Human Gene TBX3 (ENST00000349155.7_15) from GENCODE V47lift37
  Description: T-box transcription factor 3, transcript variant 1 (from RefSeq NM_005996.4)
Gencode Transcript: ENST00000349155.7_15
Gencode Gene: ENSG00000135111.16_16
Transcript (Including UTRs)
   Position: hg19 chr12:115,108,060-115,121,980 Size: 13,921 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr12:115,109,646-115,121,005 Size: 11,360 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:115,108,060-115,121,980)mRNA (may differ from genome)Protein (723 aa)
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-  Comments and Description Text from UniProtKB
  ID: TBX3_HUMAN
DESCRIPTION: RecName: Full=T-box transcription factor TBX3; Short=T-box protein 3;
FUNCTION: Transcriptional repressor involved in developmental processes. Probably plays a role in limb pattern formation.
SUBCELLULAR LOCATION: Nucleus (Potential).
TISSUE SPECIFICITY: Widely expressed.
DISEASE: Defects in TBX3 are the cause of ulnar-mammary syndrome (UMS) [MIM:181450]. UMS is characterized by ulnar ray defects, obesity, hypogenitalism, delayed puberty, hypoplasia of nipples and apocrine glands.
SIMILARITY: Contains 1 T-box DNA-binding domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/TBX3";

-  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: TBX3
Diseases sorted by gene-association score: ulnar-mammary syndrome* (1735), holt-oram syndrome (21), murcs association (18), acheiropody (11), sinoatrial node disease (8), duane-radial ray syndrome (6), mayer-rokitansky-kuster-hauser syndrome (5)
* = 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: 126.11 RPKM in Adrenal Gland
Total median expression: 697.88 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 -369.40975-0.379 Picture PostScript Text
3' UTR -435.501586-0.275 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
IPR022582 - TBX
IPR001699 - TF_T-box
IPR018186 - TF_T-box_CS

Pfam Domains:
PF00907 - T-box
PF12598 - T-box transcription factor

SCOP Domains:
49417 - p53-like transcription factors

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1H6F - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O15119
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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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  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:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001085 RNA polymerase II transcription factor binding
GO:0001102 RNA polymerase II activating transcription factor binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001501 skeletal system development
GO:0001568 blood vessel development
GO:0001701 in utero embryonic development
GO:0001947 heart looping
GO:0003007 heart morphogenesis
GO:0003151 outflow tract morphogenesis
GO:0003167 atrioventricular bundle cell differentiation
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:0007569 cell aging
GO:0008284 positive regulation of cell proliferation
GO:0008595 anterior/posterior axis specification, embryo
GO:0009887 animal organ morphogenesis
GO:0010159 specification of animal organ position
GO:0019827 stem cell population maintenance
GO:0021761 limbic system development
GO:0030539 male genitalia development
GO:0030540 female genitalia development
GO:0030857 negative regulation of epithelial cell differentiation
GO:0030879 mammary gland development
GO:0032275 luteinizing hormone secretion
GO:0035050 embryonic heart tube development
GO:0035108 limb morphogenesis
GO:0035115 embryonic forelimb morphogenesis
GO:0035116 embryonic hindlimb morphogenesis
GO:0035136 forelimb morphogenesis
GO:0042127 regulation of cell proliferation
GO:0042733 embryonic digit morphogenesis
GO:0043066 negative regulation of apoptotic process
GO:0045662 negative regulation of myoblast differentiation
GO:0045787 positive regulation of cell cycle
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0046884 follicle-stimulating hormone secretion
GO:0048332 mesoderm morphogenesis
GO:0055007 cardiac muscle cell differentiation
GO:0060021 palate development
GO:0060412 ventricular septum morphogenesis
GO:0060444 branching involved in mammary gland duct morphogenesis
GO:0060596 mammary placode formation
GO:0060923 cardiac muscle cell fate commitment
GO:0060931 sinoatrial node cell development
GO:0090398 cellular senescence
GO:2000648 positive regulation of stem cell proliferation

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AF140240 - Homo sapiens transcription factor TBX3 (TBX3) mRNA, partial cds.
AK075457 - Homo sapiens cDNA PSEC0150 fis, clone PLACE1007635.
AF216750 - Homo sapiens TBX3-iso mRNA, complete cds.
JD114354 - Sequence 95378 from Patent EP1572962.
JD101252 - Sequence 82276 from Patent EP1572962.
JD234776 - Sequence 215800 from Patent EP1572962.
BC025258 - Homo sapiens T-box 3, mRNA (cDNA clone MGC:39139 IMAGE:5458526), complete cds.
JD350313 - Sequence 331337 from Patent EP1572962.
AF074999 - Homo sapiens full length insert cDNA YH95A05.
JD466782 - Sequence 447806 from Patent EP1572962.
JD353630 - Sequence 334654 from Patent EP1572962.
JD391937 - Sequence 372961 from Patent EP1572962.
JD063767 - Sequence 44791 from Patent EP1572962.
DQ892858 - Synthetic construct clone IMAGE:100005488; FLH190361.01X; RZPDo839H0575D T-box 3 (ulnar mammary syndrome) (TBX3) gene, encodes complete protein.
AF170708 - Homo sapiens T-box protein TBX3 (TBX3) mRNA, complete cds.
DQ896106 - Synthetic construct Homo sapiens clone IMAGE:100010566; FLH190357.01L; RZPDo839H0565D T-box 3 (ulnar mammary syndrome) (TBX3) gene, encodes complete protein.
AF002228 - Homo sapiens transcription factor tbx3 (TBX3) mRNA, partial cds.
AK054604 - Homo sapiens cDNA FLJ30042 fis, clone 3NB692001538, highly similar to TBX3 PROTEIN.
AY034105 - Homo sapiens bladder cancer-related protein (XHL) gene, partial 3'UTR sequence.
AK304639 - Homo sapiens cDNA FLJ61570 complete cds, highly similar to T-box transcription factor TBX3.
JD117405 - Sequence 98429 from Patent EP1572962.
JD456995 - Sequence 438019 from Patent EP1572962.
JD327354 - Sequence 308378 from Patent EP1572962.
JD370570 - Sequence 351594 from Patent EP1572962.
JD229874 - Sequence 210898 from Patent EP1572962.
JD150409 - Sequence 131433 from Patent EP1572962.
JD513755 - Sequence 494779 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000349155.1, ENST00000349155.2, ENST00000349155.3, ENST00000349155.4, ENST00000349155.5, ENST00000349155.6, NM_005996, O15119, Q8TB20, Q9UKF8, TBX3_HUMAN, uc317xue.1, uc317xue.2
UCSC ID: ENST00000349155.7_15
RefSeq Accession: NM_005996.4
Protein: O15119 (aka TBX3_HUMAN)

-  Gene Model Information
  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.