Human Gene TCF4 (uc010xdy.1) Description and Page Index
  Description: Homo sapiens transcription factor 4 (TCF4), transcript variant 4, mRNA.
RefSeq Summary (NM_001243227): 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. In addition, an intronic CTG repeat normally numbering 10-37 repeat units can expand to >50 repeat units and cause Fuchs endothelial corneal dystrophy. Multiple alternatively spliced transcript variants that encode different proteins have been described. [provided by RefSeq, Jul 2016].
Transcript (Including UTRs)
   Position: hg19 chr18:52,889,562-53,257,045 Size: 367,484 Total Exon Count: 19 Strand: -
Coding Region
   Position: hg19 chr18:52,895,456-53,252,583 Size: 357,128 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:52,889,562-53,257,045)mRNA (may differ from genome)Protein (647 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIOMIMPubMed
Stanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: B7Z5M6_HUMAN
DESCRIPTION: SubName: Full=Transcription factor 4; SubName: Full=cDNA FLJ58684, highly similar to Transcription factor 4;
SIMILARITY: Contains 1 basic helix-loop-helix (bHLH) domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TCF4
CDC HuGE Published Literature: TCF4
Positive Disease Associations: Fuchs Endothelial Dystrophy , schizophrenia , Survival
Related Studies:
  1. Fuchs Endothelial Dystrophy
    Keith H Baratz et al. The New England journal of medicine 2010, E2-2 protein and Fuchs's corneal dystrophy., The New England journal of medicine. [PubMed 20825314]
    Genetic variation in TCF4 contributes to the development of FCD. (Funded by the National Eye Institute and others.)
  2. schizophrenia
    International Schizophrenia Consortium ,et al. 2009, Common polygenic variation contributes to risk of schizophrenia and bipolar disorder, Nature 2009 460- 7256 : 748-52. [PubMed 19571811]
  3. schizophrenia
    Stefansson ,et al. 2009, Common variants conferring risk of schizophrenia, Nature 2009 460- 7256 : 744-7. [PubMed 19571808]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TCF4
Diseases sorted by gene-association score: pitt-hopkins syndrome* (1712), corneal dystrophy, fuchs endothelial, 3* (1019), fuchs' endothelial dystrophy* (265), intellectual disability* (241), alacrima, achalasia, and mental retardation syndrome* (121), autosomal dominant non-syndromic intellectual disability* (88), cholangitis, primary sclerosing* (13), corneal dystrophy (13), non-syndromic intellectual disability (8), diabetes mellitus, insulin-dependent, 6 (6), blastic plasmacytoid dendritic cell (6), constipation (6), colorectal cancer (3), angelman syndrome (2), eye disease (1)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.72 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 355.67 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 -136.90518-0.264 Picture PostScript Text
3' UTR -1410.145704-0.247 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

SCOP Domains:
47459 - HLH, helix-loop-helix DNA-binding domain

ModBase Predicted Comparative 3D Structure on B7Z5M6
FrontTopSide
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  M74718 - Human SEF2-1A protein (SEF2-1A) mRNA, 5' end.
AK300038 - Homo sapiens cDNA FLJ54545 complete cds, highly similar to Transcription factor 4.
AK096862 - Homo sapiens cDNA FLJ39543 fis, clone PUAEN2008939, highly similar to TRANSCRIPTION FACTOR 4.
AK301144 - Homo sapiens cDNA FLJ58695 complete cds, highly similar to Transcription factor 4.
M74719 - Human SEF2-1B protein (SEF2-1B) mRNA, complete cds.
AK299169 - Homo sapiens cDNA FLJ58684 complete cds, highly similar to Transcription factor 4.
AB209741 - Homo sapiens mRNA for transcription factor 4 isoform b variant protein.
AK300636 - Homo sapiens cDNA FLJ53660 complete cds, highly similar to Transcription factor 4.
AK095041 - Homo sapiens cDNA FLJ37722 fis, clone BRHIP2019186, highly similar to TRANSCRIPTION FACTOR 4.
X52079 - H.sapiens transcription factor (ITF-2) mRNA, 3' end.
AK300612 - Homo sapiens cDNA FLJ61772 complete cds, highly similar to Transcription factor 4.
AK122765 - Homo sapiens cDNA FLJ16304 fis, clone PUAEN2003408, highly similar to TRANSCRIPTION FACTOR 4.
BC125084 - Homo sapiens transcription factor 4, mRNA (cDNA clone MGC:149723 IMAGE:40117795), complete cds.
BC125085 - Homo sapiens transcription factor 4, mRNA (cDNA clone MGC:149724 IMAGE:40117798), complete cds.
FR748222 - Homo sapiens mRNA for transcription factor 4 isoform H- (TCF4 gene).
FR748220 - Homo sapiens mRNA for transcription factor 4 isoform A+ (TCF4 gene).
FR748221 - Homo sapiens mRNA for transcription factor 4 isoform A- (TCF4 gene).
FR748218 - Homo sapiens mRNA for transcription factor 4 isoform D- (TCF4 gene).
FR748219 - Homo sapiens mRNA for transcription factor 4 isoform G- (TCF4 gene).
FR748217 - Homo sapiens mRNA for transcription factor 4 isoform F- (TCF4 gene).
FR748214 - Homo sapiens mRNA for transcription factor 4 isoform C- (TCF4 gene).
FR748215 - Homo sapiens mRNA for transcription factor 4 isoform C- delta (TCF4 gene).
FR748210 - Homo sapiens mRNA for transcription factor 4 isoform B+ (TCF4 gene).
FR748211 - Homo sapiens mRNA for transcription factor 4 isoform B- (TCF4 gene).
FR748212 - Homo sapiens mRNA for transcription factor 4 isoform B+ delta (TCF4 gene).
FR748213 - Homo sapiens mRNA for transcription factor 4 isoform B- delta (TCF4 gene).
FR748216 - Homo sapiens mRNA for transcription factor 4 isoform E- (TCF4 gene).
BC031056 - Homo sapiens transcription factor 4, mRNA (cDNA clone IMAGE:5273193).
AK316165 - Homo sapiens cDNA, FLJ79064 complete cds, highly similar to Transcription factor 4.
AK315074 - Homo sapiens cDNA, FLJ96028.
KJ897642 - Synthetic construct Homo sapiens clone ccsbBroadEn_07036 TCF4 gene, encodes complete protein.
KJ905937 - Synthetic construct Homo sapiens clone ccsbBroadEn_15607 TCF4 gene, encodes complete protein.
KR711928 - Synthetic construct Homo sapiens clone CCSBHm_00032181 TCF4 (TCF4) mRNA, encodes complete protein.
KR711929 - Synthetic construct Homo sapiens clone CCSBHm_00032187 TCF4 (TCF4) mRNA, encodes complete protein.
KR711930 - Synthetic construct Homo sapiens clone CCSBHm_00032188 TCF4 (TCF4) mRNA, encodes complete protein.
KR711931 - Synthetic construct Homo sapiens clone CCSBHm_00032190 TCF4 (TCF4) mRNA, encodes complete protein.
AB527692 - Synthetic construct DNA, clone: pF1KB6272, Homo sapiens TCF4 gene for transcription factor 4, without stop codon, in Flexi system.
KJ901782 - Synthetic construct Homo sapiens clone ccsbBroadEn_11176 TCF4 gene, encodes complete protein.
CR933675 - Homo sapiens mRNA; cDNA DKFZp781D0421 (from clone DKFZp781D0421).
FR748208 - Homo sapiens partial mRNA for transcription factor 4 isoform D (TCF4 gene).
FR748209 - Homo sapiens partial mRNA for transcription factor 4 isoform D (TCF4 gene).
FR748207 - Homo sapiens partial mRNA for transcription factor 4 isoform R (TCF4 gene).
FR748205 - Homo sapiens partial mRNA for transcription factor 4 isoform B (TCF4 gene).
AK095066 - Homo sapiens cDNA FLJ37747 fis, clone BRHIP2022986.
AK021980 - Homo sapiens cDNA FLJ11918 fis, clone HEMBB1000272.
JD021349 - Sequence 2373 from Patent EP1572962.
JD224243 - Sequence 205267 from Patent EP1572962.
JD280261 - Sequence 261285 from Patent EP1572962.
AK026674 - Homo sapiens cDNA: FLJ23021 fis, clone LNG01014, highly similar to HUMSEF21B Human SEF2-1B protein (SEF2-1B) mRNA.
JD056954 - Sequence 37978 from Patent EP1572962.
JD046741 - Sequence 27765 from Patent EP1572962.
FR748223 - Homo sapiens mRNA for transcription factor 4 isoform I- (TCF4 gene).
M74720 - Human SEF2-1D protein (SEF2-1D) mRNA, partial cds.
FR748202 - Homo sapiens partial mRNA for transcription factor 4 isoform M (TCF4 gene).
FR748206 - Homo sapiens partial mRNA for transcription factor 4 isoform E (TCF4 gene).
FR748204 - Homo sapiens partial mRNA for transcription factor 4 isoform C (TCF4 gene).
FR748203 - Homo sapiens partial mRNA for transcription factor 4 isoform L (TCF4 gene).

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z5M6, B7Z5M6_HUMAN, NM_001243227, NP_001230156
UCSC ID: uc010xdy.1
RefSeq Accession: NM_001243227
Protein: B7Z5M6 CCDS: CCDS11960.1, CCDS42438.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS59321.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene TCF4:
hirschsprung-ov (Hirschsprung Disease Overview)
pitt-hopkins (Pitt-Hopkins Syndrome)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001243227.1
exon count: 19CDS single in 3' UTR: no RNA size: 8166
ORF size: 1944CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3857.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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