Display Settings:

Format

Send to:

Choose Destination

TCF3 transcription factor 3 [ Homo sapiens (human) ]

Gene ID: 6929, updated on 7-Aug-2014
Official Symbol
TCF3provided by HGNC
Official Full Name
transcription factor 3provided by HGNC
Primary source
HGNC:11633
See related
Ensembl:ENSG00000071564; HPRD:00918; 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; 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]
See TCF3 in Epigenomics, MapViewer
Location:
19p13.3
Exon count:
21
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 19 NC_000019.10 (1609290..1652334, 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 uncharacterized LOC101928543 Neighboring gene one cut homeobox 3 Neighboring gene ATPase, aminophospholipid transporter, class I, type 8B, member 3

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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 Protein Interaction Database

  • CDO in myogenesis, organism-specific biosystem (from REACTOME)
    CDO in myogenesis, organism-specific biosystemCDO/Cdon (cell-adhesion-molecule-related/downregulated by oncogenes) is a type I transmembrane multifunctional co-receptor consisting of five immunoglobulin and three fibronectin type III (FNIII) rep...
  • Delta-Notch Signaling Pathway, organism-specific biosystem (from WikiPathways)
    Delta-Notch Signaling Pathway, organism-specific biosystemThere are 4 Notch receptors in humans (Notch 1-4) that bind to a family of 5 ligands (Jagged 1 and 2 and Delta-like 1-3). The Notch receptors are expressed on the cell surface as heterodimeric protei...
  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • HTLV-I infection, organism-specific biosystem (from KEGG)
    HTLV-I infection, organism-specific biosystemHuman T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus that is associated with adult T-cell leukemia/lymphoma (ATL). It is also strongly implicated in non-neoplastic chronic inflammato...
  • HTLV-I infection, conserved biosystem (from KEGG)
    HTLV-I infection, conserved biosystemHuman T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus that is associated with adult T-cell leukemia/lymphoma (ATL). It is also strongly implicated in non-neoplastic chronic inflammato...
  • Id Signaling Pathway, organism-specific biosystem (from WikiPathways)
    Id Signaling Pathway, organism-specific biosystemInhibitor of DNA binding (ID) proteins are members of the helix-loop-helix (HLH) family of proteins which lack a DNA binding domain themselves but bind to other family members inhibiting their DNA bi...
  • Myogenesis, organism-specific biosystem (from REACTOME)
    Myogenesis, organism-specific biosystemMyogenesis, the formation of muscle tissue, is a complex process involving steps of cell proliferation mediated by growth factor signaling, cell differentiation, reorganization of cells to form myotu...
  • Notch-mediated HES/HEY network, organism-specific biosystem (from Pathway Interaction Database)
    Notch-mediated HES/HEY network, organism-specific biosystem
    Notch-mediated HES/HEY network
  • Regulation of nuclear SMAD2/3 signaling, organism-specific biosystem (from Pathway Interaction Database)
    Regulation of nuclear SMAD2/3 signaling, organism-specific biosystem
    Regulation of nuclear SMAD2/3 signaling
  • SIDS Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
    SIDS Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...
  • Transcriptional misregulation in cancer, organism-specific biosystem (from KEGG)
    Transcriptional misregulation in cancer, organism-specific biosystem
    Transcriptional misregulation in cancer
  • Transcriptional misregulation in cancer, conserved biosystem (from KEGG)
    Transcriptional misregulation in cancer, conserved biosystem
    Transcriptional misregulation in cancer
  • Wnt Signaling Pathway NetPath, organism-specific biosystem (from WikiPathways)
    Wnt Signaling Pathway NetPath, organism-specific biosystemWnt family of proteins are a large family of cysteine-rich secreted glycoproteins that regulate cell-cell interactions. They bind to members of the Frizzled family of 7 transmembrane receptors. Bindi...
  • p38 signaling mediated by MAPKAP kinases, organism-specific biosystem (from Pathway Interaction Database)
    p38 signaling mediated by MAPKAP kinases, organism-specific biosystem
    p38 signaling mediated by MAPKAP kinases
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 
contributes_to 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 
RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription IDA
Inferred from Direct Assay
more info
PubMed 
bHLH transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
enhancer binding IC
Inferred by Curator
more info
 
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 
contributes_to sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding transcription factor activity NAS
Non-traceable Author Statement
more info
PubMed 
transcription coactivator activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
vitamin D response element binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
B cell differentiation NAS
Non-traceable Author Statement
more info
PubMed 
B cell lineage commitment IDA
Inferred from Direct Assay
more info
PubMed 
B cell lineage commitment NAS
Non-traceable Author Statement
more info
PubMed 
Peyer's patch development IEA
Inferred from Electronic Annotation
more info
 
T cell differentiation in thymus IEA
Inferred from Electronic Annotation
more info
 
cell development IEA
Inferred from Electronic Annotation
more info
 
histone H3 acetylation IEA
Inferred from Electronic Annotation
more info
 
histone H4 acetylation IEA
Inferred from Electronic Annotation
more info
 
immunoglobulin V(D)J recombination IDA
Inferred from Direct Assay
more info
PubMed 
muscle cell differentiation TAS
Traceable Author Statement
more info
 
natural killer cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of B cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell cycle IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of muscle cell differentiation TAS
Traceable Author Statement
more info
 
positive regulation of neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of sequence-specific DNA binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
protein stabilization IEA
Inferred from Electronic Annotation
more info
 
regulation of G1/S transition of mitotic cell cycle IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
response to drug IEA
Inferred from Electronic Annotation
more info
 
response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin IDA
Inferred from Direct Assay
more info
 
nuclear nucleosome IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 
protein complex IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
transcription factor E2-alpha
Names
transcription factor E2-alpha
kappa-E2-binding factor
VDR interacting repressor
transcription factor ITF-1
helix-loop-helix protein HE47
transcription factor 3 variant 3
immunoglobulin transcription factor 1
vitamin D receptor-interacting repressor
class B basic helix-loop-helix protein 21
negative vitamin D response element-binding protein
transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)

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 

    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 proteins identical to 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
    Conserved Domains (1) summary
    cd00083
    Location:544604
    Blast Score: 134
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  2. NM_003200.3NP_003191.1  transcription factor E2-alpha isoform E12

    See proteins identical to 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, OTTHUMP00000263159, ENST00000262965, OTTHUMT00000449367
    Conserved Domains (1) summary
    cd00083
    Location:547607
    Blast Score: 137
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000019.10 

    Range
    1609290..1652334
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005259620.2XP_005259677.1  

    See proteins identical to XP_005259677.1

    Conserved Domains (1) summary
    cd00083
    Location:576636
    Blast Score: 137
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  2. XM_006722859.1XP_006722922.1  

    See proteins identical to XP_006722922.1

    UniProtKB/TrEMBL
    Q2TB39
    Conserved Domains (1) summary
    cd00083
    Location:551611
    Blast Score: 137
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  3. XM_006722858.1XP_006722921.1  

    See proteins identical to XP_006722921.1

    Conserved Domains (1) summary
    cd00083
    Location:572632
    Blast Score: 134
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  4. XM_006722853.1XP_006722916.1  

    See proteins identical to XP_006722916.1

    Conserved Domains (1) summary
    cd00083
    Location:576636
    Blast Score: 137
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  5. XM_006722852.1XP_006722915.1  

    See proteins identical to XP_006722915.1

    Conserved Domains (1) summary
    cd00083
    Location:576636
    Blast Score: 137
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  6. XM_006722857.1XP_006722920.1  

    See proteins identical to XP_006722920.1

    Conserved Domains (1) summary
    cd00083
    Location:572632
    Blast Score: 134
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  7. XM_006722856.1XP_006722919.1  

    See proteins identical to XP_006722919.1

    Conserved Domains (1) summary
    cd00083
    Location:573633
    Blast Score: 134
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  8. XM_006722854.1XP_006722917.1  

    Conserved Domains (1) summary
    cd00083
    Location:575635
    Blast Score: 137
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  9. XM_006722855.1XP_006722918.1  

    See proteins identical to XP_006722918.1

    Conserved Domains (1) summary
    cd00083
    Location:573633
    Blast Score: 134
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  10. XM_006722862.1XP_006722925.1  

    Conserved Domains (1) summary
    cd00083
    Location:543603
    Blast Score: 134
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  11. XM_006722860.1XP_006722923.1  

    Conserved Domains (1) summary
    cd00083
    Location:546606
    Blast Score: 137
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  12. XM_006722863.1XP_006722926.1  

    Conserved Domains (1) summary
    cd00083
    Location:493553
    Blast Score: 134
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
  13. XM_006722861.1XP_006722924.1  

    Conserved Domains (1) summary
    cd00083
    Location:543603
    Blast Score: 134
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...

RNA

  1. XR_430152.1 RNA Sequence

  2. XR_430151.1 RNA Sequence

  3. XR_430150.1 RNA Sequence

  4. XR_430153.1 RNA Sequence

Alternate HuRef

Genomic

  1. AC_000151.1 

    Range
    1383232..1423075
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018930.2 

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