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T Gene

protein-coding   GIFtS: 62

GC06M166541
T, brachyury homolog (mouse)
(Previous name: T brachyury (mouse) homolog )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
MGC104817 2
OTTHUMP00000017588 2
TF 5
TFT 2
Descriptions
T brachyury (mouse) homolog 1
T brachyury homolog 2
T brachyury-like 2
T protein 3
T, brachyury homolog (mouse) 2
transcription factor T 2
External Ids
HGNC: 115151
Entrez Gene: 68622
UniProtKB: O151783
Ensembl: ENSG000001644587
Search outside databases for aliases for T gene

Previous GC identifers: GC06M165924 GC06M166444 GC06M166481 GC06M166482

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for T:
The protein encoded by this gene is an embryonic nuclear transcription factor that binds to a
specific DNA element, the palindromic T-site. It binds through a region in its N-terminus, called
the T-box, and effects transcription of genes required for mesoderm formation and differentiation.
The protein is localized to notochord-derived cells. [provided by RefSeq]

UniProtKB/Swiss-Prot: BRAC_HUMAN, O15178
Function: Involved in the transcriptional regulation of genes required for mesoderm formation and
differentiation. Binds to a palindromic site (called T site) and activates gene transcription when
bound to such a site

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
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Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the T gene  

Entrez Gene cytogenetic band: 6q27   Ensembl cytogenetic band:  6q27   HGNC cytogenetic band: 6q27

T Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M166541:     (about GC identifiers)

Start:
166,490,785 bp from pter
End:
166,502,121 bp from pter
Size:
11,337 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000006.10  NT_007422.13  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: BRAC_HUMAN, O15178 (See protein sequence)
Recommended Name: Brachyury protein  
Size: 435 amino acids; 47443 Da
Subunit: Monomer (By similarity)
Subcellular location: Nucleus

REFSEQ proteins: NP_003172.1  

ENSEMBL proteins: 
ENSP00000296946 ENSP00000355836 ENSP00000355841 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Browse Human Recombinant Proteins at Sigma-Aldrich  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (Brachyury / Bry)
Human Recombinant Proteins from Abnova (T)
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

2 Gene Ontology (GO) cellular component terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005634 nucleus IEA--
GO:0005737 cytoplasm IEA--
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Antibodies for T: 
Invitrogen Antibodies for T
Millipore Mono- and Polyclonal Antibodies for the study of T
Sigma-Aldrich Antibodies for T
R&D Systems Antibodies for T (Brachyury)
Antibodies from Abcam (Brachyury / Bry), each with their AbpromiseSM
Monoclonal and Polyclonal Antibodies from Abnova (T)
Novus Biologicals Antibodies for T

Assays for T: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

3 InterPro domains/families:
 IPR001699 TF_T-box
 IPR002070 TF_Brachyury
 IPR018186 TF_T-box_CS


   GeneDecks  T for the domains selected above  
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Graphical View of Domain Structure for InterPro Entry O15178

ProtoNet protein and cluster: O15178

2 Blocks protein families:
IPB001699 Transcription factor
IPB002070 Brachyury protein family signature


UniProtKB/Swiss-Prot: BRAC_HUMAN, O15178
Similarity: Contains 1 T-box DNA-binding domain

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (T)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (T)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_003181

              Applied Biosystems Silencer® siRNAs for T

              Sigma-Aldrich siRNA for T  
                     Sigma-Aldrich shRNA for T  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for T
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_003181
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_003181
                                 untagged cDNA clone in CMV expression vector: NM_003181 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_003181

UniProtKB/Swiss-Prot: BRAC_HUMAN, O15178
Function: Involved in the transcriptional regulation of genes required for mesoderm formation and
differentiation. Binds to a palindromic site (called T site) and activates gene transcription when
bound to such a site

Genatlas biochemistry entry for T:
murine T-box gene Tbx (T,brachyury) homolog,expressed in cells derived from the notochord,crucial
for mesoderm formation,no evidence of association with neural tube defects (NTD) in Netherlands
and U.K.

15/19 MGI mutant phenotypes (inferred from 37 alleles(MGI details for T) (see all 19 ):

behavior/neurologicalcraniofacialdigestive/alimentaryembryogenesis
growth/sizehearing/vestibular/earhomeostasis/metabolismlethality-postnatallethality-prenatal/perinatal
life span-post-weaning/aginglimbs/digits/tailnervous systemno phenotypic analysisother

3 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0003700 transcription factor activity NAS8963900
GO:0005515 protein binding IEA--
GO:0043565 sequence-specific DNA binding IEA--
About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section


2 Millipore Pathways for T
 Selected targets of Oct-3/4
 Selected targets of HNF1

   GeneDecks  T for the pathways selected above  
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1 Sigma-Aldrich "Your Favorite Gene" Pathway for  T  (Your Favorite Gene powered by Ingenuity) 
 Role of NANOG in Mammalian Embryonic Stem Cell Pluripotency

   GeneDecks  T for the pathways selected above  
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5/12 Interacting proteins for T (ENSP000002969463) via UniProtKB, MINT, and/or STRING (see all 12 )
InteractantInteraction Details
GeneCardExternal ID(s)
GLDCENSP000003707403STRING (score=.996)
OCA2ENSP000003466593STRING (score=.995)
AMTENSP000002735883STRING (score=.936)
DLDENSP000002054023STRING (score=.907)
GCSHENSP000003195313STRING (score=.907)
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5/13 Gene Ontology (GO) biological process terms (links to tree view) (see all 13 ):

GO IDQualified GO termEvidencePubMed IDs
GO:0001570 vasculogenesis IEA--
GO:0001756 somitogenesis IEA--
GO:0001839 neural plate morphogenesis IEA--
GO:0001843 neural tube closure IEA--
GO:0006355 regulation of transcription, DNA-dependent IEA--
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for T

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (T)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (T)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_003181

              Sigma-Aldrich siRNA for T  
                     Sigma-Aldrich shRNA for T  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_003181  

REFSEQ mRNAs for T gene: 

NM_003181.2   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_003181  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_003181
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_003181
                                 untagged cDNA clone in CMV expression vector: NM_003181 

Additional cDNA sequence: 

AJ001699.1 BC039877.1 BC098425.1 

5 DOTS entries:

DT.97837890  DT.202766  DT.97837889  DT.100737559  DT.75161871 

24/48 AceView cDNA sequences (see all 48 ):

NM_003181 BQ931406 AI341816 BG332916 BQ221957 BQ420570 BC039877 AI651456 
BQ221790 BG490984 AW003327 BE785653 BQ925830 BF512284 BU192473 AI797600 
BU164583 BF223613 BG333106 BQ951069 AI001036 AA994493 BQ924827 BQ222875 

highest scoring ESTs for T:

AJ001699 BE789773 BG332994 BG333106 BG436736 BG436820 BQ927155 BU190437 AA994493 AI001036 

Unigene Cluster for T:

T, brachyury homolog (mouse)
Hs.389457  [show with all ESTs]
Unigene Representative Sequence: NM_003181


GeneLoc Exon Structure

5 Alternative Splicing Database (ASD) splice patterns (SP) for T

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b
SP1:                          -     -                                         -     -                     
SP2:                                                                                                      
SP3:                                                                                                      
SP4:                    -     -     -                                                                     
SP5:                                                                                                      

About this scheme

ECgene alternative splicing isoforms for T

3 Ensembl transcripts including schematic representations:
ENST00000296946  ENST00000366871  ENST00000366876  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

T expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for T

1 / 2 / 3

3 probe-sets matching T gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

34966_at2, 3 U95-A 1 1.00 1.00 1.00 1.00 AJ001699 0.80 1.00 0.91 1

206524_at2, 3 U133-A 1 1.00 1.00 -- -- NM_003181 0.60 1.00 0.82 1

206524_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
About this table
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: TGAAGCAGCA

SOURCE GeneReport for Unigene cluster: Hs.389457

Expression variation in blood from EXPOLDB for T

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for T gene from 5/12 species (see all 12 )
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
T1   -- T, brachyury homolog (mouse) 89.43(n)
90.11(a)
403653  NM_001003092.1  NP_001003092.1 
chimpanzee
(Pan troglodytes)
T1   -- T, brachyury homolog (mouse) 99.77(n)
99.54(a)
472186  XM_527563.2  XP_527563.2 
cow
(Bos taurus)
T1   -- T, brachyury homolog (mouse) 88.28(n)
88.51(a)
524443  XM_864890.2  XP_869983.2 
rat
(Rattus norvegicus)
T1   -- T, brachyury homolog (mouse) 86.64(n)
92.17(a)
292301  XM_217890.4  XP_217890.3 
mouse
(Mus musculus)
T1, 5 17 (4.02 cM)5
brachyury1, 5 85.71(n)1
91.71(a)1
209971  NM_009309.21  NP_033335.11 
 BC1208075  BG0652675  (see all 6)
About this table        Species with no ortholog for T

ENSEMBL Gene Tree for T
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for T gene
TBX192  

(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/108 NCBI SNPs in T are shown (see all 108 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 132)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 6 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs30992661,2
A,C,F,H166501137(-) AGAGCG/AGGGAA 1 -- ut51 ese35Minor allele frequency- A:0.26EA EU WA 1890
rs69282161,2
A,C,F,H166503541(+) TTTCTA/GCTCTC 1 -- ng317Minor allele frequency- G:0.19EU EA WA NA 558
rs31273281,2
A,C,F,H166492035(+) GGCGCC/TGTTGC 1 G/S mis1 ese312Minor allele frequency- T:0.10NA EU EA WA 1006
rs18675941,2
A,C,F,H166503491(-) TGAAGT/CTGTAT 1 -- ng3112Minor allele frequency- C:0.23MN NA EU EA WA 1162
rs10560511,2
A,C,F,H166491569(-) GGCTTC/ACAGAT 1 -- ut31 ese38Minor allele frequency- A:0.16EU EA WA NA 2058
rs30992701,2
A,C,F,H166491515(-) CGGTGG/AAAAAA 1 -- ut318Minor allele frequency- A:0.16EA NA EU WA 2058
rs23050891,2
A,C,F,H166499260(+) GTGGAC/TCCCCA 1 G/D mis1 ese311Minor allele frequency- T:0.34EA EU WA NA 2504
rs10560531,2
A,C,F,H166491433(-) AATTTA/GTAAAC 1 -- ut319Minor allele frequency- N:0.00EA NA EU WA 2128
rs18675921,2
A,C,F,H166503726(-) GAACCG/CAGGAA 1 -- ng31 tfbs312Minor allele frequency- C:0.13MN NA EU EA WA 1160
rs11344811,2
A,C,F,H166491154(-) CTGCAC/AAATAA 1 -- ut314Minor allele frequency- A:0.24EU EA WA 412
About this table

HapMap Linkage Disequilibrium images for T (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 601397   disorders: 182940  

UniProtKB/Swiss-Prot: BRAC_HUMAN, O15178

  • Genetic variations in T are associated with susceptibility to neural tube defects (NTD)
    [MIM:182940]. NTD are common congenital malformations. Spina bifida, which results from
    malformations in the caudal region of the neural tube, is compatible with life but associated with
    significant morbidity, including lower limb paralysis
  • 3 Novoseek disease relationships for T gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    colitis 26.85 1 17923080 (1), 11994418 (1)
    inflammation 20.87 3 19412181 (1), 17723218 (1), 15498029 (1)
    asthma 4.01 1 15604153 (1)
    About this table

    Human Gene Mutation Database: T
    Human Genome Epidemiology Navigator: T (0 documents)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/82 PubMed articles for T gene (see all 82 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 6862 HGNC: 11515 AceView: T Ensembl:ENSG00000164458 euGenes: HUgn6862
    ECgene: T H-InvDB: T
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

      --
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for T:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for T Antibodies for T
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     Antibodies for T

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