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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

T Gene

protein-coding GIFtS: 57
GCID: GC06M166541

T, brachyury homolog (mouse)

(Previous name: T brachyury (mouse) homolog )

Explore 51 diseases affiliated with
T via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
T, Brachyury Homolog (Mouse)¹ ²		Brachyury Protein²
Protein T² ³		T Brachyury Homolog²
T Brachyury (Mouse) Homolog¹		TF⁵
TFT²

External Ids:	HGNC: 11515¹	Entrez Gene: 6862²	Ensembl: ENSG00000164458⁷	OMIM: 601397⁵	UniProtKB: O15178³

Export aliases for T gene to outside databases

Previous GC identifers: GC06M165924 GC06M166444 GC06M166481 GC06M166482 GC06M164037

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene 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. Two

transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2012)

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

Gene Wiki entry for T (Brachyury)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000006.11 NC_018917.1 NT_025741.15

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the T gene promoter:
SREBP-1c p300 Pax-2a HNF-4alpha2 C/EBPalpha SREBP-1b HNF-4alpha1 SREBP-1a
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: T promoter sequence

Search SABiosciences Chromatin IP Primers for T

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat T

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

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)
T gene location

GeneLoc information about chromosome 6 GeneLoc Exon Structure

GeneLoc location for GC06M166541: view genomic region (about GC identifiers)

Start:	166,571,086 bp from pter	End:	166,582,188 bp from pter
Size:	11,103 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

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

Secondary accessions: E7ERD6 Q4KMP4

Alternative splicing: 2 isoforms: O15178-1 O15178-2 (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for T: NX_O15178

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_O15178

T Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (2 alternative transcripts):

NP_001257413.1 NP_003172.1

ENSEMBL proteins:

ENSP00000296946 ENSP00000355836 ENSP00000355841 ENSP00000453512

Human Recombinant Protein Products:

	Browse Purified and Recombinant Proteins at EMD Millipore
	Browse R&D Systems for human recombinant proteins
	Browse recombinant and purified proteins available from Enzo Life Sciences
	OriGene Purified Protein: T OriGene Protein Over-expression Lysate: T OriGene Custom Protein Services for T
	GenScript Custom Purified and Recombinant Proteins Services for T
	Novus Biologicals T Proteins Novus Biologicals T Lysates
	Browse Sino Biological Recombinant Proteins
	Browse ProSpec Recombinant Proteins
	Uscn Proteins for T

Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000785	chromatin	--	--
GO:0000790	nuclear chromatin	IDA	--
GO:0005634	nucleus	--	--
GO:0005737	cytoplasm	IEA	--

T for ontologies About GeneDecksing

T Antibody Products:

	EMD Millipore Mono- and Polyclonal Antibodies for the study of T
	R&D Systems Antibodies for T (Brachyury)
	Cell Signaling Technology (CST) Antibodies for T (Brachyury)
	Browse OriGene Antibodies OriGene Custom Antibody Services for T
	GenScript Custom Superior Antibodies Services for T
	Novus Biologicals T Antibodies
	Search for Antibodies for T at Abcam
	Uscn Antibodies for T
	ThermoFisher Antibodies for T

Assay Products for T:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Immunoassay Development Browse OriGene Fluorogenic Cell Assay Kits
	R&D Systems Transcription Factor Binding & Immunoprecipitation Assays for T (Brachyury)
	GenScript Custom Assay Services for T
	Browse Enzo Life Sciences for kits & assays
	Uscn ELISAs and CLIAs for T

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

T for domains About GeneDecksing

4 InterPro domains/families:

IPR001699 TF_T-box

IPR008967 p53-like_TF_DNA-bd

IPR002070 TF_Brachyury

IPR018186 TF_T-box_CS

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 ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

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.

miRNA Products:		Browse 3'-UTR reporter clones for miRNA target validation Browse MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat T
		8/10 QIAGEN miScript miRNA Assays for microRNAs that regulate T (see all 10):
		hsa-miR-3678-3p hsa-miR-448 hsa-miR-539 hsa-miR-219-5p hsa-miR-507 hsa-miR-508-3p hsa-miR-511 hsa-miR-9

		SwitchGear 3'UTR luciferase reporter plasmid: T 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for T (see all 7) OriGene shRNA RFP: T OriGene siRNA: T
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat T

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for T

Clone Products:		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for T (see all 3) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for T OriGene custom cloning services � gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector (see all 9): T (NM_000662)
		Browse Sino Biological Human cDNA Clones
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for T
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat T

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for T
		Search LifeMap BioReagents cell lines for T

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for T

Gene Ontology (GO): 5/11 molecular function terms (GO ID links to tree view) (see all 11): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	ISS	--
GO:0000980	RNA polymerase II distal enhancer sequence-specific DNA binding	IDA	--
GO:0000981	sequence-specific DNA binding RNA polymerase II transcription factor activity	--	--
GO:0001085	RNA polymerase II transcription factor binding	ISS	--
GO:0001102	RNA polymerase II activating transcription factor binding	IPI	--

T for ontologies About GeneDecksing

Animal Models:
15/16 MGI mutant phenotypes (inferred from 35 alleles) (MGI details for T) (see all 16):

behavior/neurological	cardiovascular system	craniofacial	digestive/alimentary	embryogenesis
growth/size	homeostasis/metabolism	integument	limbs/digits/tail	mortality/aging
nervous system	no phenotypic analysis	normal	renal/urinary system	reproductive system

T for phenotypes About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways About this table

See pathways by source

Super-pathway

contained gene-specific pathways

Wnt / Hedgehog / Notch

Wnt / Hedgehog / Notch

1.00

Selected targets of HNF1

Selected targets of HNF1

1.00

Selected targets of Oct-3/4

Selected targets of Oct-3/4

1.00

Regulation of Wnt-mediated beta catenin signaling and target gene transcription

Regulation of Wnt-mediated beta catenin signaling and target gene transcription

1.00

glycine cleavage

glycine cleavage

1.00

Pathway sources
See GeneCards unified pathways
Show all pathways

2 EMD Millipore Pathways for T

	Selected targets of Oct-3/4
	Selected targets of HNF1

1 Cell Signaling Technology (CST) Pathway for T

Wnt / Hedgehog / Notch

2 BioSystems Pathways for T

	glycine cleavage
	Regulation of Wnt-mediated beta catenin signaling and target gene transcription

T for pathways About GeneDecksing

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for T

STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

5/6 Interacting proteins for T (ENSP00000296946⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 6)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
DLD	ENSP00000205402⁴	STRING: ENSP00000205402
GLDC	ENSP00000370737⁴	STRING: ENSP00000370737
LEF1	ENSP00000265165⁴	STRING: ENSP00000265165
OCA2	ENSP00000346659⁴	STRING: ENSP00000346659
CTNNB1	ENSP00000344456⁴	STRING: ENSP00000344456

About this table

Gene Ontology (GO): 5/34 biological process terms (GO ID links to tree view) (see all 34): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	ISS	--
GO:0001570	vasculogenesis	IEA	--
GO:0001756	somitogenesis	IEA	--
GO:0001839	neural plate morphogenesis	IEA	--
GO:0001843	neural tube closure	IEA	--

T for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for T
Search CenterWatch for drugs/clinical trials and news about T / BRAC

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for T gene (2 alternative transcripts):

NM_001270484.1 NM_003181.3

Unigene Cluster for T:

T, brachyury homolog (mouse)

Hs.389457 [show with all ESTs]

Unigene Representative Sequence: NM_003181

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000296946(uc003qut.1 uc003quu.1) ENST00000366871(uc003quv.1)

ENST00000366876 ENST00000461348

miRNA Products:		Browse 3'-UTR reporter clones for miRNA target validation Browse OriGene MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat T
		8/10 QIAGEN miScript miRNA Assays for microRNAs that regulate T (see all 10):
		hsa-miR-3678-3p hsa-miR-448 hsa-miR-539 hsa-miR-219-5p hsa-miR-507 hsa-miR-508-3p hsa-miR-511 hsa-miR-9

		SwitchGear 3'UTR luciferase reporter plasmid: T 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for T (see all 7) OriGene shRNA RFP: T OriGene siRNA: T
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat T

Clone Products:		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for T (see all 3) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for T OriGene custom cloning services � gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector (see all 9): T (NM_000662)
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for T
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat T

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for T Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse, rat T
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat T
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat T

Additional cDNA sequence:

AJ001699.1 BC039877.1 BC098425.1

5 DOTS entries:

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

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

NM_003181 BF512284 BU164583 BQ927155 BG490984 AW003327 BQ931406 BU192473

BG333106 BQ222875 AA994493 BC039877 BQ221790 BQ925830 BQ951069 BG332916

BQ420570 BU190437 AI001036 BQ422302 BF223613 AI797600 BQ430235 BQ221957

GeneLoc Exon Structure

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

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

ECgene alternative splicing isoforms for T

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

T expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: TGAAGCAGCA

About this image

T expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

10/15 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 15)

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Mesoderm

Mesoderm Cells

Selective marker (cell-identifying gene)

Early Embryo, Mesoderm

Primitive Streak

Anterior Primitive Streak

Mesoderm Progenitor Cells

Early Embryo, Mesoderm

Cartilage

Posterior Primitive Streak

Hemangioblasts

Blood, Endothelium

Primitive Streak

Posterior Primitive Streak

Mesoderm Progenitor Cells

Early Embryo, Mesoderm

Primitive Streak

Primitive Streak Cells

Early Embryo

Epiblast

Primordial Germ Cell Precursors

Germ Cells

Cartilage

Cervical Intervertebral Disc

Intervertebral Disc Nucleus Pulposus Cells

Cartilage

Lumbar Intervertebral Disc

Intervertebral Disc Nucleus Pulposus Cells

Cartilage

Sacral Intervertebral Disc

Intervertebral Disc Nucleus Pulposus Cells

Cartilage

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 10/37 LifeMap Cells (see all 37)

Name

Category

Embryoid bodies (Generation and expan...)

Mesoderm-like cells (Direct differentiati...)

Mesoderm

Primitive Streak Mesendoderm cells (Direct differentiati...)

Early mesoderm cells (Generation of human ...)

Primitive streak-like cells (Generation of primit...)

Activin A-induced embryoid bodies (Mouse embryonic stem...)

Mesendoderm embryoid bodies (Mouse embryonic stem...)

Anterior foregut progenitor cells (Directed differentia...)

Mesendoderm-like cells (A scalable, suspensi...)

Mesendoderm-like cells (Generation of beta c...)

See T Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for T

SOURCE GeneReport for Unigene cluster: Hs.389457

SABiosciences Expression via Pathway-Focused PCR Arrays including T:

Cell Lineage Identification in human mouse rat

WNT Signaling Targets in human mouse rat

Embryonic Stem Cells in human mouse rat

Stem Cells in human mouse rat

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for T Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse, rat T
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat T
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat T

In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for T

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for T gene from 6/21 species (see all 21) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	T¹	T, brachyury homolog (mouse)	81.13(n) 80.93(a)		395782 NM_204940.1 NP_990271.1
lizard (Anolis carolinensis)	Reptilia	T⁶ MGA⁶	--	81(a) 1(a)	1 ↔ 1 possible ortholog	GL343461.1(590323-608045) 1(41056654-41078608)
African clawed frog (Xenopus laevis)	Amphibia	Xl.514²	Xenopus laevis brachyury (T) (Xbra) gene, complete cds less	76.01(n)		M77243.1
zebrafish (Danio rerio)	Actinopterygii	ntl²	no tail	78.83(n)		30399 NM_131162.1
fruit fly (Drosophila melanogaster)	Insecta	byn^{1 , 3}	Malpighian tubule morphogenesis RNA polymerase II transcription factor less³ brachyenteron¹	68(a)³ 56.98(n)¹ 55.84(a)¹		68E3³ 39349¹ NM_079307.1¹ NP_524031.1¹
worm (Caenorhabditis elegans)	Secernentea	tbx-8³	Brachyury	42(a) (best of 2)		III(10419228-10421240) --

ENSEMBL Gene Tree for T (if available)
TreeFam Gene Tree for T (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for T gene

TBX1² TBX22² TBX19² EOMES² TBX2² TBX6² TBX21² TBX3²

TBX20² TBX5² TBX10² TBX4² TBX15² TBR1² TBX18²

14 SIMAP similar genes for T using alignment to 3 protein entries: BRAC_HUMAN (see all proteins):

TBX19 TBX6 TBX1 MGA TBX18 TBX10

TBX20 TBX5 TBX4 DKFZp762H2012 TBX2 EOMES

TBR1 TBX21

T for paralogs About GeneDecksing

2 Pseudogenes.org Pseudogenes for T
PGOHUM00000244365 PGOHUM00000235170

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 6 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs3127327^1,2	H	--	164037999(+)	`ACATTC/ATAGGG`	2	--	ut3¹ ese³		4		NS EA	420
rs1056050^1,2	C,F,H,	--	164038319(-)	`AGTAGC/TGGTGC`	2	--	ut3¹		10		MN NS EA NA WA CSA	730
rs79882341^1,2	F,	--	164038368(+)	`GTGCCG/ATGTGC`	2	--	ut3¹		1		EA	120
rs79253185^1,2	F,	--	164039051(+)	`TCAGAG/ACTCAT`	2	--	int¹		1		WA	118
rs11758476^1,2	C,F,H,	--	164039160(+)	`ggatcA/Ggctga`	2	--	int¹		5		NA WA CSA	128
rs5881682^1,2	C,F,	--	164040167(+)	`CAATTG/-AATTC`	2	--	int¹		2		NA CSA	4
rs61262328^1,2		--	164040259(+)	`TTTGAA/GGTCAA`	2	--	int¹		0	--	--	--	--
rs61432460^1,2		--	164040596(+)	`CGAAAC/TGATCT`	2	--	int¹		0	--	--	--	--
rs76792123^1,2		--	164040792(+)	`ATAGCG/ACAGCT`	2	--	int¹		1		NA	120
rs78796905^1,2		--	164040935(+)	`CCACCC/TACAGG`	2	--	int¹		1		NA	120

HapMap Linkage Disequilibrium report for T (166571086 - 166582188 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for T: --
Human Gene Mutation Database (HGMD): T

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing T

DNA2.0 Custom Variant and Variant Library Synthesis for T

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

T for disorders           About GeneDecksing

OMIM gene information: 601397
OMIM 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

T is involved in susceptibility to the development of chordoma (CHDM) [MIM:215400]. Chordomas are rare,

clinically malignant tumors derived from notochordal remnants. They occur along the length of the spinal axis,

predominantly in the sphenooccipital, vertebral and sacrococcygeal regions. They are characterized by slow growth,

local destruction of bone, extension into adjacent soft tissues and rarely, distant metastatic spread.

Note=Susceptibility to development of chordomas is due to a T gene duplication

20/51 diseases for T (see all 51): About MalaCards

neural tube defect tropical spastic paraparesis spastic paraparesis abdominal aortic aneurysm

clear cell renal cell carcinoma cervical intraepithelial neoplasia type 2 diabetes mellitus aortic aneurysm

autoimmune hemolytic anemia hemolytic anemia alopecia areata genital herpes

spina bifida hairy cell leukemia parachordoma renal cell carcinoma

allergic rhinitis aplastic anemia diabetes mellitus myoepithelioma

3 Novoseek disease relationships for T gene About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
colitis	22.3	1	17923080 (1), 11994418 (1)
inflammation	18.4	3	19412181 (1), 17723218 (1), 15498029 (1)
asthma	6.56	1	15604153 (1)

Human Genome Epidemiology (HuGE) Navigator: T (0 documents)

Export disorders for T gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for T gene, integrated from 9 sources (see all 118):
(articles sorted by number of sources associating them with T)

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The human homolog T of the mouse T(Brachyury) gene; gene structure, cDNA sequence, and assignment to chromosome 6q27. (PubMed id 8963900)^{1, 2, 3, 9} Edwards Y.H....Sowden J. (1996)
T (brachyury) gene duplication confers major suscepti bility to familial chordoma. (PubMed id 19801981)^{1, 2} Yang X.R....Kelley M.J. (2009)
The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)^{1, 2} Mungall A.J.... Beck S. (2003)
The human T locus and spina bifida risk. (PubMed id 15449172)^{2, 9} Jensen L.E....Mitchell L.E. (2004)
Genome-wide association identifies the T gene as a nov el asthma pharmacogenetic locus. (PubMed id 22538805)¹ Tantisira K.G....Israel E. (2012)
An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma. (PubMed id 22847733)¹ Nelson A.C....Flanagan A.M. (2012)
BRACHYURY confers cancer stem cell characteristics on colorectal cancer cells. (PubMed id 21365650)¹ Sarkar D....Wakeman J.A. (2012)
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. (PubMed id 22589738)¹ Fox C.S....Borecki I.B. (2012)
Expression of brachyury in hemangioblastoma: potential use in differential diagnosis. (PubMed id 22446946)¹ Barresi V....Barresi G. (2012)
P63 does not regulate brachyury expression in human ch ordomas and osteosarcomas. (PubMed id 22007675)¹ Pillay N....Flanagan A.M. (2011)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 6862	HGNC: 11515	AceView: T	Ensembl:ENSG00000164458	euGenes: HUgn6862
ECgene: T	H-InvDB: T

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for T	Pharmacogenomics, SNPs, Pathways

Intellectual Property for T gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for T gene:
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GeneCards and IP:
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T, brachyury homolog (mouse)

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