Human Gene TBX1 (ENST00000332710.8) from GENCODE V43
  Description: Homo sapiens T-box transcription factor 1 (TBX1), transcript variant C, mRNA. (from RefSeq NM_080647)
RefSeq Summary (NM_080647): 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 product shares 98% amino acid sequence identity with the mouse ortholog. DiGeorge syndrome (DGS)/velocardiofacial syndrome (VCFS), a common congenital disorder characterized by neural-crest-related developmental defects, has been associated with deletions of chromosome 22q11.2, where this gene has been mapped. Studies using mouse models of DiGeorge syndrome suggest a major role for this gene in the molecular etiology of DGS/VCFS. Several alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000332710.8
Gencode Gene: ENSG00000184058.16
Transcript (Including UTRs)
   Position: hg38 chr22:19,756,703-19,767,334 Size: 10,632 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg38 chr22:19,759,644-19,766,867 Size: 7,224 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-02-17 13:02:02

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr22:19,756,703-19,767,334)mRNA (may differ from genome)Protein (495 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSCGAPEnsemblEntrez GeneExonPrimerGencode

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=T-box transcription factor TBX1; Short=T-box protein 1; AltName: Full=Testis-specific T-box protein;
FUNCTION: Probable transcriptional regulator involved in developmental processes. Is required for normal development of the pharyngeal arch arteries (By similarity).
SUBCELLULAR LOCATION: Nucleus (Potential).
DISEASE: Note=Haploinsufficiency of the TBX1 gene is responsible for most of the physical malformations present in DiGeorge syndrome (DGS) and velocardiofacial syndrome (VCFS). DGS is characterized by the association of several malformations: hypoplastic thymus and parathyroid glands, congenital conotruncal cardiopathy, and a subtle but characteristic facial dysmorphology. VCFS is marked by the association of congenital conotruncal heart defects, cleft palate or velar insufficiency, facial dysmorpholgy and learning difficulties. It is now accepted that these two syndromes represent two forms of clinical expression of the same entity manifesting at different stages of life.
DISEASE: Defects in TBX1 are a cause of DiGeorge syndrome (DGS) [MIM:188400].
DISEASE: Defects in TBX1 are a cause of velocardiofacial syndrome (VCFS) [MIM:192430].
DISEASE: Defects in TBX1 are a cause of conotruncal heart malformations (CTHM) [MIM:217095]. CTHM consist of cardiac outflow tract defects, such as tetralogy of Fallot, pulmonary atresia, double-outlet right ventricle, truncus arteriosus communis, and aortic arch anomalies.
SIMILARITY: Contains 1 T-box DNA-binding domain.

-  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: TBX1
Diseases sorted by gene-association score: velocardiofacial syndrome* (1766), digeorge syndrome* (1270), conotruncal heart malformations* (372), tetralogy of fallot* (350), chromosome 22q11.2 microduplication syndrome* (29), ulnar-mammary syndrome (12), chromosome 6pter-p24 deletion syndrome (9), holt-oram syndrome (9), chromosomal deletion syndrome (9), esophageal atresia/tracheoesophageal fistula (8), transposition of the great arteries (6), cleft soft palate (6), inguinal hernia (6), heart disease (5), heart septal defect (4), atrioventricular septal defect (4), chromosomal disease (2), pervasive developmental disorder (1)
* = 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: 14.99 RPKM in Testis
Total median expression: 102.18 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 -61.80129-0.479 Picture PostScript Text
3' UTR -187.50467-0.401 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
4A04 - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on O43435
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     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0042803 protein homodimerization activity
GO:0043565 sequence-specific DNA binding
GO:0046983 protein dimerization activity
GO:0003700 transcription factor activity, sequence-specific DNA binding

Biological Process:
GO:0001525 angiogenesis
GO:0001568 blood vessel development
GO:0001708 cell fate specification
GO:0001755 neural crest cell migration
GO:0001934 positive regulation of protein phosphorylation
GO:0001945 lymph vessel development
GO:0002053 positive regulation of mesenchymal cell proliferation
GO:0003007 heart morphogenesis
GO:0003148 outflow tract septum morphogenesis
GO:0003151 outflow tract morphogenesis
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007368 determination of left/right symmetry
GO:0007389 pattern specification process
GO:0007498 mesoderm development
GO:0007507 heart development
GO:0007517 muscle organ development
GO:0007605 sensory perception of sound
GO:0008283 cell proliferation
GO:0008284 positive regulation of cell proliferation
GO:0009952 anterior/posterior pattern specification
GO:0021644 vagus nerve morphogenesis
GO:0030855 epithelial cell differentiation
GO:0030878 thyroid gland development
GO:0035176 social behavior
GO:0035909 aorta morphogenesis
GO:0042471 ear morphogenesis
GO:0042472 inner ear morphogenesis
GO:0042473 outer ear morphogenesis
GO:0042474 middle ear morphogenesis
GO:0042475 odontogenesis of dentin-containing tooth
GO:0042693 muscle cell fate commitment
GO:0043410 positive regulation of MAPK cascade
GO:0043587 tongue morphogenesis
GO:0044344 cellular response to fibroblast growth factor stimulus
GO:0045596 negative regulation of cell differentiation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048384 retinoic acid receptor signaling pathway
GO:0048514 blood vessel morphogenesis
GO:0048538 thymus development
GO:0048644 muscle organ morphogenesis
GO:0048701 embryonic cranial skeleton morphogenesis
GO:0048703 embryonic viscerocranium morphogenesis
GO:0048752 semicircular canal morphogenesis
GO:0048844 artery morphogenesis
GO:0050679 positive regulation of epithelial cell proliferation
GO:0060017 parathyroid gland development
GO:0060023 soft palate development
GO:0060037 pharyngeal system development
GO:0060325 face morphogenesis
GO:0060415 muscle tissue morphogenesis
GO:0060982 coronary artery morphogenesis
GO:0070166 enamel mineralization
GO:0071300 cellular response to retinoic acid
GO:0090103 cochlea morphogenesis
GO:0097152 mesenchymal cell apoptotic process
GO:2000027 regulation of organ morphogenesis
GO:2001037 positive regulation of tongue muscle cell differentiation
GO:2001054 negative regulation of mesenchymal cell apoptotic process

Cellular Component:
GO:0005634 nucleus

-  Descriptions from all associated GenBank mRNAs
  JD394840 - Sequence 375864 from Patent EP1572962.
AF373867 - Homo sapiens T-box 1 transcription factor C (TBX1C) mRNA, complete cds.
AF012130 - Homo sapiens brachyury variant A (TBX1) mRNA, complete cds.
AF012131 - Homo sapiens brachyury variant B (TBX1) mRNA, complete cds.
JD109067 - Sequence 90091 from Patent EP1572962.
JD172762 - Sequence 153786 from Patent EP1572962.
GU014843 - Synthetic construct Homo sapiens clone IMAGE:100068747; MGC:198461 T-box 1 transcription factor C (TBX1C) gene, encodes complete protein.
JD271294 - Sequence 252318 from Patent EP1572962.
JD366021 - Sequence 347045 from Patent EP1572962.
JD086293 - Sequence 67317 from Patent EP1572962.
JD385018 - Sequence 366042 from Patent EP1572962.
JD405887 - Sequence 386911 from Patent EP1572962.
JD126019 - Sequence 107043 from Patent EP1572962.
JD124991 - Sequence 106015 from Patent EP1572962.
JD129586 - Sequence 110610 from Patent EP1572962.
JD406989 - Sequence 388013 from Patent EP1572962.
JD175066 - Sequence 156090 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: C6G493, C6G494, ENST00000332710.1, ENST00000332710.2, ENST00000332710.3, ENST00000332710.4, ENST00000332710.5, ENST00000332710.6, ENST00000332710.7, NM_080647, O43435, O43436, Q96RJ2, TBX1_HUMAN, uc002zqa.1, uc002zqa.2
UCSC ID: ENST00000332710.8
RefSeq Accession: NM_080647
Protein: O43435 (aka TBX1_HUMAN)
CCDS: CCDS13767.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene TBX1:
gr_22q11deletion (22q11.2 Deletion Syndrome)

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