SampleName	Gene_1_symbol.5end_fusion_partner.	Gene_2_symbol.3end_fusion_partner.	Fusion_description	Counts_of_common_mapping_reads	Spanning_pairs	Spanning_unique_reads	Longest_anchor_found	Fusion_finding_method	Fusion_point_for_gene_1.5end_fusion_partner.	Fusion_point_for_gene_2.3end_fusion_partner.	Gene_1_id.5end_fusion_partner.	Gene_2_id.3end_fusion_partner.	Exon_1_id.5end_fusion_partner.	Exon_2_id.3end_fusion_partner.	Fusion_sequence	Predicted_effect	AnnotationGene5	AnnotationGene3
A1	TCF3	PBX1	"known_fusion,cosmic,chimerdb2,cgp,ticdb"	0	217	51	45	BOWTIE+STAR	19:1619110:-	1:164761731:+	ENSG00000071564	ENSG00000185630			CCAGCCAGGCACCCTCCCTGACCTGTCTCGGCCTCCCGACTCCTACAGTG*TTTTGAGTATCCGAGGAGCCCAGGAGGAGGAACCCACAGACCCCCAGCTG	in-frame	"This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development. Deletion of this gene or diminished activity of the encoded protein may play a role in lymphoid malignancies. This gene is also involved in several chromosomal translocations that are associated with lymphoid malignancies including pre-B-cell acute lymphoblastic leukemia (t(1;19), with PBX1), childhood leukemia (t(19;19), with TFPT) and acute leukemia (t(12;19), with ZNF384). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Sep 2011]."	"This gene encodes a nuclear protein that belongs to the PBX homeobox family of transcriptional factors. Studies in mice suggest that this gene may be involved in the regulation of osteogenesis, and required for skeletal patterning and programming. A chromosomal translocation, t(1;19) involving this gene and TCF3/E2A gene, is associated with pre-B-cell acute lymphoblastic leukemia. The resulting fusion protein, in which the DNA binding domain of E2A is replaced by the DNA binding domain of this protein, transforms cells by constitutively activating transcription of genes regulated by the PBX protein family. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]."
A2	TCF3	PBX1	"known_fusion,cosmic,chimerdb2,cgp,ticdb"	0	217	48	45	BOWTIE+BLAT	19:1619110:-	1:164761731:+	ENSG00000071564	ENSG00000185630			CCAGCCAGGCACCCTCCCTGACCTGTCTCGGCCTCCCGACTCCTACAGTG*TTTTGAGTATCCGAGGAGCCCAGGAGGAGGAACCCACAGACCCCCAGCTG	in-frame	"This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development. Deletion of this gene or diminished activity of the encoded protein may play a role in lymphoid malignancies. This gene is also involved in several chromosomal translocations that are associated with lymphoid malignancies including pre-B-cell acute lymphoblastic leukemia (t(1;19), with PBX1), childhood leukemia (t(19;19), with TFPT) and acute leukemia (t(12;19), with ZNF384). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Sep 2011]."	"This gene encodes a nuclear protein that belongs to the PBX homeobox family of transcriptional factors. Studies in mice suggest that this gene may be involved in the regulation of osteogenesis, and required for skeletal patterning and programming. A chromosomal translocation, t(1;19) involving this gene and TCF3/E2A gene, is associated with pre-B-cell acute lymphoblastic leukemia. The resulting fusion protein, in which the DNA binding domain of E2A is replaced by the DNA binding domain of this protein, transforms cells by constitutively activating transcription of genes regulated by the PBX protein family. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]."
A3	TCF3	PBX1	"known_fusion,cosmic,chimerdb2,cgp,ticdb"	0	217	24	30	BOWTIE	19:1619110:-	1:164761731:+	ENSG00000071564	ENSG00000185630	ENSE00002701060	ENSE00003472135	GGCACCCTCCCTGACCTGTCTCGGCCTCCCGACTCCTACAGTG*TTTTGAGTATCCGAGGAGCCCAGGAGGAGGAACCCACAGACCC	in-frame	"This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development. Deletion of this gene or diminished activity of the encoded protein may play a role in lymphoid malignancies. This gene is also involved in several chromosomal translocations that are associated with lymphoid malignancies including pre-B-cell acute lymphoblastic leukemia (t(1;19), with PBX1), childhood leukemia (t(19;19), with TFPT) and acute leukemia (t(12;19), with ZNF384). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Sep 2011]."	"This gene encodes a nuclear protein that belongs to the PBX homeobox family of transcriptional factors. Studies in mice suggest that this gene may be involved in the regulation of osteogenesis, and required for skeletal patterning and programming. A chromosomal translocation, t(1;19) involving this gene and TCF3/E2A gene, is associated with pre-B-cell acute lymphoblastic leukemia. The resulting fusion protein, in which the DNA binding domain of E2A is replaced by the DNA binding domain of this protein, transforms cells by constitutively activating transcription of genes regulated by the PBX protein family. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]."
A4	TCF3	PBX1	"known_fusion,cosmic,chimerdb2,cgp,ticdb"	0	217	2	34	BOWTIE+BLAT	19:1619110:-	1:164704095:+	ENSG00000071564	ENSG00000185630			CCAGCCAGGCACCCTCCCTGACCTGTCTCGGCCTCCCGACTCCTACAGTG*GAATATCTCTGAAGTAAAGAAGTATGGAATAAAGAGATAATATTATGACT	CDS(truncated)/intronic	"This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development. Deletion of this gene or diminished activity of the encoded protein may play a role in lymphoid malignancies. This gene is also involved in several chromosomal translocations that are associated with lymphoid malignancies including pre-B-cell acute lymphoblastic leukemia (t(1;19), with PBX1), childhood leukemia (t(19;19), with TFPT) and acute leukemia (t(12;19), with ZNF384). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Sep 2011]."	"This gene encodes a nuclear protein that belongs to the PBX homeobox family of transcriptional factors. Studies in mice suggest that this gene may be involved in the regulation of osteogenesis, and required for skeletal patterning and programming. A chromosomal translocation, t(1;19) involving this gene and TCF3/E2A gene, is associated with pre-B-cell acute lymphoblastic leukemia. The resulting fusion protein, in which the DNA binding domain of E2A is replaced by the DNA binding domain of this protein, transforms cells by constitutively activating transcription of genes regulated by the PBX protein family. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]."
A5	TCF3	PBX1	"known_fusion,cosmic,chimerdb2,cgp,ticdb"	0	217	2	34	BOWTIE+STAR	19:1619110:-	1:164704095:+	ENSG00000071564	ENSG00000185630			CCAGCCAGGCACCCTCCCTGACCTGTCTCGGCCTCCCGACTCCTACAGTG*GAATATCTCTGAAGTAAAGAAGTATGGAATAAAGAGATAATATTATGACT	CDS(truncated)/intronic	"This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development. Deletion of this gene or diminished activity of the encoded protein may play a role in lymphoid malignancies. This gene is also involved in several chromosomal translocations that are associated with lymphoid malignancies including pre-B-cell acute lymphoblastic leukemia (t(1;19), with PBX1), childhood leukemia (t(19;19), with TFPT) and acute leukemia (t(12;19), with ZNF384). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Sep 2011]."	"This gene encodes a nuclear protein that belongs to the PBX homeobox family of transcriptional factors. Studies in mice suggest that this gene may be involved in the regulation of osteogenesis, and required for skeletal patterning and programming. A chromosomal translocation, t(1;19) involving this gene and TCF3/E2A gene, is associated with pre-B-cell acute lymphoblastic leukemia. The resulting fusion protein, in which the DNA binding domain of E2A is replaced by the DNA binding domain of this protein, transforms cells by constitutively activating transcription of genes regulated by the PBX protein family. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]."
A6	GYPE	GYPA	cacg	95	24	9	44	BOWTIE+STAR	4:144801564:-	4:145040934:-	ENSG00000197465	ENSG00000170180			TTCAACCTCTTCTTCAGTCACAAAGAGTTACATCTCATCACAGACAAATG*ATACGCACAAACGGGACACATATGCAGCCACTCCTAGAGCTCATGAAGTT	in-frame	"The protein encoded by this gene is a sialoglycoprotein and a type I membrane protein. It is a member of a gene family with GPA and GPB genes. This encoded protein might carry the M blood group antigen. GYPA, GYPB, and GYPE are organized in tandem on chromosome 4. This gene might have derived from an ancestral gene common to the GPB gene by gene duplication. Two alternatively spliced transcript variants encoding the same protein have been described for this gene. [provided by RefSeq, Jul 2008]."	"Glycophorins A (GYPA) and B (GYPB) are major sialoglycoproteins of the human erythrocyte membrane which bear the antigenic determinants for the MN and Ss blood groups. In addition to the M or N and S or s antigens that commonly occur in all populations, about 40 related variant phenotypes have been identified. These variants include all the variants of the Miltenberger complex and several isoforms of Sta, as well as Dantu, Sat, He, Mg, and deletion variants Ena, S-s-U- and Mk. Most of the variants are the result of gene recombinations between GYPA and GYPB. [provided by RefSeq, Jul 2008].  Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.  Sequence Note: This RefSeq record represents the GYPA*0010101 allele.  Publication Note:  This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications.  "
A7	GYPE	GYPA	cacg	95	24	8	44	BOWTIE+BLAT	4:144801564:-	4:145040934:-	ENSG00000197465	ENSG00000170180			TTCAACCTCTTCTTCAGTCACAAAGAGTTACATCTCATCACAGACAAATG*ATACGCACAAACGGGACACATATGCAGCCACTCCTAGAGCTCATGAAGTT	in-frame	"The protein encoded by this gene is a sialoglycoprotein and a type I membrane protein. It is a member of a gene family with GPA and GPB genes. This encoded protein might carry the M blood group antigen. GYPA, GYPB, and GYPE are organized in tandem on chromosome 4. This gene might have derived from an ancestral gene common to the GPB gene by gene duplication. Two alternatively spliced transcript variants encoding the same protein have been described for this gene. [provided by RefSeq, Jul 2008]."	"Glycophorins A (GYPA) and B (GYPB) are major sialoglycoproteins of the human erythrocyte membrane which bear the antigenic determinants for the MN and Ss blood groups. In addition to the M or N and S or s antigens that commonly occur in all populations, about 40 related variant phenotypes have been identified. These variants include all the variants of the Miltenberger complex and several isoforms of Sta, as well as Dantu, Sat, He, Mg, and deletion variants Ena, S-s-U- and Mk. Most of the variants are the result of gene recombinations between GYPA and GYPB. [provided by RefSeq, Jul 2008].  Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.  Sequence Note: This RefSeq record represents the GYPA*0010101 allele.  Publication Note:  This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications.  "
