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    TCF3 transcription factor 3 [ Homo sapiens (human) ]

    Gene ID: 6929, updated on 12-Mar-2017
    Official Symbol
    TCF3provided by HGNC
    Official Full Name
    transcription factor 3provided by HGNC
    Primary source
    HGNC:HGNC:11633
    See related
    Ensembl:ENSG00000071564 MIM:147141; Vega:OTTHUMG00000180031
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    E2A; E47; AGM8; ITF1; VDIR; TCF-3; bHLHb21
    Summary
    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]
    Orthologs
    Location:
    19p13.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 19 NC_000019.10 (1609290..1652590, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (1609289..1652328, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene methyl-CpG binding domain protein 3 Neighboring gene ubiquinol-cytochrome c reductase, complex III subunit XI Neighboring gene RNA, U6 small nuclear 1223, pseudogene Neighboring gene uncharacterized LOC101928543 Neighboring gene one cut homeobox 3 Neighboring gene ATPase phospholipid transporting 8B3

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Agammaglobulinemia 8, autosomal dominant
    MedGen: CN236422 OMIM: 616941 GeneReviews: Not available
    not available

    NHGRI GWAS Catalog

    Description
    A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Interaction of TFIID with the HIV-1 LTR, and therefore presumably HIV-1 Tat protein, is primarily dependent on the LTR TATA element and may also be stabilized or regulated by flanking E box motifs and basic helix-loop-helix proteins such as AP-4 and E47 PubMed

    Go to the HIV-1, Human Interaction Database

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC129647, MGC129648

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    DNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    E-box binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to E-box binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to E-box binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    bHLH transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enhancer binding IC
    Inferred by Curator
    more info
    PubMed 
    mitogen-activated protein kinase kinase kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein heterodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein heterodimerization activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    repressing transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor activity, sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcription factor activity, sequence-specific DNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    vitamin D response element binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    RNA polymerase II transcription factor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear speck IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    transcription factor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    transcription factor E2-alpha
    Names
    NOL1-TCF3 fusion
    VDR interacting repressor
    class B basic helix-loop-helix protein 21
    helix-loop-helix protein HE47
    immunoglobulin transcription factor 1
    kappa-E2-binding factor
    negative vitamin D response element-binding protein
    transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)
    transcription factor 3 variant 3
    transcription factor ITF-1
    vitamin D receptor-interacting repressor

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_029953.1 RefSeqGene

      Range
      5001..48040
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001136139.2NP_001129611.1  transcription factor E2-alpha isoform E47

      See identical proteins and their annotated locations for NP_001129611.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR, lacks an exon and includes an alternate exon in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (E47, also known as Pan-1) is shorter than isoform E12.
      Source sequence(s)
      AC005321, AW028755, BG284440, BU528547, CD516687, CD674814, KC877695, M24404
      Consensus CDS
      CCDS45899.1
      UniProtKB/Swiss-Prot
      P15923
      Related
      ENSP00000468487, OTTHUMP00000263166, ENST00000588136, OTTHUMT00000449375
      Conserved Domains (1) summary
      smart00353
      Location:552605
      HLH; helix loop helix domain
    2. NM_003200.3NP_003191.1  transcription factor E2-alpha isoform E12

      See identical proteins and their annotated locations for NP_003191.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (E12). This isoform is also known as Pan-2.
      Source sequence(s)
      AC005321, KC877695, M31222
      Consensus CDS
      CCDS12074.1
      UniProtKB/Swiss-Prot
      P15923
      Related
      ENSP00000262965, ENST00000262965
      Conserved Domains (2) summary
      smart00353
      Location:555608
      HLH; helix loop helix domain
      pfam03985
      Location:496549
      Paf1; Paf1

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p7 Primary Assembly

      Range
      1609290..1652590 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017027183.1XP_016882672.1  transcription factor E2-alpha isoform X8

      Conserved Domains (2) summary
      smart00353
      Location:554607
      HLH; helix loop helix domain
      pfam03985
      Location:495548
      Paf1; Paf1
    2. XM_017027180.1XP_016882669.1  transcription factor E2-alpha isoform X6

      UniProtKB/Swiss-Prot
      P15923
      Related
      ENSP00000378813, OTTHUMP00000263165, ENST00000395423, OTTHUMT00000449374
      Conserved Domains (2) summary
      smart00353
      Location:559612
      HLH; helix loop helix domain
      pfam04592
      Location:460533
      SelP_N; Selenoprotein P, N terminal region
    3. XM_011528219.2XP_011526521.1  transcription factor E2-alpha isoform X2

      Conserved Domains (2) summary
      smart00353
      Location:583636
      HLH; helix loop helix domain
      pfam03985
      Location:524577
      Paf1; Paf1
    4. XM_006722858.3XP_006722921.1  transcription factor E2-alpha isoform X4

      See identical proteins and their annotated locations for XP_006722921.1

      UniProtKB/TrEMBL
      X6REB3
      Related
      ENSP00000396363, OTTHUMP00000263168, ENST00000453954, OTTHUMT00000449381
      Conserved Domains (1) summary
      smart00353
      Location:580633
      HLH; helix loop helix domain
    5. XM_006722853.3XP_006722916.1  transcription factor E2-alpha isoform X1

      See identical proteins and their annotated locations for XP_006722916.1

      Conserved Domains (2) summary
      smart00353
      Location:584637
      HLH; helix loop helix domain
      pfam03985
      Location:525578
      Paf1; Paf1
    6. XM_006722852.3XP_006722915.1  transcription factor E2-alpha isoform X1

      See identical proteins and their annotated locations for XP_006722915.1

      Conserved Domains (2) summary
      smart00353
      Location:584637
      HLH; helix loop helix domain
      pfam03985
      Location:525578
      Paf1; Paf1
    7. XM_017027179.1XP_016882668.1  transcription factor E2-alpha isoform X5

    8. XM_006722857.3XP_006722920.1  transcription factor E2-alpha isoform X4

      See identical proteins and their annotated locations for XP_006722920.1

      UniProtKB/TrEMBL
      X6REB3
      Conserved Domains (1) summary
      smart00353
      Location:580633
      HLH; helix loop helix domain
    9. XM_011528221.2XP_011526523.1  transcription factor E2-alpha isoform X4

      See identical proteins and their annotated locations for XP_011526523.1

      UniProtKB/TrEMBL
      X6REB3
      Conserved Domains (1) summary
      smart00353
      Location:580633
      HLH; helix loop helix domain
    10. XM_017027178.1XP_016882667.1  transcription factor E2-alpha isoform X3

      Conserved Domains (1) summary
      smart00353
      Location:581634
      HLH; helix loop helix domain
    11. XM_006722856.3XP_006722919.1  transcription factor E2-alpha isoform X3

      See identical proteins and their annotated locations for XP_006722919.1

      Conserved Domains (1) summary
      smart00353
      Location:581634
      HLH; helix loop helix domain
    12. XM_017027177.1XP_016882666.1  transcription factor E2-alpha isoform X1

      Conserved Domains (2) summary
      smart00353
      Location:584637
      HLH; helix loop helix domain
      pfam03985
      Location:525578
      Paf1; Paf1
    13. XM_011528216.2XP_011526518.1  transcription factor E2-alpha isoform X1

      See identical proteins and their annotated locations for XP_011526518.1

      Conserved Domains (2) summary
      smart00353
      Location:584637
      HLH; helix loop helix domain
      pfam03985
      Location:525578
      Paf1; Paf1
    14. XM_011528217.2XP_011526519.1  transcription factor E2-alpha isoform X1

      See identical proteins and their annotated locations for XP_011526519.1

      Conserved Domains (2) summary
      smart00353
      Location:584637
      HLH; helix loop helix domain
      pfam03985
      Location:525578
      Paf1; Paf1
    15. XM_011528226.2XP_011526528.1  transcription factor E2-alpha isoform X11

      Conserved Domains (1) summary
      smart00353
      Location:551604
      HLH; helix loop helix domain
    16. XM_011528223.2XP_011526525.1  transcription factor E2-alpha isoform X8

      Conserved Domains (2) summary
      smart00353
      Location:554607
      HLH; helix loop helix domain
      pfam03985
      Location:495548
      Paf1; Paf1
    17. XM_011528225.2XP_011526527.1  transcription factor E2-alpha isoform X10

      Conserved Domains (1) summary
      smart00353
      Location:551604
      HLH; helix loop helix domain
    18. XM_017027181.1XP_016882670.1  transcription factor E2-alpha isoform X7

      UniProtKB/Swiss-Prot
      P15923
      Conserved Domains (2) summary
      smart00353
      Location:555608
      HLH; helix loop helix domain
      pfam03985
      Location:496549
      Paf1; Paf1
    19. XM_006722855.3XP_006722918.1  transcription factor E2-alpha isoform X3

      See identical proteins and their annotated locations for XP_006722918.1

      Conserved Domains (1) summary
      smart00353
      Location:581634
      HLH; helix loop helix domain
    20. XM_011528220.2XP_011526522.1  transcription factor E2-alpha isoform X3

      See identical proteins and their annotated locations for XP_011526522.1

      Conserved Domains (1) summary
      smart00353
      Location:581634
      HLH; helix loop helix domain
    21. XM_011528227.2XP_011526529.1  transcription factor E2-alpha isoform X13

      UniProtKB/TrEMBL
      A0A0A0MRB7
      Related
      ENSP00000344375, ENST00000344749
      Conserved Domains (1) summary
      smart00353
      Location:501554
      HLH; helix loop helix domain
    22. XM_017027182.1XP_016882671.1  transcription factor E2-alpha isoform X9

      UniProtKB/Swiss-Prot
      P15923
      Conserved Domains (1) summary
      smart00353
      Location:552605
      HLH; helix loop helix domain
    23. XM_011528215.2XP_011526517.1  transcription factor E2-alpha isoform X1

      See identical proteins and their annotated locations for XP_011526517.1

      Conserved Domains (2) summary
      smart00353
      Location:584637
      HLH; helix loop helix domain
      pfam03985
      Location:525578
      Paf1; Paf1
    24. XM_017027184.1XP_016882673.1  transcription factor E2-alpha isoform X12

    RNA

    1. XR_001753745.1 RNA Sequence

    2. XR_430152.3 RNA Sequence

    3. XR_001753746.1 RNA Sequence

    4. XR_001753747.1 RNA Sequence

    5. XR_430153.3 RNA Sequence

    6. XR_001753744.1 RNA Sequence

    7. XR_001753743.1 RNA Sequence

    8. XR_001753742.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018930.2 Alternate CHM1_1.1

      Range
      1609123..1649881 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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