Human Gene TCF12 (ENST00000438423.6) from GENCODE V44
  Description: Transcriptional regulator. Involved in the initiation of neuronal differentiation. Activates transcription by binding to the E box (5'-CANNTG-3'). (from UniProt Q99081)
RefSeq Summary (NM_207036): 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].
Gencode Transcript: ENST00000438423.6
Gencode Gene: ENSG00000140262.18
Transcript (Including UTRs)
   Position: hg38 chr15:56,918,623-57,288,514 Size: 369,892 Total Exon Count: 21 Strand: +
Coding Region
   Position: hg38 chr15:56,919,914-57,282,587 Size: 362,674 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:56,918,623-57,288,514)mRNA (may differ from genome)Protein (706 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
LynxMalacardsMGIneXtProtPubMedReactome
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: HTF4_HUMAN
DESCRIPTION: RecName: Full=Transcription factor 12; Short=TCF-12; AltName: Full=Class B basic helix-loop-helix protein 20; Short=bHLHb20; AltName: Full=DNA-binding protein HTF4; AltName: Full=E-box-binding protein; AltName: Full=Transcription factor HTF-4;
FUNCTION: Transcriptional regulator. Involved in the initiation of neuronal differentiation. Activates transcription by binding to the E box (5'-CANNTG-3').
SUBUNIT: 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.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in several tissues and cell types including skeletal muscle, thymus, and a B-cell line.
DOMAIN: the 9aaTAD motif is a transactivation domain present in a large number of yeast and animal transcription factors.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/TCF12ID406.html";

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: TCF12
Diseases sorted by gene-association score: craniosynostosis 3* (1228), tcf12-related craniosynostosis* (500), isolated brachycephaly* (202), isolated plagiocephaly* (202), chondrosarcoma, extraskeletal myxoid* (183), photokeratitis (16), craniosynostosis (14), epidural abscess (10), extraosseous chondrosarcoma (10), synostosis (6), diamond-blackfan anemia (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.93 RPKM in Cervix - Endocervix
Total median expression: 381.16 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -132.60296-0.448 Picture PostScript Text
3' UTR -543.602369-0.229 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011598 - HLH_dom

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2KNH - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q99081
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0035326 enhancer binding
GO:0035497 cAMP response element binding
GO:0042803 protein homodimerization activity
GO:0043425 bHLH transcription factor binding
GO:0046332 SMAD binding
GO:0046982 protein heterodimerization activity
GO:0046983 protein dimerization activity
GO:0070888 E-box binding
GO:0071837 HMG box domain binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0006955 immune response
GO:0007275 multicellular organism development
GO:0007399 nervous system development
GO:0007517 muscle organ development
GO:0010628 positive regulation of gene expression
GO:0030154 cell differentiation
GO:0045666 positive regulation of neuron differentiation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:1902036 regulation of hematopoietic stem cell differentiation

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0005737 cytoplasm
GO:0016607 nuclear speck
GO:0043231 intracellular membrane-bounded organelle
GO:0090575 RNA polymerase II transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  AK302923 - Homo sapiens cDNA FLJ55753 complete cds, highly similar to Transcription factor 12.
AL831981 - Homo sapiens mRNA; cDNA DKFZp451F163 (from clone DKFZp451F163); complete cds.
AK294617 - Homo sapiens cDNA FLJ52589 partial cds, highly similar to Transcription factor 12.
AK312710 - Homo sapiens cDNA, FLJ93110.
AK310708 - Homo sapiens cDNA, FLJ17750.
BC050556 - Homo sapiens transcription factor 12, mRNA (cDNA clone MGC:57690 IMAGE:5767579), complete cds.
BC051769 - Homo sapiens cDNA clone IMAGE:5785263, containing frame-shift errors.
M80627 - Human HEB helix-loop-helix protein (HEB) mRNA, complete cds.
M83233 - Homo sapiens transcription factor (HTF4) mRNA, complete cds.
KJ897643 - Synthetic construct Homo sapiens clone ccsbBroadEn_07037 TCF12 gene, encodes complete protein.
CU690724 - Synthetic construct Homo sapiens gateway clone IMAGE:100021475 5' read TCF12 mRNA.
AB384761 - Synthetic construct DNA, clone: pF1KB3223, Homo sapiens TCF12 gene for transcription factor 12, complete cds, without stop codon, in Flexi system.
AM393720 - Synthetic construct Homo sapiens clone IMAGE:100002215 for hypothetical protein (TCF12 gene).
EU446662 - Synthetic construct Homo sapiens clone IMAGE:100070017; IMAGE:100011871; FLH258310.01L transcription factor 12 (HTF4, helix-loop-helix transcription factors 4) (TCF12) gene, encodes complete protein.
EU832502 - Synthetic construct Homo sapiens clone HAIB:100067531; DKFZo008F0929 transcription factor 12 (HTF4, helix-loop-helix transcription factors 4) protein (TCF12) gene, encodes complete protein.
EU832583 - Synthetic construct Homo sapiens clone HAIB:100067612; DKFZo004F0930 transcription factor 12 (HTF4, helix-loop-helix transcription factors 4) protein (TCF12) gene, encodes complete protein.
AF289510 - Homo sapiens TCF12-TEC fusion protein mRNA, partial cds.
AK294991 - Homo sapiens cDNA FLJ50514 complete cds, highly similar to Transcription factor 12.
AK304007 - Homo sapiens cDNA FLJ54640 complete cds, highly similar to Transcription factor 12.
AK308101 - Homo sapiens cDNA, FLJ98049.
BX537967 - Homo sapiens mRNA; cDNA DKFZp686K1352 (from clone DKFZp686K1352).
AM393573 - Synthetic construct Homo sapiens clone IMAGE:100001907 for hypothetical protein (TCF12 gene).
M65209 - Human transcription factor 4, Helix-loop-helix transcription factor 4 (HTF4/TCF12) mRNA, 3' end.
AK303028 - Homo sapiens cDNA FLJ51686 complete cds, highly similar to Transcription factor 12.
AK302749 - Homo sapiens cDNA FLJ52031 complete cds, highly similar to Transcription factor 12.
JD075737 - Sequence 56761 from Patent EP1572962.
JD191782 - Sequence 172806 from Patent EP1572962.
AK311359 - Homo sapiens cDNA, FLJ18401.
AK311709 - Homo sapiens cDNA, FLJ18751.
JD182053 - Sequence 163077 from Patent EP1572962.
JD260620 - Sequence 241644 from Patent EP1572962.
JD363078 - Sequence 344102 from Patent EP1572962.
JD248198 - Sequence 229222 from Patent EP1572962.
JD448689 - Sequence 429713 from Patent EP1572962.
JD037409 - Sequence 18433 from Patent EP1572962.
JD499846 - Sequence 480870 from Patent EP1572962.
JD038392 - Sequence 19416 from Patent EP1572962.
JD551459 - Sequence 532483 from Patent EP1572962.
JD301231 - Sequence 282255 from Patent EP1572962.
JD150426 - Sequence 131450 from Patent EP1572962.
JD141197 - Sequence 122221 from Patent EP1572962.
JD054124 - Sequence 35148 from Patent EP1572962.
JD358646 - Sequence 339670 from Patent EP1572962.
JD557612 - Sequence 538636 from Patent EP1572962.
JD162012 - Sequence 143036 from Patent EP1572962.
JD303657 - Sequence 284681 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q99081 (Reactome details) participates in the following event(s):

R-HSA-448962 Heterodimerization of E proteins with Myod
R-HSA-8956568 RUNX1 binds the core TAL1 complex
R-HSA-448963 Interaction of MyoD:E protein with MEF2
R-HSA-8956586 RUNX1-containing TAL1 complex binds the MYB gene enhancer
R-HSA-375170 CDO in myogenesis
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-525793 Myogenesis
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-1266738 Developmental Biology
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: BC050556, BHLHB20, ENST00000438423.1, ENST00000438423.2, ENST00000438423.3, ENST00000438423.4, ENST00000438423.5, HEB, HTF4, HTF4_HUMAN, Q7Z3D9, Q86TC1, Q86VM2, Q99081, uc002aea.1, uc002aea.2, uc002aea.3, uc002aea.4
UCSC ID: ENST00000438423.6
RefSeq Accession: NM_207036
Protein: Q99081 (aka HTF4_HUMAN)
CCDS: CCDS10159.1, CCDS10160.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.