking on an entry in full display mode will show position information and
	a list of the top-scoring elements in the window. |  | -- | Table details: 
	To view a text version of the data set, select the phastConsElements
	positional table from the Table Browser.  To view the table definition, click
	here. |  Mouse Blat This track displays alignments of mouse genome to human. The mouse genomic 
DNA is from the Arachne assembly of mouse whole genome shotgun reads available 
at the Trace Repository. 
The alignments were done with BLAT in translated protein mode requiring 2 nearby 
4-mer matches to trigger a detailed alignment. The human genome was masked with 
RepeatMasker 
and Tandem Repeats Finder 
prior to running BLAT. Regions with more than 300 aligned reads were assumed novel 
repeat elements and filtered out. Alignments of greater than 97% identity may represent 
mouse contamination of human or vice versa.
 
		| -- | Display conventions: 
	This track follows the display conventions for BLAT tracks. |  | -- | Track details: 
	Clicking on an item will show details on mouse sequence fragment and 
	alignment details. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blatMouse positional table in the Table Browser. To view the table
	definition, click here. |  Mouse Chain This track shows mouse genomic alignment to the selected genome using blastz and
axtChain. See the Human Chain track description for more information.
 Mouse Cons This track displays the conservation between the human and mouse genomes for 
50bp windows in the human genome that have at least 15bp aligned to mouse. The 
score for a window reflects the probability that the level of observed 
conservation in that 50bp region would occur by chance under neutral evolution. 
It is given on a logarithmic scale, and thus it is called the "L-score". An 
L-score of 1 means there is a 1/10 probability that the observed conservation 
level would occur by chance, an L-score of 2 means a 1/100 probability, an 
L-score of 3 means a 1/1000 probability, etc. The L-scores display as 
"mountain ranges".
 
		| -- | Display conventions:
	This track uses the display conventions for wiggle tracks. |  | -- | Track configuration: 
	The track description page contains options to configure 
	several of the graph characteristics. To read more information
	about each option, click the "Graph configuration help" link. |  | -- | Track details: 
	Clicking on one of the peaks in the track when in full display mode will 
	show human genome 
	position information for the window, as well as position information for 
	the corresponding region in the mouse genome. The details page provides 
	links to the underlying sequence for the alignment and to the sequence 
	underlying the individual alignment windows. In full mode in 
	a zoomed-out display, detailed information may not be accessible for an 
	individual feature. In this case, zoom in and try again. |  | -- | Table details: 
	To view a text version of the data set, select the 
	humMusL positional table in the Table Browser. To view the table
	definition, click here. |  Mouse EcoresThis track shows Mouse evolutionary conserved regions (ecores) computed against 
the selected assembly genome by the Exofish program at Genoscope. For 
information on this track, see the Human Ecores track description.
 Mouse ESTs This track shows alignments between mouse Expressed Sequence Tags (ESTs) -
spliced and unspliced - in GenBank and the genome. This track was generated by 
aligning mouse ESTs from GenBank against the
genome using the BLAT program. Note that the maximum intron length
allowed by BLAT is 500,000 bases, which may eliminate some ESTs with
very long introns that might otherwise align. When a single EST aligns
in multiple places, the alignment having the highest base identity is
found. Only alignments that have a base identity level within 1% of the
best are kept. Alignments must also have at least 93% base identity to be 
kept.
 
		| -- | Display conventions:
	This track uses the display conventions for EST tracks. As with other
	EST tracks, it may be necessary to zoom in to display entries in full
	display mode due to the 300 line display limit. |  | -- | Track details: 
	Clicking on an individual EST entry will show basic track information,
	the accession number, GenBank highlights, and links to EST/Genomic
	Alignments. |  | -- | Table details: 
	To view a text version of the data set, select the 
	all_est positional table in the Table Browser. To view the table
	definition, click here. |  Mouse mRNAsSee the description for Human mRNAs.
 Mouse Net This track shows the best mouse chain for every part of the selected genome.
See the Human Net track description for more information.
 Mouse Synteny (hg13+)This track shows syntenous (corresponding) regions between human and mouse 
chromosomes. The track was created by passing a 100k non-overlapping window over 
the genome and using the blastz best in mouse genome alignments to look for
high-scoring regions where at least 40% of the bases aligned with the same 
region in mouse. 100k segments were joined together if they agreed in direction 
and were within 500kb of each other in the human genome and within 4mb of each 
other in the mouse. Gaps were joined between syntenic anchors if the bases 
between two flanking regions agreed with synteny (direction and mouse location). 
The syntenic block was extended to include these areas.
 
		| -- | Display conventions:
	This track uses the display conventions for synteny tracks. |  | -- | Track details: 
	Clicking on an item in full display mode shows details of the
	mouse-human correspondence and provides a link to the genomic sequence 
	for this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	syntenyMouse positional table in the Table Browser. To view the table
	definition, click here. |  Mouse Synteny (hg12 only)This track shows orthologous (syntenic) regions between mouse and human chromosomes based on data from Michael Kamal at the Whitehead Institute.
 
		Track details: 
	Clicking on an item in full display mode will show details of the
	mouse-human correspondence, as well links to genomic dotplots, 
	additional information, and an alternative synteny map based on 
	orthologous genes.| -- | Display conventions:
	This track uses the display conventions for synteny tracks. |  | -- | Table details: 
	To view a text version of the data set, select the 
	mouseSynWhd positional table in the Table Browser. To view the table
	definition, click here. |  Multiz YeastThis track displays multiz multiple alignments of seven species of the genus 
Saccharomyces. The graphic display shows the alignment projected onto 
S. cerevisiae.
 
		| -- | Display conventions:
	In full display mode, the track displays pairwise alignments of several
	species aligned to the S. cerevisiae genome. The pairwise 
	alignments 
	are displayed in standard UCSC browser "dense" mode using a grey-scale 
	density gradient.  When zoomed-in to the base-display level, the track 
	shows the base composition of each alignment. The numbers and symbols on 
	the "hidden gap" line indicate the lengths of gaps in the S. 
	cerevisiae sequence 
	at those alignment positions. If the gap size is greater than 9, the 
	"+" symbol is displayed. The track must be zoomed-in to 30,000
	or fewer bases to access detailed information about the 
	alignments at a specific position. |  | -- | Track details: 
	Clicking on an entry in full display mode will show detailed alignment 
	information for each of the organisms. |  | -- | Table details: 
	To view a text version of the data set, select the 
	multizYeast positional table in the Table Browser. To view the 
	table definition, click here. |  NIA GenesThis track displays alignments of the National Institute on Aging (NIA) Mouse 
Gene Index (Version 3) against the mouse genome.
 
		| -- | Display conventions:
	This track uses the display conventions for Blat alignment tracks. |  | -- | Track details: 
	Clicking on an individual track item in full mode displays a page
	with alignment details and a link to the corresponding NIA Mouse Gene 
	Index entry. |  | -- | Table details: 
	To view a text version of the data set, select the 
	NIAGene positional table in the Table Browser. To view the table
	definition, click here. |  NCI60This track displays cDNA expression data for a micro-array of 8,000 genes for 
60 cell lines used in an NCI 
cancer drug screen.
 
		| -- | Display conventions:
	To understand the track, experiment with it set to 
	full mode but other tracks (except known genes) hidden, while reading its
	 
	filter page. Each column of colored boxes represents variation in 
	transcript levels for a given cDNA across array experiments; each row 
	represents the measured transcript levels for all genes in a single sample. 
	The saturation of a color corresponds to the magnitude of transcript 
	variation. Black  indicates an undetectable change in expression; gray shows 
	missing data. |  Track details: 
	Clicking on an individual track item in full mode opens a rich details 
	page.  The exon probe and experiment selected are highlighted in blue 
	under item name.| -- | Track configuration: 
	The track description page contains a filter to limit the tissue types 
	displayed and change the color scheme of the display. |  | -- | Table details: 
	To view a text version of the data set, select the 
	nci60 positional table in the Table Browser. To view the table
	definition, click here. |  Non-A. gambiae mRNAs See the description for Non-Human mRNAs.
 Non-A. mel. mRNAs mRNAs of organisms other than A. mellifera. See the description for Non-Human 
mRNAs.
 Non-Chicken mRNAs See the description for Non-Human mRNAs.
 Non-Chicken RefSeqThis track shows known protein-coding genes from organisms other than chicken, taken from 
the mRNA reference sequences collection (RefSeq) compiled at NCBI. See the Non-Dog RefSeq 
track for more information.
 Non-Chimp ESTs See the description for Non-Human ESTs.
 Non-Chimp mRNAs See the description for Non-Human mRNAs.
 Non-C. intestinalis mRNAs See the description for Non-Human mRNAs.
 Non-Ciona mRNAs See the description for Non-Human mRNAs.
 Non-Ciona RefSeqThis track shows known protein-coding genes from organisms other than 
C. intestinalis, taken from the mRNA reference sequences collection (RefSeq) 
compiled at NCBI. See the Non-Dog RefSeq track for more information.
 Non-Dog RefSeqThis track shows known protein-coding genes from organisms other than dog, taken from 
the mRNA reference sequences collection (RefSeq) compiled at NCBI.
 
		| -- | Display conventions:
	This track uses the display conventions for gene 
	predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display provides links to the 
	corresponding protein, mRNA, and genomic sequences, and related links to 
	external databases. |  | -- | Track configuration: 
	The track description page contains configuration options to
	change the feature label to display the gene name (default), the 
	accession name, both the gene and accession names, or no label at all. |  | -- | Table details: 
	To view a text version of the data set, select the 
	xenoRefGene positional table in the Table Browser. To view the table
	definition, click here. |  Non-D. anan. mRNAs mRNAs of organisms other than D. ananassae. See the description for Non-Human 
mRNAs.
 Non-D. anan. RefSeq This track shows known protein-coding genes from organisms other than D.
ananassae, taken from the mRNA reference sequences collection (RefSeq) compiled 
at NCBI. See the description for Non-Human mRNAs.
 Non-D. melanogaster mRNAs See the description for Non-Human mRNAs.
 Non-D. moj. mRNAs mRNAs of organisms other than D. mojavensis. See the description for Non-Human 
mRNAs.
 Non-D. moj. RefSeq This track shows known protein-coding genes from organisms other than D.
mojavensis, taken from the mRNA reference sequences collection (RefSeq) compiled 
at NCBI. See the description for Non-Human mRNAs.
 Non-D. pseudo. mRNAs mRNAs of organisms other than D. pseudoobscura. See the description for 
Non-Human mRNAs.
 Non-D. pseudo. RefSeq This track shows known protein-coding genes from organisms other than D.
pseudoobscura, taken from the mRNA reference sequences collection (RefSeq) compiled 
at NCBI. See the description for Non-Human mRNAs.
 Non-D. vir. mRNAs mRNAs of organisms other than D. virilis. See the description for 
Non-Human mRNAs.
 Non-D. vir. RefSeq This track shows known protein-coding genes from organisms other than D.
virilis, taken from the mRNA reference sequences collection (RefSeq) compiled 
at NCBI. See the description for Non-Human mRNAs.
 Non-D. yakuba mRNAs See the description for Non-Human mRNAs.
 Non-Fugu mRNAs See the description for Non-Human mRNAs.
 Non-Human ESTs This track displays translated BLAT alignments of non-human vertebrate
ESTs from GenBank. The alignments were passed through a piecewise
near-best-in-genome filter. In cases where ESTs align to multiple places in the 
genome, only the near-best are retained. Matches help validate human exon 
identification.
 
		| -- | Display conventions:
	This track uses the display conventions for EST tracks. As with other
	EST tracks, it may be necessary to zoom in to 
	display entries in full display mode due to the 300 line display 
	limit. |  | -- | Track details: 
	Clicking on an item in full display will show a summary of the GenBank 
	entry, a hyperlink to the full record, PubMed links by gene name, 
	product, and author, and mRNA/genomic alignment information. |  | -- | Table details: 
	To view a text version of the data set, select the 
	xenoEst positional table in the Table Browser. To view the table
	definition, click here. |  Non-Human mRNAs This track displays translated BLAT alignments of vertebrate and invertebrate 
mRNA (other than that from the selected genome) from GenBank. The alignments 
were passed through a near-best-in-genome
filter. Some mRNAs align to multiple places but only the near-best are retained. 
For a distant vertebrate, alignment requires a fairly slowly evolving gene. 
Matches are often plausible ortholog candidates.
 
		| -- | Display conventions:
	This track uses the display conventions for PSL alignment tracks. |  | -- | Track configuration: 
	The track description page contains a filter to restrict the display to 
	only those entries that match certain keywords and to change the color 
	of the selected entries. |  | -- | Track details: 
	Clicking on an entry in full display mode will show a summary of the GenBank 
	entry on that mRNA, convenient hyperlinks to major databases, and 
	base-by-base mRNA/genomic alignments. |  | -- | Table details: 
	To view a text version of the data set, select the 
	xenoMrna positional table in the Table Browser. To view the table
	definition, click here. |  Non-Mouse ESTs See the description for Non-Human ESTs.
 Non-Mouse mRNAs See the description for Non-Human mRNAs.
 Non-Opossum mRNAs See the description for Non-Human mRNAs.
 Non-Rat ESTs See the description for Non-Human ESTs.
 Non-Rat mRNAs See the description for Non-Human mRNAs.
 Non-Tetraodon mRNAs See the description for Non-Human mRNAs.
 Non-Zebrafish mRNAs See the description for Non-Human mRNAs.
 Opossum Chain This track shows opossum genomic alignments to the selected genome using 
blastz and axtChain. See the Human Chain track description for more information.
 Opossum mRNAsSee the description for Human mRNAs.
 Opossum Net This track shows the best opossum chain for every part of the selected 
genome.  See the Human Net track description for more information.
 Overlap SNPs (older archived versions only)This track shows single nucleotide polymorphisms found on overlapping contigs. 
Overlap SNPs are useful markers in mapping genes and diseases. This data was provided 
by the SNP Consortium.
 
		| -- | Display conventions: 
	SNP locations are indicated by thin grey vertical lines. |  | -- | Track details: 
	Clicking in full mode brings up a location description and 
	dbSNP link. |  | -- | Table details: 
	To view a text version of the data set, select the 
	snpNih positional table in the Table Browser. To view the table
	definition, click here. |  Parsimony P-Values (Zoo)This track displays the level of conservation of Zoo sequences at any given 
position. More precisely, it computes the p-value of observing a certain 
parsimony score for a given column of the multiple alignment under the null 
model of neutral evolution.
 
		| -- | Display conventions:
	This track uses the display conventions for wiggle tracks. |  | -- | Track configuration: 
	The track description page contains options to configure 
	several of the graph characteristics. To read more information
	about each option, click the "Graph configuration help" link. |  | -- | Track details: 
	Clicking on one of the peaks in the track when in full display mode will 
	show genome position information for the window and a link to the
	underlying DNA sequence. In full mode in 
	a zoomed-out display, detailed information may not be accessible for an 
	individual feature. In this case, zoom in and try again. |  | -- | Table details: 
	To view a text version of the data set, select the 
	parsPValues positional table in the Table Browser. To view the 
	table definition, click here. |  Perlegen (chr21 only)This track shows haplotype blocks derived from common single nucleotide 
polymorphisms (SNPs) on Chromosome 21 by Perlegen Sciences, as
described in Patil N et. al. (2001), 
"Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning", 
Science 294:1719-1723. General information on the blocks is available 
from Perlegen's Chromosome 21 Haplotype Browser.
 
		| -- | Display conventions:
	The location of each haplotype block is represented by a blue horizontal 
	line with tall vertical blue bars at the first and last SNPs of
	the block. Blocks are displayed as starting at the first SNP and ending 
	at the last SNP of the block. This is slightly different from the
	representation on the Perlegen web site in which blocks are stretched 
	until they abut each other. The shade of the blue indicates the
	minimum number of SNPs required to discriminate between haplotype 
	patterns that account for at least 80% of genotyped
	chromosomes. Darker colors indicate fewer SNPs are necessary. Individual 
	SNPs are denoted by smaller black vertical bars. At
	multi-megabase resolution in dense display mode, clusters of tall blue 
	bars may indicate hotspots for recombination. |  | -- | Track details: 
	Clicking on an entry in full display mode will show basic position
	information, SNP information for the block, and a link to sequence 
	information for the feature. To view additional information on a 
	particular block,  click on Outside Link on the item's details 
	page. |  | -- | Table details: 
	To view a text version of the data set, select the 
	perlegen positional table in the Table Browser. To view the table
	definition, click here. |  QTLThis track shows approximate positions of quantititive trait loci (QTL) based on 
reported peak LOD scores taken from Jackson Lab's 
 Mouse Genome Informatics (MGI) Database.
 
		| -- | Display conventions: 
	QTL locations are indicated by thin vertical bars. |  | -- | Track details: 
	Clicking on an item in full mode provides a link to the MGI record for the selected QTL,
	information about the QTL, and position information. |  | -- | Table details: 
	To view a text version of the data set, select the 
	jaxQTL positional table in the Table Browser. To view the table
	definition, click here. |  Quality ScoresThis track shows the sequencing quality score (between 0 and 100) 
of each base in the assembly.
 
		| -- | Display conventions:
	The height at each position of the track indicates the quality of the 
	base. When zoomed out to a large range, the heights reflect the averaged 
	scores. Scores of 40 or higher reflect high confidence in the sequence 
	(with an error rate of less than 1/10,000); scores of 20 or higher 
	reflect reasonable confidence (of working draft quality). |  | -- | Table details: 
	To view a text version of the data set, select the 
	quality positional table in the Table Browser.
	To view the table definition, click here. |  Radiation Hybrid Map (Zebrafish)This track shows alignments between zebrafish Radiation Hybrid (RH) map sequences 
(consisting of ESTs and other genetic markers) and the genome.
 
		| -- | Display conventions:
	This track uses the display conventions for EST tracks. |  | -- | Track details: 
 	Clicking in full display mode provides a link to the genomic alignment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	rhMap positional table in the Table Browser.
	To view the table definition, click here. |  Random SNPs (older archived versions only)This track displays single nucleotide polymorphisms (SNPs)found by random 
sequencing. Random SNPs are useful markers in mapping genes and complex traits.
Because these SNPs are detected from random reads, they are useful for
evolutionary studies. This data was provided by the SNP 
Consortium.
 
		| -- | Display conventions: 
	SNP locations are indicated by thin grey vertical lines. |  | -- | Track details: 
 	Clicking in full mode brings up a location description 
 	and dbSNP link. |  | -- | Table details: 
	To view a text version of the data set, select the 
	snpTsc positional table in the Table Browser. To view the table
	definition, click here. |  Rat Chain This track shows rat genomic alignment to the selected genome using blastz and
axtChain. See the Human Chain track description for more information.
 Rat EcoresThis track shows rat evolutionary conserved regions (ecores) computed against 
the selected assembly genome by the Exofish program at Genoscope. For 
information on this track, see the Human Ecores track description.
 Rat ESTs See the description for the Human ESTs track.
 Rat mRNAsSee the description for the Human mRNAs track.
 Rat Net This track shows the best rat chain for every part of the selected genome. See 
the Human Net track description for more information.
 Rat Synteny This track shows syntenous (corresponding) regions between human and rat 
chromosomes. The track was created by passing a 100k non-overlapping window over 
the genome and using the blastz best in mouse genome alignments to look for
high-scoring regions where at least 40% of the bases aligned with the same 
region in rat. 100k segments were joined together if they agreed in direction 
and were within 500kb of each other in the human genome and within 4mb of each 
other in the rat. Gaps were joined between syntenic anchors if the bases 
between two flanking regions agreed with synteny (direction and rat location). 
The syntenic block was extended to include these areas.
 
		| -- | Display conventions:
	This track uses the display conventions for synteny tracks. |  | -- | Track details: 
	Clicking on an item in full display mode shows details of the
	rat-human correspondence and provides a link to the genomic sequence 
	for this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	syntenyRat positional table in the Table Browser. To view the table
	definition, click here. |  Recomb RateThis track shows calculated sex-averaged rates of recombination based on either 
the deCODE, Marshfield, or Genethon genetic maps. The deCODE map rates are 
displayed by default.
 
		| -- | Display conventions: 
	Each 1Mb window represents the average recombination rate of the bases 
	contained within that window. Darker shades of gray correspond to higher
	recombination rates. |  | -- | Track configuration: 
	The track description page contains a filter to map distances 
	(sex-averaged distance, female distance, or male distance) for the 3 
	different types of maps. |  | -- | Track details: 
 	Clicking in full mode shows position information 
 	and a list of all the recombination rate values for that 1Mb window. |  | -- | Table details: 
	To view a text version of the data set, select the 
	recombRate positional table in the Table Browser. To view the table
	definition, click here. |  RefSeq Genes The RefSeq Gene track shows known protein coding genes taken from the mRNA
reference sequences collection (RefSeq) compiled at NCBI. Refseq mRNAs are aligned 
against the genome using the BLAT program. When a single mRNA aligns in multiple places, 
only the best alignments are kept. Alignments must also have at least 98% sequence 
identity to be kept.
 
		| -- | Display conventions:
	This track uses the display conventions for known genes and gene 
	predictions tracks. Non-coding RNA genes have their own track in some 
	assemblies. The color shading indicates the level of review that the 
	RefSeq record has undergone: predicted (light), provisional (medium), 
	reviewed (dark). |  | -- | Track details: 
	Clicking on an entry in full display provides links to the 
	corresponding protein, mRNA, and genomic sequences, and related links to 
	outside databases. |  | -- | Track configuration: 
	The track description page contains configuration options to
	change the feature label to display the gene name (default), the 
	accession name, both the gene and accession names, or no label at all. |  | -- | Table details: 
	To view a text version of the data set, select the 
	refGene positional table in the Table Browser. To view the table
	definition, click here. |  Reg. CHIP/CHIPThis track shows the location of the probes spotted on a slide in the chromatin 
immunoprecipitation/microarray hybridization (CHIP/CHIP) experiments described in 
Harbison, C.T. et al., 
Transcriptional regulatory code of a eukaryotic genome. 
Nature 431(7004), 99-104 (2004). See also the "Regulatory Code" track 
for the position of the individual motifs.
 
		| -- | Display conventions:
	Black boxes indicate the probe locations. |  | -- | Track details: 
	Clicking on an entry in full display mode shows position information, as well as
	which transcription factors pulled down DNA that is enriched for the probe 
	sequence, which transcription factor binding site motifs are present in the 
	probe, and whether these motifs are conserved in related yeast species. |  | -- | Table details: 
	To view a text version of the data set, select the 
	transRegCodeProbe positional table in the Table Browser. To view 
	the table definition, click here. |  Regulatory CodeThis track shows putative regulatory elements in S. cerevisiae that are 
supported by cross-species evidence, as described in  (Harbison, C.T. et al., 
Transcriptional regulatory code of a eukaryotic genome. 
Nature 431(7004), 99-104 (2004)). The authors performed a genome-wide 
location analysis with 203 known DNA-binding transcriptional regulators (some under 
multiple environmental conditions) and identified 11,000 high-confidence interactions 
between regulators and promoter regions. They then compiled a compendium of motifs for 
102 transcriptional regulators based on a combination of their experimental results, 
cross-species conservation data for four species of yeast, and motifs from the literature,
and finally, they mapped these motifs to the S. cerevisiae genome. This track 
shows positions at which these motifs matched the genome with high confidence and at 
which the matching sequence was well conserved across yeast species. See the 
"Reg. CHIP/CHIP" track for additional related information.
 
		| -- | Display conventions:
	Regulatory elements are represented by rectangular blocks. The darker the shade
	of the block, the stronger the evidence supporting it. |  | -- | Track details: 
	Clicking on an entry in full display mode shows the sequence at that site 
	compared to the position-specific probability matrix for the associated 
	transcriptional regulator (shown as both a table and a graphical logo). It also 
	indicates whether the binding site is supported by experimental (CHIP/CHIP) 
	results and the number of other yeast species in which it is conserved. |  | -- | Track configuration: 
	The user can set the minimum unnormalized score criteria that data must 
	meet to be displayed in the track. |  | -- | Table details: 
	To view a text version of the data set, select the 
	tranRegCode positional table in the Table Browser. To view 
	the table definition, click here. |  Regulatory ModuleThis track shows predicted transcription factor binding sites based on sequence 
similarities upstream of coordinately expressed genes. 
Clicking on a particular predicted binding site brings up a page which indicates the sequence motif associated with the predicted transcription factor, and the sequence at the predicted binding site. Where known motifs have been identified by this method, they are named, otherwise they are assigned a Motif_ number.
 
		| -- | Display conventions:
	In dense display mode, gold areas indicate the extent of the area 
	searched for binding sites; black boxes indicate the actual binding 
	sites. In fuller display modes, the gold areas disappear and only the 
	binding sites are displayed. |  | -- | Track details: 
	Clicking on an entry in full display mode provides positional and
	score information about the item, and a link to display the DNA
	underlying the feature. |  | -- | Track configuration: 
	The user can set the minimum unnormalized score criteria that data must 
	meet to be displayed in the track. |  | -- | Table details: 
	To view a text version of the data set, select the 
	esRegGeneToMotif positional table in the Table Browser. To view 
	the table definition, click here. |  RepeatMaskerThe track shows dispersed repeats as determined by 
RepeatMasker
using the
Repbase Update
library of repetitive sequences from the Genetic Information Research 
Institute.  
These elements include SINE, LINE, LTR, DNA, simple, low complexity, 
micro-satellite, tRNA, and other repeat families.
 
		| -- | Display conventions:
	Darker gray boxes indicates a more recent age (as dated by alignment to a 
	canonical repeat). In dense mode for large chromosomal regions, the black 
	boxes representing repeats may merge into misleading single blocks in the 
	display. Full display mode shows 9 tracks representing the major repeat 
	classes. |  | -- | Table details: 
	To view a text version of the data set, select the 
	rmsk positional table in the Table Browser. To view the table
	definition, click here. |  Retroposed GenesThis track shows processed mRNAs that have been inserted back into the genome after the 
mouse/human split. Retrogenes can be functional genes that have acquired a promoter 
from a neighboring gene, non-functional pseudogenes, or transcribed pseudogenes.
 
		| -- | Display conventions: 
	This track follows the display conventions used by gene prediction tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show detailed information
	about the pseudogene's characteristics, alignment links, and Genome Browser
	annotation links for the gene locus that spawned the retrogene. |  | -- | Table details: 
	To view a text version of the data set, select the 
	pseudoGeneLink positional table in the Table Browser. To view the table
	definition, click here. |  RGD ESTs This track shows alignments expressed sequence tags (ESTs) from the Rat Genome
Database (RGD).
 
		| -- | Display conventions:
	This track uses the display conventions for EST tracks. As with other
	EST tracks, it may be necessary to zoom in to display entries in full
	display mode due to the 300 line display limit. |  | -- | Track details: 
	Clicking on an individual EST entry will show basic track information,
	the accession number, GenBank highlights, links to EST/genomic
	alignments, and an external link to the RGD EST report. |  | -- | Table details: 
	To view a text version of the data set, select the 
	rgdEst positional table in the Table Browser. To view the table
	definition, click here. |  RGD GenesThis track shows RefSeq genes curated by the Rat Genome Database (RGD).
 
		| -- | Display conventions: 
	This track follows the display conventions used by gene prediction tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will display position 
	information, links to sequence displays, and links to outside sources
	showing additional information. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn
	on codon coloring for the track. Click the "Codon coloring help"
	link on the page for more information about this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	rgdGene positional table in the Table Browser. To view the table
	definition, click here. |  RGD QTLThis track shows quantitative trait loci (QTLs) curated by the Rat Genome 
Database (RGD).
 
		| -- | Display conventions: 
	Loci positions are represented by blocks. |  | -- | Track details: 
	Clicking on an entry in full display mode will display genomic 
	information and a link to the corresponding entry in the RGD. |  | -- | Table details: 
	To view a text version of the data set, select the 
	rgdQtl positional table in the Table Browser. To view the table
	definition, click here. |  RGD SSLPThis track shows simple sequence length polymorphisms (SSLPs), also known as
microsatellite DNA, from the Rat Genome Database (RGD). SSLPs consist of 
1 - 6 simple nucleotide repeat sequences, highly polymorphic in repeat length 
among strains. They are often used as genetic markers for genotyping.
 
		| -- | Display conventions: 
	SSLP positions are represented by thin blocks. |  | -- | Track details: 
	Clicking on an entry in full display mode will display genomic 
	information and a link to the corresponding entry in the RGD. |  | -- | Table details: 
	To view a text version of the data set, select the 
	rgdSslp positional table in the Table Browser. To view the table
	definition, click here. |  Rinn Sex ExpThis track shows gene expression differences between adult male and female tissues as 
described in Rinn, JL et al. (2004) 
Major Molecular Differences between Mammalian Sexes Are Involved in Drug 
Metabolism and Renal Function. Developmental Cell 6:791-800.
 
		| -- | Display conventions: 
	This track follows display conventions similar to PSL alignment tracks. |  | -- | Track details: 
	In dense or packed display mode, the track shows averages of related
	tissues. In full display mode, all tissues are displayed. Click on an 
	individual tissue entry to show a gene expression map for all tissues in 
	the experiment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	rinnSex positional table in the Table Browser. To view the table
	definition, click here. |  RNA GenesThis track shows human non-protein-coding RNA genes and RNA pseudogenes. This 
includes tRNAs, rRNAs, SRPs, methylation guide snoRNAs, U2-U6 RNA-like, and 
similar elements both known and predicted (by tRNAscanSE etc). The density of 
these elements can range from 1-4 per million bp in some chromosomes. Protein 
coding genes are displayed elsewhere in the RefSeq Genes track.
 
		| -- | Display conventions: 
	RNA genes are represented by light-colored blocks. Pseudogenes are
	represented by darker blocks. |  | -- | Track details: 
	Clicking on an entry in full display mode will display feature 
	classification, method of prediction, location, reliability score, and
	a link to DNA sequence for the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	rnaGene positional table in the Table Browser. To view the table
	definition, click here. |  RosettaThis track displays microarray tissue 
expression data provided by Rosetta Inpharmatics. 
It helps catalogue genes and transcriptome, complements computational gene 
predictions, and seeks to define gene boundaries via co-regulated expression 
of nearby exons.
 
		| -- | Display conventions:
	The data is stratified by various tissue and disease-specific 
	conditions of gene expression.  Confirmed and predicted exons are placed in 
	separate tracks. Click on the mini-button to the left of the track to
	display a track description page containing more information. |  | -- | Track configuration: 
	The track description page contains a filter to fine-tune the track 
	display. The following display options are configurable: 
		o Reference Sample: Determines which of the 69 different
		experiments are displayed, based on the reference sample
		used.o Exons Shown: Determines whether data is shown for probes 
		corresponding to confirmed, predicted, or all exons.
 o Color Scheme: Data are presented using two color false display. 
		The default colors can be changed for those who are colorblind. Gray 
		values indicate missing data.
 
 |  | -- | Track details: 
	Clicking on a Rosetta exon in full display mode will show an averaged display 
	that can be expanded via checkboxes to a graph of actual intensities for an 
	individual experiment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	rosetta positional table in the Table Browser. To view the table
	definition, click here. |  Sanger 22 and Sanger 22 PseudoThese tracks contain the Sanger Centre annotations of chromosome 22.
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on the track while in full display mode will show details of
	the methods used to construct this track as well as the contributors. |  | -- | Table details: 
	To view a text version of the data set, select the 
	sanger22 positional table in the Table Browser. To view the table
	definition, click here. |  S. cerevisiae ESTsSee the Human ESTs track description.
 S. cerevisiae mRNAsSee the Human mRNAs track description.
 Scaffolds (Chimp)This track shows the chromosome-based version of the November 2003 Arachne chimp assembly 
(panTro1) from the Chimp Genome Sequencing Consortium.
 
		| -- | Display conventions:
	In dense display mode, this track depicts in alternating gold and brown the 
	individual scaffolds used to create the assembled sequence. 
	Where gaps exist in the path, spaces are shown between the gold and brown blocks. 
	Relative order and orientation of the scaffolds, as determined from the human/chimp 
	alignments, is implied for the non-random chromosomes.  The display must be 
	sufficiently zoomed in to view the gap features. |  | -- | Track details: 
	Clicking on an item in full display mode will show information about the
	scaffold fragment and bases and position information. |  | -- | Table details: 
	To view a text version of the data set, select the 
	gold positional table in the Chimp Table Browser. To view the table
	definition, click here. |  Scaffolds (Fugu, Zebrafish, Tetraodon)This track shows the draft and finished clones that comprise the assembly.
 
		| -- | Display conventions:
	In dense display mode, this track depicts in alternating gold and brown the 
	individual clones used to create the assembled sequence. 
	Where gaps exist in the path, spaces are shown between the gold and brown blocks. 
	If the relative order and orientation of the contigs between the two blocks is 
	known, a line is drawn to bridge the blocks.  The display must be 
	sufficiently zoomed in to view the gap features. |  | -- | Track details: 
	Clicking on an item in full display mode will show contig and position information. |  | -- | Table details: 
	To view a text version of the data set, select the 
	gold positional table in the Fugu or Zebrafish Table Browser. To view 
	the table definition, click here. |  Segmental DuplicationsThis track shows regions detected as putative genomic duplications within the 
golden path. 
For a description of the 'fuguization' detection method,
see Bailey JA et. al. (2001). 
"Segmental duplications: organization and impact within the current human genome 
project assembly". Genome Res 11:1005-17.
 
		| -- | Display conventions:
	Orange, yellow, dark-light gray represent
	similarities of greater than 99%, 99-98% and 98-90% respectively. Duplications 
	greater than 98% similarity that lack sufficient SDD evidence (likely 
	missed overlaps) are shown as red. Cut off values were at least 1 kb of 
	total sequence aligned (containing at least 500 bp non-RepeatMasked 
	sequence) and at least 90% sequence identity. |  | -- | Track details: 
	Clicking on an entry in full display mode provides position, filter,
	and alignment information as well as links to the corresponding genomic
	sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	genomicSuperDups positional table in the Table Browser. To view the table
	definition, click here. |  Self Chain This track shows alignments of the selected genome with itself using blastz and
axtChain.
 
		| -- | Display conventions:
	This track uses the display conventions for chain tracks. |  | -- | Track details: 
	Clicking on an item in full display mode shows position information, the 
	chain ID and score, and provides 
	links to view details of parts of the chain or to open the browser 
	to the corresponding aligning position. |  | -- | Table details: 
	To view a text version of the data set, select the 
	chainSelf positional table in the Table Browser. To view the 
	table definition, click here. |  SGD Genes This track shows annotated genes and open reading frames (ORFs) of 
Saccharomyces cerevisiae obtained from the Saccharomyces Genome 
Database (SGD).
 
		| -- | Display conventions:
	This track uses the display conventions for known genes and gene 
	predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode provides a wealth of 
	genomic, mRNA, and protein information about the gene as well as 
	links to several associated external sites. |  | -- | Table details: 
	To view a text version of the data set, select the 
	sgdGene positional table in the Table Browser. To view the table
	definition, click here. |  SGD Other This track shows a variety of features in the Saccharomyces cerevisiae
genome, including tRNAs, transposons, centromeres, and open reading frames (ORFs) classified as dubious. 
The data was downloaded from the Saccharomyces Genome Database 
(SGD).
 
		| -- | Display conventions:
	This track uses the display conventions for known genes and gene 
	predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode provides genomic information 
	and a link to view the DNA underlying the track. |  | -- | Table details: 
	To view a text version of the data set, select the 
	sgdOther positional table in the Table Browser. To view the table
	definition, click here. |  SGP Genes This track shows gene predictions from the SGP program, which is being developed 
at the Grup de Recerca en Informàtica Biomèdica (GRIB) at Institut Municipal 
d'Investigació Mèdica (IMIM) in Barcelona. To predict genes in a genomic query, 
SGP combines geneid predictions with tblastx comparisons of the genomic query 
against other genomic sequences.
 
		| -- | Display conventions:
	This track uses the display conventions for known genes and gene 
	predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode provides position information
	as well as links to the corresponding protein, mRNA, genomic, and 
	comparative sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	sgpGene positional table in the Table Browser. To view the table
	definition, click here. |  Short MatchThis track shows all occurrences of a selected short motif within the displayed 
position range of the assembly sequence. It is useful for finding 
oligonucleotides, restriction sites, or other recurring short sequences within 
the assembly.
 
		| -- | Display conventions:
	Perfect matches are indicated by a solid rectangle. In full display mode,
	each occurrence is labeled by the strand on which the match is located,
	followed by the starting coordinate of the match. In cases where the 
	input motif sequence is identical to its reverse complement, only the 
	match on the "+" strand is shown. |  | -- | Track details: 
	Clicking on an entry in full display mode provides position information
	about the match. |  | -- | Track configuration: 
	The track may be configured to search for any short sequence of 2-30 
	bases in length. To change the sequence, type a new sequence into the 
	text box at the top of the track description page. |  | -- | Table details: 
	Unlike most annotations in the Genome Browser, this track is not 
	table-based. |  Simple RepeatsThis track displays simple tandem repeats (possibly imperfect) located by 
Tandem Repeats Finder, 
which is specialized to this purpose. These repeats can occur within coding regions of 
genes and may be quite polymorphic. Repeat expansions are sometimes associated with 
specific diseases.
 
		| -- | Display conventions: 
	Repeats are represented by block boxes that indicate location in the
	assembly. |  | -- | Track details: 
	Clicking on an item in full display mode will show the simple repeat 
	sequence, copy number, and quality of match statistics. |  | -- | Table details: 
	To view a text version of the data set, select the 
	simpleRepeats positional table in the Table Browser. To view the table
	definition, click here. |  Slam Human, Slam Mouse, Slam RatThese tracks predict coding exons and conserved noncoding regions in a pair of 
homologous DNA sequences, incorporating both statistical sequence properties and 
the degree of conservation in making the predictions. The model is symmetric: the 
same gene structure (with possibly different exon lengths) is predicted in both 
sequences.
 
		| -- | Display conventions: 
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show basic track
	information, plus links to the predicted mRNA, 
	genomic sequence, and comparative sequence. |  | -- | Table details: 
	To view a text version of the data set, select the appropriate
	slam positional table in the Table Browser (e.g. slamHuman, 
	slamMouse, slamRat). To view the table
	definition, click here. |  SlamHumanNonCoding, SlamMouseNonCoding, SlamRatNonCodingThese tables show slam predictions of conserved noncoding regions in homologous 
DNA sequences.
 
		| -- | Display conventions: 
	The data in these tables are displayed as part of the Slam Human, 
	Slam Mouse, and Slam Rat tracks. See the track descriptions for these
	tracks for display information. |  | -- | Table details: 
	To view a text version of the data set, select the appropriate
	slamNonCoding positional table in the Table Browser (e.g. slamHumanNonCoding, 
	slamMouseNonCoding, slamRatNonCoding). To view the table
	definition, click here. |  SNAP Genes (C. intestinalis)This track shows gene predictions determined by SNAP (Semi-HMM-based Nucleic Acid Parser),
a general purpose gene-finding program written by Ian Korf. SNAP is suitable for both 
eukaryotic and prokaryotic genomes. For this set of gene predictions, it was trained on 
gene annotations from the DOE Joint Genome Institute (JGI).
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode brings up basic track
	information, plus links to the translated protein, predicted mRNA, and
	genomic sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	snapGene positional table in the Table Browser. To view the table
	definition, click here. |  Sno/miRNAThis track displays positions of four different types of RNA in the human genome: 
microRNAs from the miRNA Registry at the Wellcome Trust Sanger Institute, small nucleolar 
RNAs (C/D box and H/ACA box snoRNAs) and Cajal body-specific RNAs (scaRNAs) from the 
snoRNA-LBME-DB maintained at the Laboratoire de Biologie Moléculaire Eucaryote. C/D box 
and H/ACA box snoRNAs are guides for the 2'O-ribose methylation and the pseudouridilation,
respectively, of rRNAs and snRNAs, although many of them have no documented target RNA. 
The scaRNAs guide modifications of the spliceosomal snRNAs transcribed by RNA polymerase 
II, and often contain both C/D and H/ACA domains.
 
		| -- | Display conventions:
	Mature miRNAs (miRs) are represented by thick red blocks; the predicted stem-loop 
	portions of the primary transcripts are indicated by thinner blocks. When a 
	single precursor produces two mature miRs from its 5' and 3' parts, both positions
	of the mature miRNA are individually displayed. C/D box, H/ACA box snoRNAs and 
	scaRNAs are represented by blue, green and magenta blocks, respectively. At a 
	zoomed-in resolution, arrows superimposed on the blocks indicate the sense 
	orientation of the snoRNAs. |  | -- | Track details: 
	Clicking on an entry in full display mode provides a link to the miRNA
	Registry, the RNA type, position information, and a link to the DNA sequence
	associated with the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	wgRna positional table in the Table Browser. To view the table
	definition, click here. |  SNPs (Human assemblies hg17 and later) This track displays all the known Simple Nucleotide Polymorphisms (SNPs) that
can be mapped against the current genome assembly. These data were obtained from
dbSNP and 
commercially-available genotyping arrays and include known point 
mutations (Single Nucleotide Polymorphisms), insertions, deletions, multiple
See the track description page for more information about the SNP 
classifications.
These data were provided by the SNP Consortium and 
Affymetric, Inc..
 
		| -- | Display conventions: 
	Variants are drawn a single tick marks at most zoom levels. 
	When viewing the track at or near base-level resolution, the displayed 
	width of the SNP corresponds to the width of the variant in the 
	reference sequence. Insertions are indicated by a single tick mark 
	displayed between two nucleotides, single nucleotide polymorphisms are 
	displayed as the width of a single base, and multiple nucleotide 
	variants are represented by a block that spans two or more bases. |  | -- | Track details: 
 	Clicking in full mode brings up position information about the reference
	sequence, detailed information about the variant, and a link to the
	record in dbSNP. |  | -- | Track configuration: 
	The colors of variants may be changed to highlight their source, 
	molecule type, variant class, validation status, or functional 
	classification. Variants can be excluded from the display based on 
	these same criteria or if they fall below the user-specified minimum 
	average heterozygosity. |  | -- | Table details: 
	To view a text version of the data set, select the 
	snp positional table in the Table Browser. To view the table
	definition, click here. |  SNPs (Human assemblies prior to hg17) This track displays all the known Simple Nucleotide Polymorphisms (SNPs) that
can be mapped against the current genome assembly. These include known point 
mutations (Single Nucleotide Polymorphisms), insertions, deletions, and 
segmental mutations from the current build of dbSnp (shown in the Genome
Browser release log). See the track
description page for more information about major cases that are not mapped.
These data were provided by the SNP 
Consortium.
 
		| -- | Display conventions: 
	SNP locations are indicated by thin grey vertical lines. |  | -- | Track details: 
 	Clicking in full mode brings up a location description 
 	and dbSNP link. |  | -- | Table details: 
	To view a text version of the data set, select the 
	snpMap positional table in the Table Browser. To view the table
	definition, click here. |  Spliced ESTsThe Spliced EST track displays the subset of Expressed Sequence Tags (ESTs)
from GenBank that show signs of splicing when aligned against
the genome. ESTs are single read (typically approximately 500 base) sequences 
that usually represent fragments of transcribed genes. By requiring splicing, 
the level of contamination in the EST databases is drastically reduced at the 
expense of eliminating many genuine 3' ESTs. This track may also suggest 
alternate splices. The GT-AG splice donor/acceptor rule has not been applied.  
For a display of all ESTs (including unspliced), see the Human EST 
track.
This track was generated by aligning human ESTs from GenBank against the
genome using the BLAT program. Note that the maximum intron length
allowed by BLAT is 500,000 bases, which may eliminate some ESTs with
very long introns that might otherwise align. When a single EST aligns
in multiple places, the alignment having the highest base identity is
found. Only alignments that have a base identity level within 1% of the
best are kept. Alignments must also have at least 93% base identity to be 
kept.
 
		| -- | Display conventions:
	This track uses the display conventions for EST tracks 
	As with other EST tracks, it may be necessary to zoom in to 
	display entries in full display mode due to the 300 line display 
	limit. |  | -- | Track details: 
	Clicking on an individual EST entry will show basic track information,
	the accession number, GenBank highlights, and links to translated
	protein, predicted mRNA, and genomic sequences. |  | -- | Table details: 
	To view a text version of the data set, select the 
	intronEst positional table in the Table Browser. To view the table
	definition, click here. |  STS Markers (human)This track shows the locations of Sequence Tagged Site (STS) markers along
the draft assembly. The STS markers have been mapped using either
genetic (Genethon and Marshfield maps), radiation hybridization (the Stanford,
Whitehead RH, and GeneMap99 maps) or YAC mapping (the Whitehead YAC map)
techniques. In releases prior to August 2001, this track also shows the 
approximate position of FISH mapped clones. Starting with the August 2001 assembly, 
the FISH clones have been moved into a separate track.
 
		| -- | Display conventions:
	Genetic map markers are shown in blue, and radiation hybrid
	map markers are shown in black. When a marker maps to multiple
	positions in the genome, it is shown in a lighter color. |  | -- | Track details: 
	Clicking on a specific marker in full display mode will show synonyms, 
	position information, primers, YAC map position, and uniSTS and GDB links. |  | -- | Table details: 
	To view a text version of the data set, select the 
	stsMap positional table in the Table Browser. To view the table
	definition, click here. |  STS Markers (mouse)This track shows the locations of Sequence Tagged Site (STS) markers
along the draft assembly of the mouse genome. These STS markers appear on the MGI consensus
mouse genetic map. Information about the genetic map and STS marker
primer sequences are provided by the  Mouse Genome Informatics database group at The Jackson 
Laboratory.
 
		| -- | Display conventions:
	Genetic map markers are shown as thin black boxes. |  | -- | Track details: 
	Clicking on a specific marker in full display mode will show position 
	information, primers, genetic map position, genomic alignments, and MGI
	links. |  | -- | Table details: 
	To view a text version of the data set, select the 
	stsMapMouse positional table in the Table Browser. To view the table
	definition, click here. |  STS Markers (rat)This track shows locations of Sequence Tagged Site (STS) markers along the draft 
assembly of the rat genome. These STSs have been mapped using either
genetic (rat FHH x ACI F2 intercross genetic map, rat SHRSP x BN F2 intercross genetic map) or radiation hybridization (RH
map.2.2).
 
		| -- | Display conventions:
	Genetic map markers are shown as thin black boxes. |  | -- | Track details: 
	Clicking on a specific marker in full display mode will show position 
	information, primers, genetic map position, and links to the corresponding
	UniSTS and RGD entries. |  | -- | Table details: 
	To view a text version of the data set, select the 
	stsMapRat positional table in the Table Browser. To view the table
	definition, click here. |  Superfamily The Superfamily track shows proteins having homologs with known structures or 
functions. Each entry in the track shows the coding region of a gene (based on 
Ensembl gene prediction). The label, shown in Full mode at the left
hand side of each entry, consists of the names of all known protein domains 
coded by this gene. This usually contains structural and/or function descriptions
that provide valuable information for getting a quick grasp of the biological 
significance for the gene.
 
		| -- | Display conventions:
	Coding regions are indicated by red blocks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show the Superfamily 
	domains of the corresponding protein and provide a link to the Superfamily	  database entry. |  | -- | Table details: 
	To view a text version of the data set, select the 
	superfamily positional table in the Table Browser. To view the table
	definition, click here. |  Tetraodon Chain This track shows Tetraodon genomic alignments to the selected 
genome using blastz and axtChain. See the Human Chain track description for 
more information.
 Tetraodon EcoresThis track shows Tetraodon evolutionary conserved regions (ecores) computed 
against the selected assembly genome by the Exofish program at Genoscope. For 
information on this track, see the Human Ecores track description.
 Tetraodon Net This track shows the best Tetraodon chain for every part of the selected genome.
See the Human Net track description for more information.
 TFBS ConservedThis tracks shows the location and score of transcription factor binding sites 
(TFBSs) conserved in a multiple species alignment. A binding site is considered 
to be conserved across the alignment if its score meets the threshold score for 
that binding site in all aligned species. The score and threshold are computed 
with the Transfac Matrix Database created by Biobase. The data are purely 
computational, and as such not all binding sites listed here are biologically 
functional binding sites.
 
		| -- | Display conventions: TFBSs are represented by thin blocks.
	The darker the shading, the better the match of the binding site. |  | -- | Track details: 
	Clicking on a block in full display mode will show the the entry's 
	Transfac ID, positional information, and a link to its Transfac Matrix
	(free registration with Transfac is required). |  | -- | Table details: 
	To view a text version of the data set, select the 
	tfbsCons positional table in the Table Browser. To view the table
	definition, click here. |  Tight MouseThis track displays Blastz alignments of the specified mouse
draft assembly to the human genome, filtered by axtBest and
subsetAxt with very stringent constraints. See the track's description
page for more details.
 
		| -- | Display conventions:
	This track uses the display conventions for cross-species synteny 
	tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show human and 
	mouse position information, alignment details, and a link to a detailed
	view of parts of the alignment. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn 
	on the chromosome color track or to filter the display output by 
	chromosome. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blastzTightMouse positional table in the Table Browser. To view the table
	definition, click here. |  Tight RatThis track displays Blastz alignments of the Nov. 2002 rat
draft assembly to the mouse genome, filtered by axtBest and
subsetAxt with very stringent constraints. See the track's description
page for more details.
 
		| -- | Display conventions:
	This track uses the display conventions for cross-species synteny 
	tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show mouse and 
	rat position information, alignment details, and a link to a detailed
	view of parts of the alignment. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn 
	on the chromosome color track or to filter the display output by 
	chromosome. |  | -- | Table details: 
	To view a text version of the data set, select the 
	blastzTightRat positional table in the Table Browser. To view the table
	definition, click here. |  Tigr Gene IndexThis track displays alignments of the 
TIGR Gene Index (TGI) 
against the human genome. The TGI is based largely on assemblies of EST
sequences from the public databases and TIGR.  Entries are 
actual assemblies providing a consensus sequence, not simply clusters of 
overlapping sequences, but generally don't predict whole genes. Gene
indices for mouse, rat, cow, and pig also contribute to this track.
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show basic track
	information, links to the  predicted mRNA and
	genomic sequences, and a link to supporting information in the TIGR
	Human Gene Index. |  | -- | Table details: 
	To view a text version of the data set, select the 
	tigrGeneIndex positional table in the Table Browser. To view the table
	definition, click here. |  TranscriptomeThis track shows transcriptome data for chromosomes 21 and 22 from Affymetrix, 
as described in "Large-Scale Transcriptional Activity in Chromosomes 21 and 22", 
Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S, Strausberg, R. L., 
Fodor, S.P.A. and Gingeras, T.R.. In general, the data presented is the perfect 
match - mismatch value. Different experiments were normalized by setting the 
average value to be the same for each chip.
 
		| -- | Display conventions:
	This track uses the display conventions for wiggle tracks. To present a 
	more interpretable display when zoomed out, averages have been 
	precalculated over the chromosome at two different resolutions in 
	addition to the raw data. For example, when zoomed out, there may appear 
	to be a peak at the center of a gene rather than a signal at every exon. 
	Zooming in will reveal the raw data for that region. |  | -- | Track details: 
	In dense mode (or at the top of the track in full mode), the 
	transcriptome wiggle track displays the maximum value over all 
	experiments for that probe, the idea 
	being to paint as many transcribed regions as possible. In full mode, 
	the track displays a separate wiggle track for each cell type, showing 
	the data produced by averaging together replicates for that cell type.
	Clicking on an individual data point will show positional information and
	a link to view the sequence for the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	affyTranscriptome positional table in the Table Browser. To view the table
	definition, click here. |  Twinscan Gene PredictionsThis track displays Twinscan gene predictions. Twinscan predicts genes in a 
manner similar to Genscan, except that Twinscan takes advantage of genome 
comparison to improve gene prediction accuracy. More information and a web 
server can be found at the Washington University St. Louis 
Twinscan web page.
 
		| -- | Display conventions:
	This track uses the display conventions for gene predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show basic track
	information, links to the  predicted protein, predicted mRNA, 
	genomic sequence, and comparative sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	twinscan positional table in the Table Browser. To view the table
	definition, click here. |  UCSC Synteny (hg12)See description for Mouse Synteny (hg13+).
 UniGeneThis track shows UniGene 
clusters of ESTs aligned to the genome using BLAT. This data imperfectly 
indicates exon/intron boundaries and to a lesser extent genes. The Serial 
Analysis of Gene Expression 
(SAGE) project at NCBI - a quantitative measurement of gene expression in 
various tissues and disease states - mapped small 10bp bar-coded expression 
markers onto these UniGene clusters in the SageMap project. The Genome Browser 
uses this mapping to provide access to the SAGE data associated with the 
UniGene track in the assembled and annotated genome.
 
		| -- | Display conventions:
	This track uses the display conventions for PSL alignment tracks. |  | -- | Track details: 
	Clicking on a UniGene feature will show an elaborate display of tabular and 
	graphical data from the SAGE project relevant to that cluster. |  | -- | Table details: 
	To view a text version of the data set, select the 
	uniGene positional table in the Table Browser. To view the table
	definition, click here. |  Vega Genes (selected human chromosomes only)This track shows genes from the Vertebrate Genome Annotation (VEGA) database, a central repository for manual annotation of different vertebrate finished genome sequence. In collaboration with the genome sequencing centers, Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analysed on a clone by clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery.
 
		| -- | Display conventions:
	This track uses the display conventions for gene prediction tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show basic track
	information, a link to the Vega web page for the item, and links to the 
	predicted protein, predicted mRNA, 
	genomic sequence, and comparative sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	vegaGene positional table in the Table Browser. To view the table
	definition, click here. |  Vega Pseudogenes (selected human chromosomes only)This track shows annotated pseudogenes and immunoglobulin segments from the Vertebrate Genome Annotation (VEGA) database, a central repository for manual annotation of different vertebrate finished genome sequence. In collaboration with the genome sequencing centers, Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analysed on a clone by clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery.
 
		| -- | Display conventions:
	This track uses the display conventions for gene prediction tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show basic track
	information, a link to the Vega web page for the item, and links to the 
	predicted mRNA, genomic sequence, and comparative sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	vegaPseudoGene positional table in the Table Browser. To view the table
	definition, click here. |  WashU ClonesThis track displays the location of clones (mostly lambda and cosmid clones) 
from Washington University in St. Louis using the names assigned by that group. 
The data was downloaded from the Saccharomyces Genome Database 
(SGD).
 
		| -- | Display conventions:
	The clone positions are shown in black. |  | -- | Track details: 
	Clicking on an entry in full display mode brings up genomic 
	information and a link to the American Type Culture Collection (ATCC) 
	website. |  | -- | Table details: 
	To view a text version of the data set, select the 
	sgdClone positional table in the Table Browser. To view the table
	definition, click here. |  WormBase GenesThis track shows Sanger Gene predictions from the Wormbase files 
downloaded from the Sanger Institute FTP site. The data shown is the subset
annotated with "curated", "DNA", or "RNA" followed by one of these strings: 
"intron", "exon", "cds", "sequence", or "transcri".
 
		| -- | Display conventions:
	This track uses the display conventions for gene prediction tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show a wealth of 
	information about the gene and its associated mRNA and protein, as
	well as links to many related external sites. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn
	on codon coloring for the track. Click the "Codon coloring 
	help" link on the page for more information about this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	sangerGene positional table in the Table Browser. To view 
	the table definition, click here. |  WormBase Genefinder This track shows Sanger Gene predictions from the Wormbase files 
downloaded from the Sanger Institute FTP site. The data shown is the subset
annotated with the string "Genefinder" and found by the gene prediction 
program, Genefinder.
 
		| -- | Display conventions:
	This track uses the display conventions for gene prediction tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show genomic
	information  and links to the 
	translated protein, predicted mRNA, genomic sequence. |  | -- | Track configuration: 
	The track description page contains a filter that can be used to turn
	on codon coloring for the track. Click the "Codon coloring 
	help" link on the page for more information about this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	sangerGenefinder positional table in the Table Browser. To view 
	the table definition, click here. |  WSSD CoverageThis track represents coverage of clones that were assayed for segmental duplications 
using high-depth Celera reads. Absent regions were not assessed by this version of the 
Segmental Duplication Database (SDD). For a description of the whole-genome shotgun 
sequence detection (WSSD) "fuguization" method, see Bailey, JA. et al.,
Segmental duplications: organization and impact within the current human 
genome project assembly, Genome Res. 11(6), 1005-17 (2001).
 
		| -- | Display conventions:
	Rectangular blocks indicate the positions of clones. |  | -- | Track details: 
	Clicking on an entry in full display mode will show position information and a 
	link to the underlying DNA for the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	celeraCoverage positional table in the Table Browser. To view 
	the table definition, click here. |  WSSD Duplication High-depth sequence reads from the Celera project were used to detect paralogy in the 
human genome reference sequence. This track shows confirmed segmental duplications, 
defined as having similarity to sequences in the Segmental Duplication Database (SDD) 
of greater than 90% over more than 250 bp of repeatmasked sequence. For a description 
of the whole-genome shotgun sequence detection (WSSD) 'fuguization' method, see 
Bailey, JA. et al., 
Segmental duplications: organization and impact within the current human 
genome project assembly, Genome Res. 11(6), 1005-17 (2001).
 
		| -- | Display conventions:
	Rectangular blocks indicate the positions of duplications. |  | -- | Track details: 
	Clicking on an entry in full display mode will show the WSSD ID number, 
	position information, and a link to the underlying DNA for the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	celeraDupPositive positional table in the Table Browser. To view 
	the table definition, click here. |  WSSD OverlayThis track shows regions detected as overlays of Celera whole-genome shotgun sequence 
assembly on the public human assembly.
 
		| -- | Display conventions:
	Regions are represented by rectangular blocks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show position information and a 
	link to the underlying DNA for the feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	celeraOverlay positional table in the Table Browser. To view 
	the table definition, click here. |  X. tropicalis Chain This track shows X. tropicalis genomic alignments to the selected 
genome using blastz and axtChain. See the Human Chain track description for 
more information.
 X. tropicalis ESTs See the description for the Human ESTs track.
 X. tropicalis mRNAsSee the description for the Human mRNAs track.
 X. tropicalis Net This track shows the best X. tropicalis chain for every part of the selected genome. See 
the Human Net track description for more information.
 Yale PseudoThis track shows pseudogenes identified in the 
Yale Pseudogene 
Database.
 
		| -- | Display conventions:
	This track uses the display conventions for gene prediction tracks. |  | -- | Track details: 
	Clicking on an entry in full display mode will show genomic
	information, a link to the corresponding pseudogene entry in the 
	Yale Pseudogene Database, and links to predicted mRNA and genomic 
	sequence. |  | -- | Track configuration: 
	The track description page provides an option to turn
	on codon coloring for the track. Click the "Codon coloring 
	help" link on the page for more information about this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	pseudoYale positional table in the Table Browser. To view 
	the table definition, click here. |  Zebrafish Chain This track shows zebrafish genomic alignments to the selected 
genome using blastz and axtChain. See the Human Chain track description for 
more information.
 Zebrafish ESTsSee the Human ESTs track description.
 Zebrafish mRNAsSee the Human mRNAs track description.
 Zebrafish Net This track shows the best Zebrafish chain for every part of the selected genome.
See the Human Net track description for more information.
 Zfish WZ EST Clusters(Zebrafish)
This track shows alignments between zebrafish WZ expressed sequence tags (ESTs) from 
WashU-Zebrafish Genome Resources and the genome. These WZ ESTs are compiled to produce 
longer reads by clustering together ESTs that originate from the same transcript.
 
		| -- | Display conventions:
	This track uses the display conventions for EST tracks.  Hatch marks on the 
	introns indicate the direction of transcription. 
	As with otherEST tracks, it may be necessary to zoom 
	in to display entries in full display mode due to the 300 line display 
	limit. |  | -- | Track details: 
	Clicking on an individual EST entry displays a link to the genomic alignment. |  | -- | Table details: 
	To view a text version of the data set, select the 
	wz_ests positional table in the Table Browser. To view the table
	definition, click here. |  ZGC Genes  (Zebrafish)This track shows alignments to the genome of zebrafish mRNAs from the Mammalian Gene 
Collection (MGC) having full-length open reading frames (ORFs).
 
		| -- | Display conventions:
	This track uses the display conventions for known genes and gene 
	predictions tracks. |  | -- | Track details: 
	Clicking on an entry in full display provides links to the 
	corresponding protein, mRNA, and genomic sequences, and related links to 
	outside databases. |  | -- | Track configuration: 
	The track description page offers configuration options that can be used to turn
	on codon coloring for the track. Click the "Codon coloring 
	help" link on the page for more information about this feature. |  | -- | Table details: 
	To view a text version of the data set, select the 
	mgcGenes positional table in the Table Browser. To view the table
	definition, click here. |  ZooSeq (Zoo)This track displays the level of conservation for each zoo species based on 
blastz pair-wise alignments.
 
		| -- | Display conventions:
	This track uses the display conventions for wiggle tracks. 
	Gray horizontal bars denote a mapping/sequencing gap. Percent identities 
	of less than 50% are not shown because they fall below the minimum
	y-axis value. |  | -- | Track configuration: 
	The track description page contains options to configure 
	several of the graph characteristics. To read more information
	about each option, click the "Graph configuration help" link. |  | -- | Track details: 
	Clicking on an entry in full display mode will show basic track
	information, a link to the Vega web page for the item, and links to the 
	predicted mRNA, genomic sequence, and comparative sequence. |  | -- | Table details: 
	To view a text version of the data set, select the 
	zoo positional table in the Table Browser. To view the table
	definition, click here. |  Last updated on 3 Mar. 2005. 
Questions and feedback welcome.
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