Human Gene TBX5 (ENST00000310346.8) from GENCODE V44
  Description: Homo sapiens T-box transcription factor 5 (TBX5), transcript variant 1, mRNA. (from RefSeq NM_000192)
RefSeq Summary (NM_000192): This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. This gene is closely linked to related family member T-box 3 (ulnar mammary syndrome) on human chromosome 12. The encoded protein may play a role in heart development and specification of limb identity. Mutations in this gene have been associated with Holt-Oram syndrome, a developmental disorder affecting the heart and upper limbs. Several transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000310346.8
Gencode Gene: ENSG00000089225.20
Transcript (Including UTRs)
   Position: hg38 chr12:114,353,931-114,408,442 Size: 54,512 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg38 chr12:114,355,532-114,403,898 Size: 48,367 Coding Exon Count: 8 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:114,353,931-114,408,442)mRNA (may differ from genome)Protein (518 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=T-box transcription factor TBX5; Short=T-box protein 5;
FUNCTION: Involved in the transcriptional regulation of genes required for mesoderm differentiation. Probably plays a role in limb pattern formation.
SUBUNIT: Monomer.
INTERACTION: Q08369:Gata4 (xeno); NbExp=2; IntAct=EBI-297043, EBI-297008; P52952:NKX2-5; NbExp=6; IntAct=EBI-304423, EBI-936601;
SUBCELLULAR LOCATION: Nucleus (Potential).
DISEASE: Defects in TBX5 are the cause of Holt-Oram syndrome (HOS) [MIM:142900]. HOS is a developmental disorder affecting the heart and upper limbs. It is characterized by thumb anomaly and atrial septal defects.
SIMILARITY: Contains 1 T-box DNA-binding domain.
WEB RESOURCE: Name=GeneReviews; URL="";

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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: TBX5
Diseases sorted by gene-association score: holt-oram syndrome* (1637), aortic valve disease 2* (283), heart disease* (263), tbx5-related holt-oram syndrome* (100), ulnar-mammary syndrome (33), lung agenesis (17), ventricular septal defect (16), duane-radial ray syndrome (15), heart septal defect (15), atrial heart septal defect (14), pallister-killian syndrome (13), murcs association (12), acro-renal-ocular syndrome (10), acheiropody (9), mayer-rokitansky-kuster-hauser syndrome (8), atrioventricular septal defect (8), atrioventricular block (7), pulmonary valve stenosis (6), pulmonary valve disease (6), tetralogy of fallot (6), char syndrome (6), patent ductus arteriosus (6), patent foramen ovale (6), apert syndrome (6), atrial fibrillation (5), dilated cardiomyopathy (3), autosomal genetic disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 40.64 RPKM in Heart - Atrial Appendage
Total median expression: 90.02 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 -230.20667-0.345 Picture PostScript Text
3' UTR -375.701601-0.235 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
IPR008967 - p53-like_TF_DNA-bd
IPR001699 - TF_T-box
IPR018186 - TF_T-box_CS

Pfam Domains:
PF00907 - T-box

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2X6U - X-ray MuPIT 2X6V - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q99593
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 BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
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:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory 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:0043565 sequence-specific DNA binding

Biological Process:
GO:0002009 morphogenesis of an epithelium
GO:0003166 bundle of His development
GO:0003181 atrioventricular valve morphogenesis
GO:0003197 endocardial cushion development
GO:0003218 cardiac left ventricle formation
GO:0003229 ventricular cardiac muscle tissue development
GO:0003281 ventricular septum development
GO:0003283 atrial septum development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006367 transcription initiation from RNA polymerase II promoter
GO:0007267 cell-cell signaling
GO:0007275 multicellular organism development
GO:0007389 pattern specification process
GO:0007507 heart development
GO:0008285 negative regulation of cell proliferation
GO:0010719 negative regulation of epithelial to mesenchymal transition
GO:0030324 lung development
GO:0030326 embryonic limb morphogenesis
GO:0030336 negative regulation of cell migration
GO:0035115 embryonic forelimb morphogenesis
GO:0035136 forelimb morphogenesis
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0051891 positive regulation of cardioblast differentiation
GO:0055007 cardiac muscle cell differentiation
GO:0060039 pericardium development
GO:0060044 negative regulation of cardiac muscle cell proliferation
GO:0060045 positive regulation of cardiac muscle cell proliferation
GO:0060413 atrial septum morphogenesis
GO:0060980 cell migration involved in coronary vasculogenesis
GO:0072513 positive regulation of secondary heart field cardioblast proliferation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0032991 macromolecular complex
GO:0032993 protein-DNA complex

-  Descriptions from all associated GenBank mRNAs
  BC027942 - Homo sapiens T-box 5, mRNA (cDNA clone MGC:35581 IMAGE:5204163), complete cds.
JD048418 - Sequence 29442 from Patent EP1572962.
JD237468 - Sequence 218492 from Patent EP1572962.
JD491097 - Sequence 472121 from Patent EP1572962.
JD184688 - Sequence 165712 from Patent EP1572962.
JD241772 - Sequence 222796 from Patent EP1572962.
JD520028 - Sequence 501052 from Patent EP1572962.
JD126391 - Sequence 107415 from Patent EP1572962.
JD502402 - Sequence 483426 from Patent EP1572962.
AK300251 - Homo sapiens cDNA FLJ57197 complete cds, highly similar to T-box transcription factor TBX5.
AF086146 - Homo sapiens full length insert cDNA clone ZB04C08.
JD253282 - Sequence 234306 from Patent EP1572962.
JD247088 - Sequence 228112 from Patent EP1572962.
AF221714 - Homo sapiens T-box 5 (TBX5) mRNA, complete cds.
Y09445 - H.sapiens mRNA for transcription factor TBX5.
AB051068 - Homo sapiens TBX5 mRNA for transcription factor T-box 5, complete cds.
JD513430 - Sequence 494454 from Patent EP1572962.
AK290611 - Homo sapiens cDNA FLJ76260 complete cds, highly similar to Homo sapiens T-box 5 (TBX5), transcript variant 1, mRNA.
JD359726 - Sequence 340750 from Patent EP1572962.
JD328400 - Sequence 309424 from Patent EP1572962.
U89353 - Homo sapiens transcription factor T-box 5 (TBX5) mRNA, alternatively spliced, complete cds.
EU446658 - Synthetic construct Homo sapiens clone IMAGE:100069830; IMAGE:100011867; FLH258553.01L T-box 5 (TBX5) gene, encodes complete protein.
AB527531 - Synthetic construct DNA, clone: pF1KB5967, Homo sapiens TBX5 gene for T-box protein 5, without stop codon, in Flexi system.
U80987 - Human transcription factor TBX5 mRNA, complete cds.
JD138089 - Sequence 119113 from Patent EP1572962.
JD204957 - Sequence 185981 from Patent EP1572962.
BC011028 - Homo sapiens T-box 5, mRNA (cDNA clone IMAGE:4042787), partial cds.
JD148661 - Sequence 129685 from Patent EP1572962.
JD461983 - Sequence 443007 from Patent EP1572962.
JD148660 - Sequence 129684 from Patent EP1572962.
JD461982 - Sequence 443006 from Patent EP1572962.
JD303725 - Sequence 284749 from Patent EP1572962.
JD129120 - Sequence 110144 from Patent EP1572962.
JD110971 - Sequence 91995 from Patent EP1572962.
JD110970 - Sequence 91994 from Patent EP1572962.

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

Protein Q99593 (Reactome details) participates in the following event(s):

R-HSA-2032794 WWTR1 (TAZ), TBX5, and PCAF form a complex
R-HSA-2032785 YAP1- and WWTR1 (TAZ)-stimulated gene expression
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: ENST00000310346.1, ENST00000310346.2, ENST00000310346.3, ENST00000310346.4, ENST00000310346.5, ENST00000310346.6, ENST00000310346.7, NM_000192, O15301, Q99593, Q9Y4I2, TBX5_HUMAN, uc001tvp.1, uc001tvp.2, uc001tvp.3, uc001tvp.4
UCSC ID: ENST00000310346.8
RefSeq Accession: NM_000192
Protein: Q99593 (aka TBX5_HUMAN)
CCDS: CCDS9173.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene TBX5:
hos (Holt-Oram Syndrome)

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