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Aliases for TCF12 Gene

Aliases for TCF12 Gene

  • Transcription Factor 12 2 3
  • HTF4 3 4 6
  • Class B Basic Helix-Loop-Helix Protein 20 3 4
  • Helix-Loop-Helix Transcription Factor 4 2 3
  • Transcription Factor HTF-4 3 4
  • DNA-Binding Protein HTF4 3 4
  • E-Box-Binding Protein 3 4
  • BHLHb20 3 4
  • TCF-12 3 4
  • CRS3 3 6
  • HEB 3 4
  • HsT17266 3

External Ids for TCF12 Gene

Summaries for TCF12 Gene

Entrez Gene Summary for TCF12 Gene

  • The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for TCF12 Gene

TCF12 (Transcription Factor 12) is a Protein Coding gene. Diseases associated with TCF12 include craniosynostosis 3 and isolated brachycephaly. Among its related pathways are L1CAM interactions and ERK Signaling. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and transcription regulatory region DNA binding. An important paralog of this gene is TCF4.

UniProtKB/Swiss-Prot for TCF12 Gene

  • Transcriptional regulator. Involved in the initiation of neuronal differentiation. Activates transcription by binding to the E box (5-CANNTG-3)

Gene Wiki entry for TCF12 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TCF12 Gene

Genomics for TCF12 Gene

Genomic Location for TCF12 Gene

56,918,623 bp from pter
57,299,281 bp from pter
380,659 bases
Plus strand

Genomic View for TCF12 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for TCF12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TCF12 Gene

Regulatory Elements for TCF12 Gene

Proteins for TCF12 Gene

  • Protein details for TCF12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Transcription factor 12
    Protein Accession:
    Secondary Accessions:
    • B4E1W1
    • Q7Z3D9
    • Q86TC1
    • Q86VM2

    Protein attributes for TCF12 Gene

    682 amino acids
    Molecular mass:
    72965 Da
    Quaternary structure:
    • Efficient DNA binding requires dimerization with another bHLH protein. Forms homo- or heterooligomers with myogenin, E12 and ITF2 proteins. Interacts with PTF1A. Interacts with NEUROD2 (By similarity). Interacts with RUNX1T1.

    Three dimensional structures from OCA and Proteopedia for TCF12 Gene

    Alternative splice isoforms for TCF12 Gene


neXtProt entry for TCF12 Gene

Proteomics data for TCF12 Gene at MOPED

Post-translational modifications for TCF12 Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys110, Lys151, and Lys571

No data available for DME Specific Peptides for TCF12 Gene

Domains for TCF12 Gene

Gene Families for TCF12 Gene

  • bHLH :Basic helix-loop-helix proteins

Protein Domains for TCF12 Gene

Graphical View of Domain Structure for InterPro Entry



  • the 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.:
    • Q99081
  • Contains 1 bHLH (basic helix-loop-helix) domain.:
    • Q99081
genes like me logo Genes that share domains with TCF12: view

Function for TCF12 Gene

Molecular function for TCF12 Gene

GENATLAS Biochemistry: transcription factor 12,involved in differentiation of muscle cells and in regulation of gene expression during hematopoiesis
UniProtKB/Swiss-Prot Function: Transcriptional regulator. Involved in the initiation of neuronal differentiation. Activates transcription by binding to the E box (5-CANNTG-3)

Gene Ontology (GO) - Molecular Function for TCF12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA 11802795
GO:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription IDA 11802795
GO:0003677 DNA binding --
GO:0003700 sequence-specific DNA binding transcription factor activity IDA 11802795
GO:0005515 protein binding IPI 11802795
genes like me logo Genes that share ontologies with TCF12: view
genes like me logo Genes that share phenotypes with TCF12: view

Animal Models for TCF12 Gene

MGI Knock Outs for TCF12:
Targeting motifs for TCF12 Gene
HOMER Transcription Factor Regulatory Elements motif TCF12
  • Consensus sequence: ACAGCTGCTG Submotif: canonical Cell Type: GM12878 GeoId: GSE32465

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targeting for TCF12 Gene

Localization for TCF12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TCF12 Gene

Subcellular locations from

Jensen Localization Image for TCF12 Gene COMPARTMENTS Subcellular localization image for TCF12 gene
Compartment Confidence
nucleus 5
plasma membrane 1

Gene Ontology (GO) - Cellular Components for TCF12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IDA 21828274
GO:0005634 nucleus IDA --
GO:0005667 transcription factor complex --
GO:0005737 cytoplasm IDA 21828274
GO:0090575 RNA polymerase II transcription factor complex IDA 11802795
genes like me logo Genes that share ontologies with TCF12: view

Pathways for TCF12 Gene

genes like me logo Genes that share pathways with TCF12: view

Pathways by source for TCF12 Gene

1 BioSystems pathway for TCF12 Gene
3 Reactome pathways for TCF12 Gene

Gene Ontology (GO) - Biological Process for TCF12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006357 regulation of transcription from RNA polymerase II promoter TAS 8163514
GO:0006955 immune response TAS 1312219
GO:0007517 muscle organ development TAS 1312219
GO:0010628 positive regulation of gene expression --
genes like me logo Genes that share ontologies with TCF12: view

Transcripts for TCF12 Gene

Unigene Clusters for TCF12 Gene

Transcription factor 12:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for TCF12 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e ^ 3a · 3b · 3c · 3d · 3e ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a ·
SP1: - - - - - - -
SP2: - - - - - -
SP3: - - - - - -
SP4: - - - - - - -
SP6: - - - - - - - - -
SP7: -
SP8: - -
SP9: - -
SP12: - - -
SP13: -

ExUns: 17b ^ 18 ^ 19a · 19b ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26a · 26b ^ 27a · 27b · 27c
SP1: - - -
SP2: - - -
SP3: - - - -
SP4: - - - -
SP5: - - - -
SP11: -

Relevant External Links for TCF12 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for TCF12 Gene

mRNA expression in normal human tissues for TCF12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for TCF12 Gene

SOURCE GeneReport for Unigene cluster for TCF12 Gene Hs.511504

mRNA Expression by UniProt/SwissProt for TCF12 Gene

Tissue specificity: Expressed in several tissues and cell types including skeletal muscle, thymus, and a B-cell line
genes like me logo Genes that share expressions with TCF12: view

No data available for mRNA differential expression in normal tissues for TCF12 Gene

Orthologs for TCF12 Gene

This gene was present in the common ancestor of animals.

Orthologs for TCF12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia TCF12 35
  • 99.72 (n)
  • 99.43 (a)
TCF12 36
  • 99 (a)
(Bos Taurus)
Mammalia TCF12 35
  • 95.41 (n)
  • 98.68 (a)
TCF12 36
  • 98 (a)
(Canis familiaris)
Mammalia TCF12 35
  • 95.9 (n)
  • 98.14 (a)
TCF12 36
  • 98 (a)
(Mus musculus)
Mammalia Tcf12 35
  • 91.45 (n)
  • 95.61 (a)
Tcf12 16
Tcf12 36
  • 96 (a)
(Monodelphis domestica)
Mammalia TCF12 36
  • 96 (a)
(Ornithorhynchus anatinus)
Mammalia TCF12 36
  • 87 (a)
(Rattus norvegicus)
Mammalia Tcf12 35
  • 91.83 (n)
  • 96.03 (a)
(Gallus gallus)
Aves TCF12 35
  • 83.39 (n)
  • 88.74 (a)
TCF12 36
  • 83 (a)
(Anolis carolinensis)
Reptilia TCF12 36
  • 78 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.8165 35
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.13108 35
tcf12 35
  • 79.99 (n)
  • 84.24 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10475 35
(Danio rerio)
Actinopterygii tcf12 35
  • 69.8 (n)
  • 73.64 (a)
tcf12 36
  • 67 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008814 35
  • 48.95 (n)
  • 48.11 (a)
fruit fly
(Drosophila melanogaster)
Insecta da 36
  • 25 (a)
da 37
  • 65 (a)
(Caenorhabditis elegans)
Secernentea hlh-2 36
  • 25 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4501 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 26 (a)
Species with no ortholog for TCF12:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 TCF12 Gene

Gene Tree for TCF12 (if available)
Gene Tree for TCF12 (if available)

Paralogs for TCF12 Gene

Paralogs for TCF12 Gene

genes like me logo Genes that share paralogs with TCF12: view

Variants for TCF12 Gene

Sequence variations from dbSNP and Humsavar for TCF12 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type MAF
rs169892 -- 56,942,445(+) TAATC(C/T)TCAGG intron-variant
rs169893 -- 56,925,533(-) GTTTA(C/T)TGCCC intron-variant
rs190039 -- 56,941,300(+) aaatc(A/G)aggct intron-variant
rs213145 -- 56,953,488(+) taatt(A/G)gtatt intron-variant
rs213146 -- 56,953,575(+) gtttt(A/T)aacta intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TCF12 Gene

Variant ID Type Subtype PubMed ID
nsv833020 CNV Gain+Loss 17160897
nsv457162 CNV Gain 19166990
esv9081 CNV Gain 19470904
nsv904250 CNV Loss 21882294
nsv904251 CNV Loss 21882294
esv2749733 CNV Deletion 23290073
nsv94861 CNV Loss 16902084
nsv457164 CNV Loss 19166990
nsv833021 CNV Gain 17160897
nsv1546 CNV Insertion 18451855
nsv526342 CNV Gain 19592680
nsv94818 CNV Insertion 16902084
nsv94799 CNV Insertion 16902084

Relevant External Links for TCF12 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TCF12 Gene

Disorders for TCF12 Gene

(1) OMIM Diseases for TCF12 Gene (600480)


  • Craniosynostosis 3 (CRS3) [MIM:615314]: A primary abnormality of skull growth involving premature fusion of one or more cranial sutures. The growth velocity of the skull often cannot match that of the developing brain resulting in an abnormal head shape and, in some cases, increased intracranial pressure, which must be treated promptly to avoid permanent neurodevelopmental disability. {ECO:0000269 PubMed:23354436, ECO:0000269 PubMed:25271085}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for TCF12 Gene

Relevant External Links for TCF12

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with TCF12: view

Publications for TCF12 Gene

  1. Genomic organization of human TCF12 gene and spliced mRNA variants producing isoforms of transcription factor HTF4. (PMID: 12826747) Gan T.I. … Bina M. (Cytogenet. Genome Res. 2002) 3 4 23
  2. HEB, a helix-loop-helix protein related to E2A and ITF2 that can modulate the DNA-binding ability of myogenic regulatory factors. (PMID: 1312219) Hu J.S. … Kingston R.E. (Mol. Cell. Biol. 1992) 3 4 23
  3. HTF4: a new human helix-loop-helix protein. (PMID: 1886779) Zhang Y. … Bina M. (Nucleic Acids Res. 1991) 2 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  5. Mutations in TCF12, encoding a basic helix-loop-helix partner of TWIST1, are a frequent cause of coronal craniosynostosis. (PMID: 23354436) Sharma V.P. … Wilkie A.O. (Nat. Genet. 2013) 3 4

Products for TCF12 Gene

Sources for TCF12 Gene

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