Mouse Gene T (ENSMUST00000074667.8) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus brachyury, T-box transcription factor T (T), mRNA. (from RefSeq NM_009309)
Gencode Transcript: ENSMUST00000074667.8
Gencode Gene: ENSMUSG00000062327.10
Transcript (Including UTRs)
   Position: mm10 chr17:8,434,423-8,442,496 Size: 8,074 Total Exon Count: 8 Strand: +
Coding Region
   Position: mm10 chr17:8,434,531-8,441,869 Size: 7,339 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Data last updated at UCSC: 2019-09-20

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr17:8,434,423-8,442,496)mRNA (may differ from genome)Protein (436 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=Brachyury; SubName: Full=Brachyury, isoform CRA_a;
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

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

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -32.90108-0.305 Picture PostScript Text
3' UTR -164.60627-0.263 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

SCOP Domains:
49417 - p53-like transcription factors

ModBase Predicted Comparative 3D Structure on Q78ZW9
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
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:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001570 vasculogenesis
GO:0001756 somitogenesis
GO:0001839 neural plate morphogenesis
GO:0001843 neural tube closure
GO:0003007 heart morphogenesis
GO:0003257 positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor 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:0007341 penetration of zona pellucida
GO:0007498 mesoderm development
GO:0007509 mesoderm migration involved in gastrulation
GO:0008284 positive regulation of cell proliferation
GO:0009653 anatomical structure morphogenesis
GO:0009952 anterior/posterior pattern specification
GO:0014028 notochord formation
GO:0022414 reproductive process
GO:0023019 signal transduction involved in regulation of gene expression
GO:0030509 BMP signaling pathway
GO:0030903 notochord development
GO:0036342 post-anal tail morphogenesis
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048706 embryonic skeletal system development
GO:0060070 canonical Wnt signaling pathway
GO:0060349 bone morphogenesis
GO:0060395 SMAD protein signal transduction
GO:0061371 determination of heart left/right asymmetry
GO:0071300 cellular response to retinoic acid

Cellular Component:
GO:0000785 chromatin
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005737 cytoplasm

-  Descriptions from all associated GenBank mRNAs
  X51683 - M.musculus T mRNA.
BC120807 - Mus musculus brachyury, mRNA (cDNA clone MGC:156044 IMAGE:40129730), complete cds.

-  Other Names for This Gene
  Alternate Gene Symbols: brachyury(T), mCG_19345, NM_009309, Q78ZW9, Q78ZW9_MOUSE, uc008ajq.1
UCSC ID: uc008ajq.1
RefSeq Accession: NM_009309
Protein: Q78ZW9 CCDS: CCDS28383.1

-  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.