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TCF3 transcription factor 3 [ Homo sapiens (human) ]

Gene ID: 6929, updated on 17-Jun-2018
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; 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
See TCF3 in Genome Data Viewer
Location:
19p13.3
Exon count:
21
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (1609284..1652546, 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: C4310786 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 
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity 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 proximal promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II transcription factor activity, sequence-specific DNA binding ISA
Inferred from Sequence Alignment
more info
 
RNA polymerase II transcription factor activity, sequence-specific DNA binding ISM
Inferred from Sequence Model
more info
PubMed 
RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS
Non-traceable Author Statement
more info
PubMed 
bHLH transcription factor binding IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
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 binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific 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 NAS
Non-traceable Author Statement
more info
PubMed 
immunoglobulin V(D)J recombination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
immunoglobulin V(D)J recombination IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of DNA-binding transcription factor activity 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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II 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
 
regulation of hematopoietic stem cell differentiation TAS
Traceable Author Statement
more info
 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
transcription, DNA-templated 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 TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 
transcription factor complex IBA
Inferred from Biological aspect of Ancestor
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_001136139.3NP_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, AW028755, BG284440, BU528547, CD516687, CD674814, KC877695, M24404
    Consensus CDS
    CCDS45899.1
    UniProtKB/Swiss-Prot
    P15923
    Related
    ENSP00000468487.1, OTTHUMP00000263166, ENST00000588136.5
    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_001351778.1NP_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, AW968445, KC877695, M31222
    Conserved Domains (2) summary
    smart00353
    Location:554607
    HLH; helix loop helix domain
    pfam03985
    Location:495549
    Paf1; Paf1
  3. NM_001351779.1NP_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, 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_003200.4NP_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 longestisoform (E12). This isoform is also known as Pan-2.
    Source sequence(s)
    AC005321, KC877695, M31222
    Consensus CDS
    CCDS12074.1
    UniProtKB/Swiss-Prot
    P15923
    Related
    ENSP00000262965.4, ENST00000262965.9
    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 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    1609284..1652546 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, OTTHUMP00000263165, 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, OTTHUMP00000263168, ENST00000453954.6, OTTHUMT00000449381
    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_017027182.1XP_016882671.1  transcription factor E2-alpha isoform X14

    UniProtKB/Swiss-Prot
    P15923
    Conserved Domains (2) summary
    smart00353
    Location:552605
    HLH; helix loop helix domain
    cl25732
    Location:495622
    SMC_N; RecF/RecN/SMC N terminal domain
  28. 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
  29. 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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