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TCF3 transcription factor 3 [ Homo sapiens (human) ]

Gene ID: 6929, updated on 24-Dec-2022

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; AllianceGenome:HGNC:11633
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; AGM8A; AGM8B; 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
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Genomic context

See TCF3 in Genome Data Viewer
Location:
19p13.3
Exon count:
21
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (1609292..1652615, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (1580117..1623781, complement)
105.20220307 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 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1795609-1796421 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
Agammaglobulinemia 8, autosomal dominant
MedGen: C4310786 OMIM: 616941 GeneReviews: Not available
Compare labs
AGAMMAGLOBULINEMIA 8B, AUTOSOMAL RECESSIVE
MedGen: C5676958 OMIM: 619824 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

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

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 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 DNA-templated transcription 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 IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
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 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 (1) summary
    cd18943
    Location:538611
    bHLH_E-protein_E47-like; basic helix-loop-helix (bHLH) domain found in transcription factor E47 and similar proteins
  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 (1) summary
    cd18943
    Location:538611
    bHLH_E-protein_E47-like; basic helix-loop-helix (bHLH) domain found in transcription factor E47 and similar proteins
  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, Q9UPI9
    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 Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_047439298.1XP_047295254.1  transcription factor E2-alpha isoform X12

  2. XM_047439297.1XP_047295253.1  transcription factor E2-alpha isoform X10

    UniProtKB/TrEMBL
    A0A0A0MRB7
  3. XM_047439296.1XP_047295252.1  transcription factor E2-alpha isoform X11

    Related
    ENSP00000378813.3, ENST00000395423.7
  4. XM_047439294.1XP_047295250.1  transcription factor E2-alpha isoform X11

  5. XM_047439290.1XP_047295246.1  transcription factor E2-alpha isoform X9

  6. XM_047439286.1XP_047295242.1  transcription factor E2-alpha isoform X8

  7. XM_011528226.3XP_011526528.1  transcription factor E2-alpha isoform X8

    Conserved Domains (1) summary
    smart00353
    Location:551604
    HLH; helix loop helix domain
  8. XM_047439279.1XP_047295235.1  transcription factor E2-alpha isoform X5

  9. XM_047439285.1XP_047295241.1  transcription factor E2-alpha isoform X7

  10. XM_011528225.3XP_011526527.1  transcription factor E2-alpha isoform X7

    Conserved Domains (1) summary
    smart00353
    Location:551604
    HLH; helix loop helix domain
  11. XM_047439284.1XP_047295240.1  transcription factor E2-alpha isoform X6

  12. XM_047439283.1XP_047295239.1  transcription factor E2-alpha isoform X6

  13. XM_047439278.1XP_047295234.1  transcription factor E2-alpha isoform X4

    UniProtKB/Swiss-Prot
    Q9UPI9
  14. XM_047439277.1XP_047295233.1  transcription factor E2-alpha isoform X4

    UniProtKB/Swiss-Prot
    Q9UPI9
  15. XM_017027181.2XP_016882670.1  transcription factor E2-alpha isoform X4

    UniProtKB/Swiss-Prot
    P15923, Q9UPI9
    Conserved Domains (2) summary
    smart00353
    Location:555608
    HLH; helix loop helix domain
    pfam03985
    Location:496549
    Paf1; Paf1
  16. XM_047439261.1XP_047295217.1  transcription factor E2-alpha isoform X2

  17. XM_017027178.2XP_016882667.1  transcription factor E2-alpha isoform X3

    Conserved Domains (1) summary
    smart00353
    Location:581634
    HLH; helix loop helix domain
  18. XM_047439262.1XP_047295218.1  transcription factor E2-alpha isoform X3

    Related
    ENSP00000396363.3, ENST00000453954.6
  19. XM_006722855.5XP_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_047439259.1XP_047295215.1  transcription factor E2-alpha isoform X1

  21. XM_047439260.1XP_047295216.1  transcription factor E2-alpha isoform X1

  22. XM_047439295.1XP_047295251.1  transcription factor E2-alpha isoform X11

  23. XM_047439291.1XP_047295247.1  transcription factor E2-alpha isoform X9

  24. XM_047439280.1XP_047295236.1  transcription factor E2-alpha isoform X5

  25. XM_047439289.1XP_047295245.1  transcription factor E2-alpha isoform X7

  26. XM_047439287.1XP_047295243.1  transcription factor E2-alpha isoform X7

  27. XM_047439282.1XP_047295238.1  transcription factor E2-alpha isoform X6

  28. XM_047439281.1XP_047295237.1  transcription factor E2-alpha isoform X6

  29. XM_047439276.1XP_047295232.1  transcription factor E2-alpha isoform X4

    UniProtKB/Swiss-Prot
    Q9UPI9
  30. XM_047439258.1XP_047295214.1  transcription factor E2-alpha isoform X1

  31. XM_047439293.1XP_047295249.1  transcription factor E2-alpha isoform X10

    UniProtKB/TrEMBL
    A0A0A0MRB7
  32. XM_047439292.1XP_047295248.1  transcription factor E2-alpha isoform X10

    UniProtKB/TrEMBL
    A0A0A0MRB7
  33. XM_047439275.1XP_047295231.1  transcription factor E2-alpha isoform X9

  34. XM_047439274.1XP_047295230.1  transcription factor E2-alpha isoform X8

  35. XM_047439273.1XP_047295229.1  transcription factor E2-alpha isoform X8

  36. XM_047439271.1XP_047295227.1  transcription factor E2-alpha isoform X8

  37. XM_047439267.1XP_047295223.1  transcription factor E2-alpha isoform X5

  38. XM_047439266.1XP_047295222.1  transcription factor E2-alpha isoform X5

  39. XM_047439288.1XP_047295244.1  transcription factor E2-alpha isoform X7

  40. XM_047439272.1XP_047295228.1  transcription factor E2-alpha isoform X7

  41. XM_047439270.1XP_047295226.1  transcription factor E2-alpha isoform X7

  42. XM_047439269.1XP_047295225.1  transcription factor E2-alpha isoform X6

  43. XM_047439268.1XP_047295224.1  transcription factor E2-alpha isoform X6

  44. XM_047439265.1XP_047295221.1  transcription factor E2-alpha isoform X4

    UniProtKB/Swiss-Prot
    Q9UPI9
  45. XM_047439264.1XP_047295220.1  transcription factor E2-alpha isoform X4

    UniProtKB/Swiss-Prot
    Q9UPI9
  46. XM_047439263.1XP_047295219.1  transcription factor E2-alpha isoform X4

    UniProtKB/Swiss-Prot
    Q9UPI9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    1580117..1623781 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)