Human Gene TBX6 (ENST00000395224.7) from GENCODE V44
  Description: Homo sapiens T-box transcription factor 6 (TBX6), mRNA. (from RefSeq NM_004608)
RefSeq Summary (NM_004608): 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. Knockout studies in mice indicate that this gene is important for specification of paraxial mesoderm structures. [provided by RefSeq, Aug 2008].
Gencode Transcript: ENST00000395224.7
Gencode Gene: ENSG00000149922.12
Transcript (Including UTRs)
   Position: hg38 chr16:30,085,793-30,091,924 Size: 6,132 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg38 chr16:30,086,225-30,091,193 Size: 4,969 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: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:30,085,793-30,091,924)mRNA (may differ from genome)Protein (436 aa)
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HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TBX6_HUMAN
DESCRIPTION: RecName: Full=T-box transcription factor TBX6; Short=T-box protein 6;
FUNCTION: T-box transcription factor that plays an essential role in the determination of the fate of axial stem cells: neural vs mesodermal. Acts in part by down-regulating, a specific enhancer (N1) of SOX2, to inhibit neural development. Seems to play also an essential role in left/right axis determination and acts through effects on Notch signaling around the node as well as through an effect on the morphology and motility of the nodal cilia (By similarity).
SUBUNIT: Forms a dimeric complex with DNA (in vitro).
SUBCELLULAR LOCATION: Nucleus (Potential).
TISSUE SPECIFICITY: Expressed in fetal tail bud, posterior spinal tissue, intervertebral disk and testis. Also expressed in adult testis, kidney, lung, muscle and thymus.
DEVELOPMENTAL STAGE: Expressed during gastrulation and during a second phase in some adult tissues.
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: TBX6
Diseases sorted by gene-association score: spondylocostal dysostosis 5* (1279), spondylocostal dysostosis 5, autosomal dominant* (100), dysostosis (13), spondylocostal dysostosis 3, autosomal recessive (8), ulnar-mammary syndrome (6), scoliosis (3)
* = 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: 4.42 RPKM in Esophagus - Mucosa
Total median expression: 46.96 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 -34.20100-0.342 Picture PostScript Text
3' UTR -136.60432-0.316 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
IPR002070 - TF_Brachyury
IPR001699 - TF_T-box
IPR018186 - TF_T-box_CS

Pfam Domains:
PF00907 - T-box

ModBase Predicted Comparative 3D Structure on O95947
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-  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:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001085 RNA polymerase II transcription factor binding
GO:0001102 RNA polymerase II activating transcription factor binding
GO:0001191 transcriptional repressor activity, RNA polymerase II transcription factor binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001707 mesoderm formation
GO:0001708 cell fate specification
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0007498 mesoderm development
GO:0009653 anatomical structure morphogenesis
GO:0010977 negative regulation of neuron projection development
GO:0014043 negative regulation of neuron maturation
GO:0023019 signal transduction involved in regulation of gene expression
GO:0032525 somite rostral/caudal axis specification
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AJ007989 - Homo sapiens mRNA for transcription factor TBX6.
JD302213 - Sequence 283237 from Patent EP1572962.
BC026031 - Homo sapiens T-box 6, mRNA (cDNA clone MGC:39231 IMAGE:5460190), complete cds.
JD123150 - Sequence 104174 from Patent EP1572962.
JD107267 - Sequence 88291 from Patent EP1572962.
JD098014 - Sequence 79038 from Patent EP1572962.
JD218145 - Sequence 199169 from Patent EP1572962.
JD413221 - Sequence 394245 from Patent EP1572962.
JD200871 - Sequence 181895 from Patent EP1572962.
JD341939 - Sequence 322963 from Patent EP1572962.
JD038551 - Sequence 19575 from Patent EP1572962.
JD365673 - Sequence 346697 from Patent EP1572962.
JD157121 - Sequence 138145 from Patent EP1572962.
JD321864 - Sequence 302888 from Patent EP1572962.
EU446659 - Synthetic construct Homo sapiens clone IMAGE:100069856; IMAGE:100011868; FLH258573.01L T-box 6 (TBX6) gene, encodes complete protein.
KJ534981 - Homo sapiens clone TBX6_iso-B_fetal-F12 T-box 6 isoform B (TBX6) mRNA, partial cds, alternatively spliced.
KJ535035 - Homo sapiens clone TBX6_iso-A_adult-A16 T-box 6 isoform A (TBX6) mRNA, complete cds, alternatively spliced.
AB464285 - Synthetic construct DNA, clone: pF1KB7737, Homo sapiens TBX6 gene for T-box 6, without stop codon, in Flexi system.
AK022330 - Homo sapiens cDNA FLJ12268 fis, clone MAMMA1001627, highly similar to Homo sapiens mRNA for transcription factor TBX6.
CU693110 - Synthetic construct Homo sapiens gateway clone IMAGE:100021979 5' read TBX6 mRNA.
JD441605 - Sequence 422629 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000395224.1, ENST00000395224.2, ENST00000395224.3, ENST00000395224.4, ENST00000395224.5, ENST00000395224.6, NM_004608, O95947, Q8TAS4, TBX6_HUMAN, uc010veh.1, uc010veh.2, uc010veh.3, uc010veh.4
UCSC ID: ENST00000395224.7
RefSeq Accession: NM_004608
Protein: O95947 (aka TBX6_HUMAN)
CCDS: CCDS10670.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene TBX6:
cdh-ov (Congenital Diaphragmatic Hernia Overview)
spondylocostal-d (Spondylocostal Dysostosis, Autosomal Recessive)

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