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    TCF3 transcription factor 3 [ Homo sapiens (human) ]

    Gene ID: 6929, updated on 11-Jul-2021

    Summary

    Official Symbol
    TCF3provided by HGNC
    Official Full Name
    transcription factor 3provided by HGNC
    Primary source
    HGNC:HGNC:11633
    See related
    Ensembl:ENSG00000071564 MIM:147141
    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; p75; 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]
    Expression
    Broad expression in testis (RPKM 16.2), lymph node (RPKM 12.8) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TCF3 in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (1609292..1652615, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (1609291..1652614, 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

    Genomic regions, transcripts, and products

    Expression

    • 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus.
    GeneReviews: Not available
    Agammaglobulinemia 8, autosomal dominant
    MedGen: C4310786 OMIM: 616941 GeneReviews: Not available
    Compare labs

    HIV-1 interactions

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC129647, MGC129648

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription factor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
     
    enables DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to E-box binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables 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
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables bHLH transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables cis-regulatory region sequence-specific DNA binding IC
    Inferred by Curator
    more info
    PubMed 
    enables mitogen-activated protein kinase kinase kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein heterodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables vitamin D response element binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in B cell differentiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in B cell lineage commitment NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in immunoglobulin V(D)J recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within immunoglobulin V(D)J recombination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in regulation of transcription, DNA-templated NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in euchromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of transcription regulator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    part_of transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    transcription factor E2-alpha
    Names
    E2A-HLF fusion transcript protein
    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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_029953.2 RefSeqGene

      Range
      4932..48255
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1325

    mRNA and Protein(s)

    1. NM_001136139.4NP_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. Variants 2 and 4 encode the same isoform (E47).
      Source sequence(s)
      AC005321, AC006274, AW028755, BG284440, BU528547, CD516687, CD674814, KC877695, M24404
      Consensus CDS
      CCDS45899.1
      UniProtKB/Swiss-Prot
      P15923
      Related
      ENSP00000468487.1, ENST00000588136.7
      Conserved Domains (2) summary
      smart00353
      Location:552605
      HLH; helix loop helix domain
      cl25732
      Location:495622
      SMC_N; RecF/RecN/SMC N terminal domain
    2. NM_001351778.2NP_001338707.1  transcription factor E2-alpha isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the central coding region, and contains an alternate splice structure in the 3' region, resulting in differences in the 3' UTR. The encoded isoform (3) has the same N- and C-termini, but is one aa shorter than isoform 1.
      Source sequence(s)
      AA251176, AC006274, AW968445, KC877695, M31222
      Conserved Domains (2) summary
      smart00353
      Location:554607
      HLH; helix loop helix domain
      pfam03985
      Location:495549
      Paf1; Paf1
    3. NM_001351779.2NP_001338708.1  transcription factor E2-alpha isoform E47

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate penultimate exon compared to variant 1. The encoded isoform (E47, also known as Pan-1) is shorter than isoform E12. Variants 2 and 4 encode the same isoform (E47).
      Source sequence(s)
      AC005321, AC006274, AW028755, BG284440, KC877695, M24404, M31222
      Consensus CDS
      CCDS45899.1
      Conserved Domains (2) summary
      smart00353
      Location:552605
      HLH; helix loop helix domain
      cl25732
      Location:495622
      SMC_N; RecF/RecN/SMC N terminal domain
    4. NM_003200.5NP_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 longest transcript and encodes the longest isoform (E12). This isoform is also known as Pan-2.
      Source sequence(s)
      AC005321, AC006274, KC877695, M31222
      Consensus CDS
      CCDS12074.1
      UniProtKB/Swiss-Prot
      P15923
      Related
      ENSP00000262965.5, ENST00000262965.12
      Conserved Domains (2) summary
      smart00353
      Location:555608
      HLH; helix loop helix domain
      pfam03985
      Location:496549
      Paf1; Paf1

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

      Range
      1609292..1652615 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528227.3XP_011526529.1  transcription factor E2-alpha isoform X17

      UniProtKB/TrEMBL
      A0A0A0MRB7
      Related
      ENSP00000344375.6, ENST00000344749.9
      Conserved Domains (1) summary
      smart00353
      Location:501554
      HLH; helix loop helix domain
    2. XM_017027180.2XP_016882669.1  transcription factor E2-alpha isoform X11

      UniProtKB/Swiss-Prot
      P15923
      Related
      ENSP00000378813.3, ENST00000395423.7
      Conserved Domains (2) summary
      smart00353
      Location:559612
      HLH; helix loop helix domain
      pfam04592
      Location:460533
      SelP_N; Selenoprotein P, N terminal region
    3. XM_024451674.1XP_024307442.1  transcription factor E2-alpha isoform X1

      Conserved Domains (2) summary
      smart00353
      Location:611664
      HLH; helix loop helix domain
      pfam03985
      Location:552606
      Paf1
    4. XM_024451673.1XP_024307441.1  transcription factor E2-alpha isoform X1

      Conserved Domains (2) summary
      smart00353
      Location:611664
      HLH; helix loop helix domain
      pfam03985
      Location:552606
      Paf1
    5. XM_024451678.1XP_024307446.1  transcription factor E2-alpha isoform X3

      Conserved Domains (2) summary
      smart00353
      Location:607660
      HLH; helix loop helix domain
      cl25732
      Location:551677
      SMC_N; RecF/RecN/SMC N terminal domain
    6. XM_024451677.1XP_024307445.1  transcription factor E2-alpha isoform X3

      Conserved Domains (2) summary
      smart00353
      Location:607660
      HLH; helix loop helix domain
      cl25732
      Location:551677
      SMC_N; RecF/RecN/SMC N terminal domain
    7. XM_024451676.1XP_024307444.1  transcription factor E2-alpha isoform X2

      Conserved Domains (2) summary
      smart00353
      Location:608661
      HLH; helix loop helix domain
      cl25732
      Location:551678
      SMC_N; RecF/RecN/SMC N terminal domain
    8. XM_024451672.1XP_024307440.1  transcription factor E2-alpha isoform X1

      Conserved Domains (2) summary
      smart00353
      Location:611664
      HLH; helix loop helix domain
      pfam03985
      Location:552606
      Paf1
    9. XM_024451669.1XP_024307437.1  transcription factor E2-alpha isoform X1

      Conserved Domains (2) summary
      smart00353
      Location:611664
      HLH; helix loop helix domain
      pfam03985
      Location:552606
      Paf1
    10. XM_024451671.1XP_024307439.1  transcription factor E2-alpha isoform X1

      Conserved Domains (2) summary
      smart00353
      Location:611664
      HLH; helix loop helix domain
      pfam03985
      Location:552606
      Paf1
    11. XM_017027179.2XP_016882668.1  transcription factor E2-alpha isoform X9

    12. XM_011528219.2XP_011526521.1  transcription factor E2-alpha isoform X5

      Conserved Domains (2) summary
      smart00353
      Location:583636
      HLH; helix loop helix domain
      pfam03985
      Location:524577
      Paf1; Paf1
    13. XM_006722858.3XP_006722921.1  transcription factor E2-alpha isoform X8

      See identical proteins and their annotated locations for XP_006722921.1

      UniProtKB/TrEMBL
      X6REB3
      Related
      ENSP00000396363.3, ENST00000453954.6
      Conserved Domains (1) summary
      smart00353
      Location:580633
      HLH; helix loop helix domain
    14. XM_006722857.4XP_006722920.1  transcription factor E2-alpha isoform X8

      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
    15. XM_017027177.2XP_016882666.1  transcription factor E2-alpha isoform X4

      Conserved Domains (2) summary
      smart00353
      Location:584637
      HLH; helix loop helix domain
      pfam03985
      Location:525578
      Paf1; Paf1
    16. XM_024451675.1XP_024307443.1  transcription factor E2-alpha isoform X2

      Conserved Domains (2) summary
      smart00353
      Location:608661
      HLH; helix loop helix domain
      cl25732
      Location:551678
      SMC_N; RecF/RecN/SMC N terminal domain
    17. XM_011528223.3XP_011526525.1  transcription factor E2-alpha isoform X13

      Conserved Domains (2) summary
      smart00353
      Location:554607
      HLH; helix loop helix domain
      pfam03985
      Location:495549
      Paf1; Paf1
    18. XM_024451679.1XP_024307447.1  transcription factor E2-alpha isoform X6

      Conserved Domains (2) summary
      smart00353
      Location:582635
      HLH; helix loop helix domain
      pfam03985
      Location:523577
      Paf1
    19. XM_011528221.2XP_011526523.1  transcription factor E2-alpha isoform X8

      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
    20. XM_017027178.1XP_016882667.1  transcription factor E2-alpha isoform X7

      Conserved Domains (1) summary
      smart00353
      Location:581634
      HLH; helix loop helix domain
    21. XM_006722855.4XP_006722918.1  transcription factor E2-alpha isoform X7

      See identical proteins and their annotated locations for XP_006722918.1

      Conserved Domains (1) summary
      smart00353
      Location:581634
      HLH; helix loop helix domain
    22. XM_011528216.2XP_011526518.1  transcription factor E2-alpha isoform X4

      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
    23. XM_011528226.2XP_011526528.1  transcription factor E2-alpha isoform X16

      Conserved Domains (1) summary
      smart00353
      Location:551604
      HLH; helix loop helix domain
    24. XM_011528225.2XP_011526527.1  transcription factor E2-alpha isoform X15

      Conserved Domains (1) summary
      smart00353
      Location:551604
      HLH; helix loop helix domain
    25. XM_017027181.1XP_016882670.1  transcription factor E2-alpha isoform X12

      UniProtKB/Swiss-Prot
      P15923
      Conserved Domains (2) summary
      smart00353
      Location:555608
      HLH; helix loop helix domain
      pfam03985
      Location:496549
      Paf1; Paf1
    26. XM_011528220.2XP_011526522.1  transcription factor E2-alpha isoform X7

      See identical proteins and their annotated locations for XP_011526522.1

      Conserved Domains (1) summary
      smart00353
      Location:581634
      HLH; helix loop helix domain
    27. XM_024451670.1XP_024307438.1  transcription factor E2-alpha isoform X1

      Conserved Domains (2) summary
      smart00353
      Location:611664
      HLH; helix loop helix domain
      pfam03985
      Location:552606
      Paf1
    28. XM_024451680.1XP_024307448.1  transcription factor E2-alpha isoform X10

      Conserved Domains (2) summary
      smart00353
      Location:611663
      HLH; helix loop helix domain
      pfam03985
      Location:552606
      Paf1

    RNA

    1. XR_002958351.1 RNA Sequence

    2. XR_002958350.1 RNA Sequence

    3. XR_002958349.1 RNA Sequence

    4. XR_002958348.1 RNA Sequence

    5. XR_001753745.1 RNA Sequence

    6. XR_001753747.1 RNA Sequence

    7. XR_002958347.1 RNA Sequence

    8. XR_002958346.1 RNA Sequence

    9. XR_001753743.2 RNA Sequence

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