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Aliases for TCF3 Gene

Aliases for TCF3 Gene

  • Transcription Factor 3 2 3 4 5
  • Immunoglobulin Transcription Factor 1 2 3 4
  • Kappa-E2-Binding Factor 2 3 4
  • Class B Basic Helix-Loop-Helix Protein 21 3 4
  • Transcription Factor E2-Alpha 2 3
  • Transcription Factor ITF-1 3 4
  • VDR Interacting Repressor 2 3
  • BHLHb21 3 4
  • TCF-3 3 4
  • ITF1 3 4
  • E2A 3 4
  • Transcription Factor 3 (E2A Immunoglobulin Enhancer Binding Factors E12/E47) 3
  • Negative Vitamin D Response Element-Binding Protein 3
  • E2A Immunoglobulin Enhancer-Binding Factor E12/E47 2
  • Immunoglobulin Enhancer-Binding Factor E12/E47 4
  • Vitamin D Receptor-Interacting Repressor 3
  • Transcription Factor 3 Variant 3 3
  • Helix-Loop-Helix Protein HE47 3
  • NOL1-TCF3 Fusion 3
  • AGM8 3
  • VDIR 3
  • E47 3

External Ids for TCF3 Gene

Previous GeneCards Identifiers for TCF3 Gene

  • GC19M001671
  • GC19M001549
  • GC19M001560
  • GC19M001384

Summaries for TCF3 Gene

Entrez Gene Summary for TCF3 Gene

  • 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]

GeneCards Summary for TCF3 Gene

TCF3 (Transcription Factor 3) is a Protein Coding gene. Diseases associated with TCF3 include Agammaglobulinemia 8, Autosomal Dominant and Agammaglobulinemia, Non-Bruton Type. Among its related pathways are Ectoderm Differentiation and PAK Pathway. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is TCF4.

UniProtKB/Swiss-Prot for TCF3 Gene

  • Transcriptional regulator. Involved in the initiation of neuronal differentiation. Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5-CANNTG-3. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. Binds to IEB1 and IEB2, which are short DNA sequences in the insulin gene transcription control region.

Gene Wiki entry for TCF3 Gene

Additional gene information for TCF3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TCF3 Gene

Genomics for TCF3 Gene

GeneHancer (GH) Regulatory Elements for TCF3 Gene

Promoters and enhancers for TCF3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I001647 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 592.7 +2.1 2149 6.6 CLOCK ZFP64 FEZF1 DMAP1 YY1 E2F8 ZNF143 SP3 NFYC MEF2D TCF3 SF3A2 LOC100288123 DAZAP1 DOT1L TMEM259 STK11 CIRBP AP3D1 MUM1
GH19I001236 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 89.1 +395.7 395746 41.1 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 CIRBP C19orf24 MIDN CBARP ATP5F1D SF3A2 TCF3 TMEM259 LOC100288123 PTBP1
GH19I001382 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 75.2 +268.6 268579 2.2 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NDUFS7 PIR43938 PIR60227 TRF-GAA1-6 TRN-GTT2-6 CIRBP SF3A2 TMEM259 MUM1 TCF3
GH19I001437 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 72.2 +213.1 213122 4.3 MLX DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC RPS15 ENSG00000268798 SF3A2 TCF3 TMEM259 LOC100288123 PTBP1 DAZAP1 MED16 ENSG00000267317
GH19I001019 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 66.5 +631.4 631398 4.4 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF143 TMEM259 GC19P001025 RNU6-2 TCF3 LOC100288123 DAZAP1 GRIN3B PTBP1 CIRBP MED16
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TCF3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TCF3 gene promoter:

Genomic Locations for TCF3 Gene

Genomic Locations for TCF3 Gene
chr19:1,609,290-1,652,605
(GRCh38/hg38)
Size:
43,316 bases
Orientation:
Minus strand
chr19:1,609,291-1,652,604
(GRCh37/hg19)

Genomic View for TCF3 Gene

Genes around TCF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TCF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TCF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TCF3 Gene

Proteins for TCF3 Gene

  • Protein details for TCF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P15923-TFE2_HUMAN
    Recommended name:
    Transcription factor E2-alpha
    Protein Accession:
    P15923
    Secondary Accessions:
    • P15883
    • Q14208
    • Q14635
    • Q14636
    • Q2TB39
    • Q2TB40
    • Q9UPI9

    Protein attributes for TCF3 Gene

    Size:
    654 amino acids
    Molecular mass:
    67600 Da
    Quaternary structure:
    • Forms a heterodimer with ASH1 and TWIST2. Isoform E12 interacts with RALGAPA1 and FIGLA. Efficient DNA binding requires dimerization with another bHLH protein. Component of a nuclear TAL-1 complex composed at least of CBFA2T3, LDB1, TAL1 and TCF3. Interacts with NEUROD2, PTF1A and TGFB1I1. Forms a heterodimer with MYOG; heterodimerization enhances MYOG DNA-binding and transcriptional activities (By similarity). Homodimer. Heterodimer. Forms a heterodimer with NEUROD1; the heterodimer is inhibited in presence of ID2, but not NR0B2, to E-box element. Interacts with EP300 and UBE2I. Interacts with BHLHA9 (PubMed:25466284). Forms a heterodimer with ATOH8; repress transcription of TCF3 and TCF3/NEUROG3 dimer-induced transactivation of E box-dependent promoters (By similarity).
    SequenceCaution:
    • Sequence=AAA52331.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TCF3 Gene

    Alternative splice isoforms for TCF3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TCF3 Gene

Post-translational modifications for TCF3 Gene

No data available for DME Specific Peptides for TCF3 Gene

Domains & Families for TCF3 Gene

Gene Families for TCF3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for TCF3 Gene

Suggested Antigen Peptide Sequences for TCF3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P15923

UniProtKB/Swiss-Prot:

TFE2_HUMAN :
  • the 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.
Domain:
  • the 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.
genes like me logo Genes that share domains with TCF3: view

Function for TCF3 Gene

Molecular function for TCF3 Gene

GENATLAS Biochemistry:
transcription factor 3,heterodimerizing with all myogenic bHLH vproteins and binding DNA cooperatively with PBXs/MEISs/PKNOX1
UniProtKB/Swiss-Prot Function:
Transcriptional regulator. Involved in the initiation of neuronal differentiation. Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell fate during embryogenesis, like muscle or early B-cell differentiation. Dimers bind DNA on E-box motifs: 5-CANNTG-3. Binds to the kappa-E2 site in the kappa immunoglobulin gene enhancer. Binds to IEB1 and IEB2, which are short DNA sequences in the insulin gene transcription control region.

Phenotypes From GWAS Catalog for TCF3 Gene

Gene Ontology (GO) - Molecular Function for TCF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 14576336
GO:0001078 transcriptional repressor activity, RNA polymerase II proximal promoter sequence-specific DNA binding IDA 14576336
GO:0003677 DNA binding NAS 2105528
GO:0003700 DNA binding transcription factor activity NAS 2493990
GO:0003713 transcription coactivator activity IDA 14752053
genes like me logo Genes that share ontologies with TCF3: view
genes like me logo Genes that share phenotypes with TCF3: view

Human Phenotype Ontology for TCF3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TCF3 Gene

MGI Knock Outs for TCF3:

Animal Model Products

Transcription Factor Targets for TCF3 Gene

Selected GeneGlobe predicted Target genes for TCF3
Targeted motifs for TCF3 Gene
HOMER Transcription Factor Regulatory Elements motif TCF3
  • Consensus sequence: ANACAGCTGC Submotif: canonical Cell Type: proBcell GEO ID: GSE21978

Clone Products

  • Addgene plasmids for TCF3

No data available for Enzyme Numbers (IUBMB) for TCF3 Gene

Localization for TCF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TCF3 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TCF3 gene
Compartment Confidence
nucleus 5
plasma membrane 2
cytosol 2
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TCF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IDA 21828274
GO:0005634 nucleus NAS 2493990
GO:0005654 nucleoplasm TAS,IDA --
GO:0005667 transcription factor complex IDA 10775504
GO:0005737 cytoplasm IDA 21828274
genes like me logo Genes that share ontologies with TCF3: view

Pathways & Interactions for TCF3 Gene

genes like me logo Genes that share pathways with TCF3: view

SIGNOR curated interactions for TCF3 Gene

Activates:
Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for TCF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 14576336
GO:0002326 B cell lineage commitment NAS 12435739
GO:0006351 transcription, DNA-templated IDA,IEA 10775504
GO:0006355 regulation of transcription, DNA-templated NAS 2493990
GO:0007399 nervous system development IEA --
genes like me logo Genes that share ontologies with TCF3: view

Drugs & Compounds for TCF3 Gene

No Compound Related Data Available

Transcripts for TCF3 Gene

Unigene Clusters for TCF3 Gene

Transcription factor 3:
Representative Sequences:

Clone Products

  • Addgene plasmids for TCF3

Alternative Splicing Database (ASD) splice patterns (SP) for TCF3 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b · 17c ^ 18a · 18b · 18c · 18d ·
SP1: -
SP2:
SP3:
SP4: - - - -
SP5:
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:

ExUns: 18e · 18f ^ 19a · 19b ^ 20a · 20b · 20c · 20d ^ 21a · 21b · 21c · 21d · 21e · 21f · 21g ^ 22a · 22b · 22c ^ 23 ^ 24a · 24b · 24c
SP1: - - - -
SP2: - - - - - - - - -
SP3: - - - -
SP4:
SP5:
SP6:
SP7:
SP8: - - - - - - -
SP9: -
SP10: - - -
SP11: - - - - - - - - - -
SP12: - - - - - - - - - - -
SP13: - - - - - -
SP14: - - - - - -
SP15: - - - - - - - - -
SP16: -
SP17: - -
SP18: - - - - -
SP19: - - -
SP20: - - - - - - -
SP21:

Relevant External Links for TCF3 Gene

GeneLoc Exon Structure for
TCF3
ECgene alternative splicing isoforms for
TCF3

Expression for TCF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TCF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TCF3 Gene

This gene is overexpressed in Placenta (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TCF3 Gene



Protein tissue co-expression partners for TCF3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TCF3 Gene:

TCF3

SOURCE GeneReport for Unigene cluster for TCF3 Gene:

Hs.371282

Evidence on tissue expression from TISSUES for TCF3 Gene

  • Nervous system(3.5)
  • Lung(3.2)
  • Bone marrow(3)
  • Blood(2.8)
  • Intestine(2.7)
  • Lymph node(2.3)
  • Spleen(2.3)
  • Kidney(2.1)
  • Muscle(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TCF3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • meninges
  • middle ear
  • mouth
  • neck
  • outer ear
  • sinus
  • skull
Thorax:
  • bronchus
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • biliary tract
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
Pelvis:
  • pelvis
  • rectum
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with TCF3: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for TCF3 Gene

Orthologs for TCF3 Gene

This gene was present in the common ancestor of animals.

Orthologs for TCF3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TCF3 33 34
  • 98.64 (n)
cow
(Bos Taurus)
Mammalia TCF3 33 34
  • 84.69 (n)
dog
(Canis familiaris)
Mammalia TCF3 33 34
  • 83.92 (n)
mouse
(Mus musculus)
Mammalia Tcf3 33 16 34
  • 79.9 (n)
rat
(Rattus norvegicus)
Mammalia Tcf3 33
  • 79.19 (n)
oppossum
(Monodelphis domestica)
Mammalia TCF3 34
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TCF3 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves TCF3 33 34
  • 71.34 (n)
lizard
(Anolis carolinensis)
Reptilia TCF3 34
  • 54 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tcf3 33
  • 61.9 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC52608 33
zebrafish
(Danio rerio)
Actinopterygii tcf3b 33 34
  • 61.29 (n)
tcf3a 34
  • 49 (a)
OneToMany
e12 33
fruit fly
(Drosophila melanogaster)
Insecta da 35 34
  • 56 (a)
worm
(Caenorhabditis elegans)
Secernentea hlh-2 34
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 23 (a)
OneToMany
Species where no ortholog for TCF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TCF3 Gene

ENSEMBL:
Gene Tree for TCF3 (if available)
TreeFam:
Gene Tree for TCF3 (if available)

Paralogs for TCF3 Gene

Paralogs for TCF3 Gene

Pseudogenes.org Pseudogenes for TCF3 Gene

genes like me logo Genes that share paralogs with TCF3: view

Variants for TCF3 Gene

Sequence variations from dbSNP and Humsavar for TCF3 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs376780559 A colorectal cancer sample 1,650,226(-) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs879255271 pathogenic, Agammaglobulinemia 8, autosomal dominant 1,612,357(-) C/T coding_sequence_variant, downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs201725633 likely-benign, not provided 1,622,040(-) G/A intron_variant
rs879255378 uncertain-significance, not specified 1,619,219(-) G/A/C coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1000002388 -- 1,629,272(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TCF3 Gene

Variant ID Type Subtype PubMed ID
dgv1971e59 CNV duplication 20981092
dgv6205n54 CNV loss 21841781
dgv6206n54 CNV loss 21841781
dgv6207n54 CNV loss 21841781
dgv6208n54 CNV gain+loss