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TCF4 Gene(Protein Coding)

Transcription Factor 4

GCID:
GC18M055222
GIFtS:
67
Genes Participants
UDN Logo

Aliases for TCF4 Gene

Aliases for TCF4 Gene

  • Transcription Factor 4 2 3 5
  • Class B Basic Helix-Loop-Helix Protein 19 3 4
  • Immunoglobulin Transcription Factor 2 3 4
  • SL3-3 Enhancer Factor 2 3 4
  • BHLHb19 3 4
  • ITF-2 3 4
  • SEF-2 3 4
  • TCF-4 3 4
  • ITF2 3 4
  • SEF2 3 4
  • SEF2-1A 3
  • SEF2-1B 3
  • SEF2-1D 3
  • SEF2-1 3
  • FECD3 3
  • E2-2 3
  • PTHS 3

External Ids for TCF4 Gene

Previous GeneCards Identifiers for TCF4 Gene

  • GC18M052983
  • GC18M052797
  • GC18M052679
  • GC18M051043
  • GC18M051045
  • GC18M052889
  • GC18M049599

Summaries for TCF4 Gene

Entrez Gene Summary for TCF4 Gene

  • This gene encodes transcription factor 4, a basic helix-loop-helix transcription factor. The encoded protein recognizes an Ephrussi-box ('E-box') binding site ('CANNTG') - a motif first identified in immunoglobulin enhancers. This gene is broadly expressed, and may play an important role in nervous system development. Defects in this gene are a cause of Pitt-Hopkins syndrome. Multiple alternatively spliced transcript variants that encode different proteins have been described. [provided by RefSeq, Aug 2011]

GeneCards Summary for TCF4 Gene

TCF4 (Transcription Factor 4) is a Protein Coding gene. Diseases associated with TCF4 include Pitt-Hopkins Syndrome and Corneal Dystrophy, Fuchs Endothelial, 3. Among its related pathways are ERK Signaling and Corticotropin-releasing hormone. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and protein heterodimerization activity. An important paralog of this gene is TCF3.

UniProtKB/Swiss-Prot for TCF4 Gene

  • Transcription factor that binds to the immunoglobulin enchancer Mu-E5/KE5-motif. Involved in the initiation of neuronal differentiation. Activates transcription by binding to the E box (5-CANNTG-3). Binds to the E-box present in the somatostatin receptor 2 initiator element (SSTR2-INR) to activate transcription (By similarity). Preferentially binds to either 5-ACANNTGT-3 or 5-CCANNTGG-3.

Gene Wiki entry for TCF4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TCF4 Gene

Genomics for TCF4 Gene

Products:

  1. Regulatory Element

Regulatory Elements for TCF4 Gene

Enhancers for TCF4 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around TCF4 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the TCF4 gene promoter:

Genomic Location for TCF4 Gene

Chromosome:
18
Start:
55,222,331 bp from pter
End:
55,664,787 bp from pter
Size:
442,457 bases
Orientation:
Minus strand

Genomic View for TCF4 Gene

Genes around TCF4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TCF4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TCF4 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TCF4 Gene

Proteins for TCF4 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for TCF4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P15884-ITF2_HUMAN
    Recommended name:
    Transcription factor 4
    Protein Accession:
    P15884
    Secondary Accessions:
    • B3KT62
    • B3KUC0
    • B4DT37
    • B4DUG3
    • B7Z5M6
    • B7Z6Y1
    • G0LNT9
    • G0LNU0
    • G0LNU1
    • G0LNU2
    • G0LNU4
    • G0LNU5
    • G0LNU8
    • G0LNU9
    • G0LNV0
    • G0LNV1
    • G0LNV2
    • H3BPQ1
    • Q08AP2
    • Q08AP3
    • Q15439
    • Q15440
    • Q15441

    Protein attributes for TCF4 Gene

    Size:
    667 amino acids
    Molecular mass:
    71308 Da
    Quaternary structure:
    • Efficient DNA binding requires dimerization with another bHLH protein. Forms homo- or heterooligomers with myogenin. Interacts with HIVEP2. Interacts with NEUROD2 (By similarity). Interacts with AGBL1. Interacts with BHLHA9.
    SequenceCaution:
    • Sequence=AAA60310.1; Type=Miscellaneous discrepancy; Note=Incomplete and probable erroneous sequence.; Evidence={ECO:0000305}; Sequence=AAA60312.1; Type=Miscellaneous discrepancy; Note=Incomplete and probable erroneous sequence.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TCF4 Gene

    Alternative splice isoforms for TCF4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TCF4 Gene

Proteomics data for TCF4 Gene at MOPED

Protein Expression for TCF4 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TCF4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TCF4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TCF4 Gene

Domains & Families for TCF4 Gene

Gene Families for TCF4 Gene

HGNC:

Protein Domains for TCF4 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TCF4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P15884

UniProtKB/Swiss-Prot:

ITF2_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.
  • Contains 1 bHLH (basic helix-loop-helix) domain.
genes like me logo Genes that share domains with TCF4: view

Function for TCF4 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for TCF4 Gene

GENATLAS Biochemistry:
transcription factor 4,with several alternatively spliced isoforms
UniProtKB/Swiss-Prot Function:
Transcription factor that binds to the immunoglobulin enchancer Mu-E5/KE5-motif. Involved in the initiation of neuronal differentiation. Activates transcription by binding to the E box (5-CANNTG-3). Binds to the E-box present in the somatostatin receptor 2 initiator element (SSTR2-INR) to activate transcription (By similarity). Preferentially binds to either 5-ACANNTGT-3 or 5-CCANNTGG-3.

Gene Ontology (GO) - Molecular Function for TCF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding ISS 8978694
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding ISS 8978694
GO:0003682 chromatin binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding IDA 2105528
GO:0003714 transcription corepressor activity IEA --
genes like me logo Genes that share ontologies with TCF4: view

Phenotypes for TCF4 Gene

MGI mutant phenotypes for TCF4:
inferred from 4 alleles
GenomeRNAi human phenotypes for TCF4:
genes like me logo Genes that share phenotypes with TCF4: view

Human Phenotype Ontology for TCF4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TCF4 Gene

MGI Knock Outs for TCF4:

Animal Model Products

miRNA for TCF4 Gene

miRTarBase miRNAs that target TCF4

Transcription Factor Targets for TCF4 Gene

Selected GeneGlobe predicted Target genes for TCF4

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) and HOMER Transcription for TCF4 Gene

Localization for TCF4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TCF4 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for TCF4 Gene COMPARTMENTS Subcellular localization image for TCF4 gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1
endoplasmic reticulum 1

No data available for Gene Ontology (GO) - Cellular Components for TCF4 Gene

Pathways & Interactions for TCF4 Gene

genes like me logo Genes that share pathways with TCF4: view

SIGNOR curated interactions for TCF4 Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for TCF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006367 transcription initiation from RNA polymerase II promoter ISS 8978694
GO:0045893 positive regulation of transcription, DNA-templated IDA 2105528
GO:1900746 regulation of vascular endothelial growth factor signaling pathway IEA --
genes like me logo Genes that share ontologies with TCF4: view

Drugs & Compounds for TCF4 Gene

Products:

  1. Drug

(2) Additional Compounds for TCF4 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with TCF4: view

Transcripts for TCF4 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for TCF4 Gene

(43) REFSEQ mRNAs :
(41) Additional mRNA sequences :
(512) Selected AceView cDNA sequences:
(75) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TCF4 Gene

Transcription factor 4:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for TCF4 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b · 17c ^ 18 ^ 19 ^ 20 ^ 21a · 21b ^ 22a ·
SP1: - - - - - - -
SP2: - - - - - - -
SP3: - - - - - -
SP4: - - - - -
SP5: -
SP6: -
SP7: - - -
SP8: - -
SP9: -
SP10:
SP11: - - -
SP12: -
SP13:

ExUns: 22b ^ 23 ^ 24a · 24b · 24c ^ 25a · 25b ^ 26 ^ 27a · 27b
SP1: - -
SP2: -
SP3: - -
SP4: -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for TCF4 Gene

GeneLoc Exon Structure for
TCF4
ECgene alternative splicing isoforms for
TCF4

Expression for TCF4 Gene

Products:

  1. Primer

mRNA expression in normal human tissues for TCF4 Gene

mRNA expression in normal human tissues for TCF4 Gene
mRNA expression by BioGPS for TCF4 GenemRNA expression by GTEx for TCF4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TCF4 Gene

This gene is overexpressed in NK cells (59.0) and Blymphocyte (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for TCF4 Gene



SOURCE GeneReport for Unigene cluster for TCF4 Gene Hs.605153

mRNA Expression by UniProt/SwissProt for TCF4 Gene

P15884-ITF2_HUMAN
Tissue specificity: Expressed in adult heart, brain, placenta, skeletal muscle and to a lesser extent in the lung. In developing embryonic tissues, expression mostly occurs in the brain.
genes like me logo Genes that share expression patterns with TCF4: view

Primer Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for TCF4 Gene

Orthologs for TCF4 Gene

This gene was present in the common ancestor of animals.

Orthologs for TCF4 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
 Mammalia TCF4 35
  • 91.96 (n)
  • 97.94 (a)
TCF7L2 36
  • 98 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia TCF4 35
  • 95.48 (n)
  • 99.07 (a)
TCF4 36
  • 99 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Tcf4 35
  • 92.64 (n)
  • 98.2 (a)
Tcf4 16
Tcf4 36
  • 98 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Tcf4 35
  • 91.62 (n)
  • 97.44 (a)
oppossum
(Monodelphis domestica)
 Mammalia TCF4 36
  • 98 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia TCF4 36
  • 97 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia TCF4 36
  • 99 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves TCF4 36
  • 81 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia TCF4 36
  • 95 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia tcf4 35
  • 80.34 (n)
  • 89.01 (a)
zebrafish
(Danio rerio)
 Actinopterygii CABZ01109624.1 36
  • 78 (a)
 OneToMany
tcf4 36
  • 77 (a)
 OneToMany
fruit fly
(Drosophila melanogaster)
 Insecta da 37
  • 78 (a)
da 36
  • 24 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea hlh-2 36
  • 24 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 36
  • 26 (a)
 OneToMany
Species with no ortholog for TCF4:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 TCF4 Gene

ENSEMBL:
Gene Tree for TCF4 (if available)
TreeFam:
Gene Tree for TCF4 (if available)

Paralogs for TCF4 Gene

Paralogs for TCF4 Gene

(85) SIMAP similar genes for TCF4 Gene using alignment to 31 proteins:

genes like me logo Genes that share paralogs with TCF4: view

Variants for TCF4 Gene

Sequence variations from dbSNP and Humsavar for TCF4 Gene

SNP ID Clin Chr 18 pos Sequence Context AA Info Type
VAR_034704 Pitt-Hopkins syndrome (PTHS)
VAR_034705 Pitt-Hopkins syndrome (PTHS)
rs11660217 - 55,254,497(+) CTTAC(C/T)ATGAG reference, missense
VAR_058632 Pitt-Hopkins syndrome (PTHS)
VAR_058633 Pitt-Hopkins syndrome (PTHS)

Structural Variations from Database of Genomic Variants (DGV) for TCF4 Gene

Variant ID Type Subtype PubMed ID
nsv2315 CNV Loss 18451855
esv273068 CNV Insertion 20981092
nsv438291 CNV Loss 16468122
esv274560 CNV Insertion 20981092
esv271560 CNV Insertion 20981092
esv2659569 CNV Deletion 23128226
esv2635967 CNV Deletion 19546169
esv2487089 CNV Deletion 19546169
dgv496e201 CNV Deletion 23290073
esv2717133 CNV Deletion 23290073
nsv828246 CNV Gain 20364138
nsv131347 CNV Insertion 16902084

Variation tolerance for TCF4 Gene

Residual Variation Intolerance Score: 13.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.67; 14.20% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TCF4 Gene

Human Gene Mutation Database (HGMD)
TCF4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TCF4 Gene

Disorders for TCF4 Gene

MalaCards: The human disease database

(10) MalaCards diseases for TCF4 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
pitt-hopkins syndrome
  • intellectual disability, wide mouth, distinctive facial features, and intermittent hyperventilation followed by apnea
corneal dystrophy, fuchs endothelial, 3
  • fuchs endothelial corneal dystrophy, late-onset
fuchs' endothelial dystrophy
  • fced
diabetes mellitus, noninsulin-dependent
  • diabetes mellitus, noninsulin-dependent, 2
autosomal dominant non-syndromic intellectual disability
  • autosomal dominant mental retardation
- elite association - COSMIC cancer census association via MalaCards
Search TCF4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

ITF2_HUMAN
  • Corneal dystrophy, Fuchs endothelial, 3 (FECD3) [MIM:613267]: A late-onset form of Fuchs endothelial corneal dystrophy, a disease caused by loss of endothelium of the central cornea. It is characterized by focal wart-like guttata that arise from Descemet membrane and develop in the central cornea, epithelial blisters, reduced vision and pain. Descemet membrane is thickened by abnormal collagenous deposition. {ECO:0000269 PubMed:24255041, ECO:0000269 PubMed:25168903, ECO:0000269 PubMed:25593321}. Note=The disease is caused by mutations affecting the gene represented in this entry. Causative mutations are heterozygous TCF4 intronic trinucleotide repeat expansions (CTG)n. {ECO:0000269 PubMed:24255041, ECO:0000269 PubMed:25168903, ECO:0000269 PubMed:25593321}.
  • Pitt-Hopkins syndrome (PTHS) [MIM:610954]: A syndrome characterized by mental retardation, wide mouth and distinctive facial features, and intermittent hyperventilation followed by apnea. Features include intellectual disability with severe speech impairment, normal growth parameters at birth, postnatal microcephaly, breathing anomalies, severe motor developmental delay, motor incoordination, ocular anomalies, constipation, seizures, typical behavior and subtle brain abnormalities. {ECO:0000269 PubMed:17436254, ECO:0000269 PubMed:17436255, ECO:0000269 PubMed:18728071, ECO:0000269 PubMed:19235238, ECO:0000269 PubMed:20184619, ECO:0000269 PubMed:22045651}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for TCF4

Genetic Association Database (GAD)
TCF4
Human Genome Epidemiology (HuGE) Navigator
TCF4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TCF4
genes like me logo Genes that share disorders with TCF4: view

No data available for Genatlas for TCF4 Gene

Publications for TCF4 Gene

  1. A novel, heritable, expanding CTG repeat in an intron of the SEF2-1 gene on chromosome 18q21.1. (PMID: 9302263) Breschel T.S. … Ross C.A. (Hum. Mol. Genet. 1997) 2 3 4 67
  2. Common variants conferring risk of schizophrenia. (PMID: 19571808) Stefansson H. … Collier D.A. (Nature 2009) 3 23
  3. Disruption of the TCF4 gene in a girl with mental retardation but without the classical Pitt-Hopkins syndrome. (PMID: 18627065) Kalscheuer V.M. … Ropers H.H. (Am. J. Med. Genet. A 2008) 3 23
  4. CpG methylation in exon 1 of transcription factor 4 increases with age in normal gastric mucosa and is associated with gene silencing in intestinal-type gastric cancers. (PMID: 18635522) Kim S.K. … Kim Y.S. (Carcinogenesis 2008) 3 23
  5. Development of human plasmacytoid dendritic cells depends on the combined action of the basic helix-loop-helix factor E2-2 and the Ets factor Spi-B. (PMID: 18792017) Nagasawa M. … Blom B. (Eur. J. Immunol. 2008) 3 23

Products for TCF4 Gene

  • Addgene plasmids for TCF4

Sources for TCF4 Gene

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