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T (T brachyury transcription factor)

Identity

Alias_namesT
HGNC (Hugo) T
LocusID (NCBI) 6862
Atlas_Id 50265
Location 6q27  [Link to chromosome band 6q27]
Location_base_pair Starts at 166571146 and ends at 166582157 bp from pter ( according to hg19-Feb_2009)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)T   11515
Cards
Entrez_Gene (NCBI)T  6862  T brachyury transcription factor
AliasesSAVA; TFT
GeneCards (Weizmann)T
Ensembl hg19 (Hinxton)ENSG00000164458 [Gene_View]  chr6:166571146-166582157 [Contig_View]  T [Vega]
Ensembl hg38 (Hinxton)ENSG00000164458 [Gene_View]  chr6:166571146-166582157 [Contig_View]  T [Vega]
ICGC DataPortalENSG00000164458
TCGA cBioPortalT
AceView (NCBI)T
Genatlas (Paris)T
WikiGenes6862
SOURCE (Princeton)T
Genetics Home Reference (NIH)T
Genomic and cartography
GoldenPath hg19 (UCSC)T  -     chr6:166571146-166582157 -  6q27   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)T  -     6q27   [Description]    (hg38-Dec_2013)
EnsemblT - 6q27 [CytoView hg19]  T - 6q27 [CytoView hg38]
Mapping of homologs : NCBIT [Mapview hg19]  T [Mapview hg38]
OMIM182940   601397   615709   
Gene and transcription
Genbank (Entrez)AJ001699 BC039877 BC098425 BE785653 BG436736
RefSeq transcript (Entrez)NM_001270484 NM_003181
RefSeq genomic (Entrez)NC_000006 NC_018917 NG_012135 NT_025741 NW_004929328
Consensus coding sequences : CCDS (NCBI)T
Cluster EST : UnigeneHs.742027 [ NCBI ]
CGAP (NCI)Hs.742027
Alternative Splicing GalleryENSG00000164458
Gene ExpressionT [ NCBI-GEO ]   T [ EBI - ARRAY_EXPRESS ]   T [ SEEK ]   T [ MEM ]
Gene Expression Viewer (FireBrowse)T [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6862
GTEX Portal (Tissue expression)T
Protein : pattern, domain, 3D structure
UniProt/SwissProtO15178   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO15178  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO15178
Splice isoforms : SwissVarO15178
PhosPhoSitePlusO15178
Domaine pattern : Prosite (Expaxy)TBOX_1 (PS01283)    TBOX_2 (PS01264)    TBOX_3 (PS50252)   
Domains : Interpro (EBI)p53-like_TF_DNA-bd    TF_Brachyury    TF_T-box    TF_T-box_CS   
Domain families : Pfam (Sanger)T-box (PF00907)   
Domain families : Pfam (NCBI)pfam00907   
Domain families : Smart (EMBL)TBOX (SM00425)  
Conserved Domain (NCBI)T
DMDM Disease mutations6862
Blocks (Seattle)T
SuperfamilyO15178
Human Protein AtlasENSG00000164458
Peptide AtlasO15178
HPRD03236
IPIIPI00005203   IPI00619896   
Protein Interaction databases
DIP (DOE-UCLA)O15178
IntAct (EBI)O15178
FunCoupENSG00000164458
BioGRIDT
STRING (EMBL)T
ZODIACT
Ontologies - Pathways
QuickGOO15178
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  nuclear chromatin  RNA polymerase II core promoter proximal region sequence-specific DNA binding  RNA polymerase II distal enhancer sequence-specific DNA binding  RNA polymerase II transcription factor binding  RNA polymerase II activating transcription factor binding  transcriptional repressor activity, RNA polymerase II transcription factor binding  vasculogenesis  somitogenesis  neural plate morphogenesis  neural tube closure  heart morphogenesis  positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation  transcription factor activity, sequence-specific DNA binding  transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding  nucleus  cytoplasm  transcription, DNA-templated  signal transduction  penetration of zona pellucida  mesoderm development  mesoderm migration involved in gastrulation  positive regulation of cell proliferation  anterior/posterior axis specification, embryo  notochord formation  signal transduction involved in regulation of gene expression  BMP signaling pathway  post-anal tail morphogenesis  embryonic skeletal system development  canonical Wnt signaling pathway  bone morphogenesis  SMAD protein signal transduction  determination of heart left/right asymmetry  cellular response to retinoic acid  primitive streak formation  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  nuclear chromatin  RNA polymerase II core promoter proximal region sequence-specific DNA binding  RNA polymerase II distal enhancer sequence-specific DNA binding  RNA polymerase II transcription factor binding  RNA polymerase II activating transcription factor binding  transcriptional repressor activity, RNA polymerase II transcription factor binding  vasculogenesis  somitogenesis  neural plate morphogenesis  neural tube closure  heart morphogenesis  positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation  transcription factor activity, sequence-specific DNA binding  transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding  nucleus  cytoplasm  transcription, DNA-templated  signal transduction  penetration of zona pellucida  mesoderm development  mesoderm migration involved in gastrulation  positive regulation of cell proliferation  anterior/posterior axis specification, embryo  notochord formation  signal transduction involved in regulation of gene expression  BMP signaling pathway  post-anal tail morphogenesis  embryonic skeletal system development  canonical Wnt signaling pathway  bone morphogenesis  SMAD protein signal transduction  determination of heart left/right asymmetry  cellular response to retinoic acid  primitive streak formation  
NDEx NetworkT
Atlas of Cancer Signalling NetworkT
Wikipedia pathwaysT
Orthology - Evolution
OrthoDB6862
GeneTree (enSembl)ENSG00000164458
Phylogenetic Trees/Animal Genes : TreeFamT
HOVERGENO15178
HOGENOMO15178
Homologs : HomoloGeneT
Homology/Alignments : Family Browser (UCSC)T
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerT [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)T
dbVarT
ClinVarT
1000_GenomesT 
Exome Variant ServerT
ExAC (Exome Aggregation Consortium)T (select the gene name)
Genetic variants : HAPMAP6862
Genomic Variants (DGV)T [DGVbeta]
DECIPHER (Syndromes)6:166571146-166582157  ENSG00000164458
CONAN: Copy Number AnalysisT 
Mutations
ICGC Data PortalT 
TCGA Data PortalT 
Broad Tumor PortalT
OASIS PortalT [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICT  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDT
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch T
DgiDB (Drug Gene Interaction Database)T
DoCM (Curated mutations)T (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)T (select a term)
intoGenT
Cancer3DT(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM182940    601397    615709   
Orphanet20199    20198    20197    20196    20195    20194    20192    20188    20189    20190    20191    20187    6023    22705   
MedgenT
Genetic Testing Registry T
NextProtO15178 [Medical]
TSGene6862
GENETestsT
Huge Navigator T [HugePedia]
snp3D : Map Gene to Disease6862
BioCentury BCIQT
ClinGenT
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6862
Chemical/Pharm GKB GenePA36296
Clinical trialT
Miscellaneous
canSAR (ICR)T (select the gene name)
Probes
Litterature
PubMed57 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineT
EVEXT
GoPubMedT
iHOPT
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Fri Nov 18 19:53:11 CET 2016

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