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TBX6 Gene(Protein Coding)

T-Box 6

GCID:
GC16M030097
GIFtS:
48
Genes Participants
UDN Logo

Aliases for TBX6 Gene

Aliases for TBX6 Gene

  • T-Box 6 2 3 5
  • T-Box Protein 6 3 4
  • T-Box Transcription Factor TBX6 3
  • SCDO5 3

External Ids for TBX6 Gene

Previous GeneCards Identifiers for TBX6 Gene

  • GC16P029057
  • GC16M030419
  • GC16M030095
  • GC16M030134
  • GC16M030004
  • GC16M027758

Summaries for TBX6 Gene

Entrez Gene Summary for TBX6 Gene

  • 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]

GeneCards Summary for TBX6 Gene

TBX6 (T-Box 6) is a Protein Coding gene. Diseases associated with TBX6 include Spondylocostal Dysostosis 5 and Dysostosis. Among its related pathways are Mesodermal Commitment Pathway and Neural Crest Differentiation. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and RNA polymerase II activating transcription factor binding. An important paralog of this gene is TBX2.

UniProtKB/Swiss-Prot for TBX6 Gene

  • 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).

Additional gene information for TBX6 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TBX6 Gene

Genomics for TBX6 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for TBX6 Gene

Promoters and enhancers for TBX6 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH16I030089 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 573.5 -1.6 -1555 8.1 MLX DMAP1 IRF4 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC MEF2D YPEL3 TBX6 STX4 INO80E SMG1P2 SMG1P5 RNF40 PRR14 FBRS SRCAP
GH16I030112 Promoter/Enhancer 1.5 EPDnew ENCODE 20.3 -22.9 -22911 5.5 HDGF ARID4B SIN3A GLI4 ZNF2 ZBTB7B ZNF48 YY1 ZNF121 ZNF143 GDPD3 GC16P030116 TBX6 MAPK3 CORO1A SLX1A SLX1A-SULT1A3 BOLA2B CD2BP2 DOC2A
GH16I029742 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 8.4 +346.8 346805 5.4 HDGF BMI1 BATF KLF5 IRF4 ZNF207 ETV6 BCLAF1 IKZF2 RUNX3 C16orf54 ENSG00000260719 RN7SKP127 TBX6 YPEL3 MYLPF CORO1A PPP4C GC16M029747
GH16I030051 Enhancer 0.9 Ensembl ENCODE 18.2 +40.3 40275 1.1 ZNF639 ZNF189 JUN OSR2 ZNF335 ZSCAN21 ZSCAN23 ZNF121 ZFHX2 ZNF366 ALDOA FAM57B GC16P030051 TBX6 C16orf92 PPP4C DOC2A HIRIP3 INO80E NPIPB12
GH16I029819 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5.7 +269.0 269023 7.5 HDGF PKNOX1 CLOCK SIN3A ZNF48 YY1 GLIS2 ZNF143 FOS RUNX3 MVP ENSG00000238045 GC16M029840 INO80E SRCAP ENSG00000260853 NPIPB12 GDPD3 ATXN2L NFATC2IP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TBX6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TBX6 gene promoter:

Genomic Locations for TBX6 Gene

Genomic Locations for TBX6 Gene
chr16:30,085,793-30,091,937
(GRCh38/hg38)
Size:
6,145 bases
Orientation:
Minus strand
chr16:30,097,114-30,103,208
(GRCh37/hg19)

Genomic View for TBX6 Gene

Genes around TBX6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBX6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBX6 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TBX6 Gene

Proteins for TBX6 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for TBX6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95947-TBX6_HUMAN
    Recommended name:
    T-box transcription factor TBX6
    Protein Accession:
    O95947
    Secondary Accessions:
    • Q8TAS4
    • Q9HA44

    Protein attributes for TBX6 Gene

    Size:
    436 amino acids
    Molecular mass:
    47045 Da
    Quaternary structure:
    • Forms a dimeric complex with DNA (in vitro).

    Alternative splice isoforms for TBX6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBX6 Gene

Post-translational modifications for TBX6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TBX6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TBX6 Gene

Domains & Families for TBX6 Gene

Gene Families for TBX6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for TBX6 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TBX6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with TBX6: view

No data available for UniProtKB/Swiss-Prot for TBX6 Gene

Function for TBX6 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for TBX6 Gene

GENATLAS Biochemistry:
murine T-box gene Tbx6 (T,brachyury) homolog,expressed during gastrulation and in some adult tissues,including testis,involved in paraxial mesoderm formation and somitogenesis
UniProtKB/Swiss-Prot 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).

Phenotypes From GWAS Catalog for TBX6 Gene

Gene Ontology (GO) - Molecular Function for TBX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding IEA --
GO:0001085 RNA polymerase II transcription factor binding ISS --
GO:0001102 RNA polymerase II activating transcription factor binding ISS --
GO:0001191 transcriptional repressor activity, RNA polymerase II transcription factor binding ISS --
GO:0003677 DNA binding IEA,TAS 9933572
genes like me logo Genes that share ontologies with TBX6: view
genes like me logo Genes that share phenotypes with TBX6: view

Human Phenotype Ontology for TBX6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TBX6 Gene

MGI Knock Outs for TBX6:

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for TBX6 Gene

Localization for TBX6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBX6 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TBX6 gene
Compartment Confidence
nucleus 4
cytosol 2
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TBX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with TBX6: view

Pathways & Interactions for TBX6 Gene

genes like me logo Genes that share pathways with TBX6: view

Gene Ontology (GO) - Biological Process for TBX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II ISS --
GO:0001707 mesoderm formation IEA --
GO:0001708 cell fate specification IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with TBX6: view

No data available for SIGNOR curated interactions for TBX6 Gene

Drugs & Compounds for TBX6 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for TBX6 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for TBX6 Gene

(5) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(27) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TBX6 Gene

T-box 6:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for TBX6 Gene

No ASD Table

Relevant External Links for TBX6 Gene

GeneLoc Exon Structure for
TBX6
ECgene alternative splicing isoforms for
TBX6

Expression for TBX6 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TBX6 Gene

mRNA expression in normal human tissues for TBX6 Gene
mRNA expression by GTEx for TBX6 GenemRNA expression by BioGPS for TBX6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TBX6 Gene

This gene is overexpressed in Esophagus - Mucosa (x6.2).

NURSA nuclear receptor signaling pathways regulating expression of TBX6 Gene:

TBX6

SOURCE GeneReport for Unigene cluster for TBX6 Gene:

Hs.198301

mRNA Expression by UniProt/SwissProt for TBX6 Gene:

O95947-TBX6_HUMAN
Tissue specificity: Expressed in fetal tail bud, posterior spinal tissue, intervertebral disk and testis. Also expressed in adult testis, kidney, lung, muscle and thymus.

Evidence on tissue expression from TISSUES for TBX6 Gene

  • Blood(4)
  • Lymph node(4)
  • Spleen(4)
  • Nervous system(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TBX6 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • eye
  • eyelid
  • face
  • head
  • neck
  • nose
  • skull
Thorax:
  • chest wall
  • lung
  • rib
  • rib cage
  • sternum
Pelvis:
  • pelvis
General:
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with TBX6: view

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for TBX6 Gene

Orthologs for TBX6 Gene

This gene was present in the common ancestor of animals.

Orthologs for TBX6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia TBX6 33 34
  • 99.46 (n)
cow
(Bos Taurus)
 Mammalia TBX6 33 34
  • 88.53 (n)
dog
(Canis familiaris)
 Mammalia TBX6 33 34
  • 87.31 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia TBX6 34
  • 86 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Tbx6 33 16 34
  • 85.02 (n)
rat
(Rattus norvegicus)
 Mammalia Tbx6 33
  • 84.79 (n)
oppossum
(Monodelphis domestica)
 Mammalia TBX6 34
  • 82 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves TBX6 34
  • 33 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia TBX6 34
  • 49 (a)
 OneToOne
zebrafish
(Danio rerio)
 Actinopterygii tbx6 34
  • 21 (a)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta Doc2 35 34
  • 57 (a)
Doc3 35 34
  • 54 (a)
Doc1 35 34
  • 52 (a)
Species where no ortholog for TBX6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TBX6 Gene

ENSEMBL:
Gene Tree for TBX6 (if available)
TreeFam:
Gene Tree for TBX6 (if available)

Paralogs for TBX6 Gene

Paralogs for TBX6 Gene

(15) SIMAP similar genes for TBX6 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with TBX6: view

Variants for TBX6 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for TBX6 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs201620629 pathogenic, Spondylocostal dysostosis 5 30,086,847(-) G/A/C coding_sequence_variant, missense_variant, non_coding_transcript_variant, stop_gained
rs202193096 pathogenic, Spondylocostal dysostosis 5, Spondylocostal dysostosis 5 (SCDO5) [MIM:122600] 30,089,130(-) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs2289292 pathogenic, benign, Spondylocostal dysostosis 5, not specified 30,086,309(-) C/G/T coding_sequence_variant, downstream_transcript_variant, genic_downstream_transcript_variant, synonymous_variant
rs3809624 pathogenic, Spondylocostal dysostosis 5 30,091,481(-) T/C 5_prime_UTR_variant, intron_variant, non_coding_transcript_variant
rs3809627 pathogenic, Spondylocostal dysostosis 5 30,091,839(-) C/A 5_prime_UTR_variant, intron_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for TBX6 Gene

Variant ID Type Subtype PubMed ID
esv2758642 CNV gain 17122850
nsv1160384 CNV duplication 26073780
nsv833187 CNV loss 17160897

Variation tolerance for TBX6 Gene

Residual Variation Intolerance Score: 43.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.33; 41.57% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBX6 Gene

Human Gene Mutation Database (HGMD)
TBX6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBX6

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TBX6 Gene

Disorders for TBX6 Gene

MalaCards: The human disease database

(6) MalaCards diseases for TBX6 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search TBX6 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TBX6_HUMAN
  • Spondylocostal dysostosis 5 (SCDO5) [MIM:122600]: A rare condition of variable severity characterized by vertebral and costal anomalies. The main feature include dwarfism, vertebral fusion, hemivertebrae, posterior rib fusion, reduced rib number, and other rib malformations. SCDO5 inheritance can be autosomal dominant or recessive. {ECO:0000269 PubMed:23335591, ECO:0000269 PubMed:25564734}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TBX6

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TBX6: view

No data available for Genatlas for TBX6 Gene

Publications for TBX6 Gene

  1. Identification, mapping, and phylogenomic analysis of four new human members of the T-box gene family: EOMES, TBX6, TBX18, and TBX19. (PMID: 9888994) Yi CH … Brook JD (Genomics 1999) 2 3 4 58
  2. The human TBX6 gene: cloning and assignment to chromosome 16p11.2. (PMID: 9933572) Papapetrou C … Edwards YH (Genomics 1999) 2 3 4 58
  3. Compound Heterozygosity for Null Mutations and a Common Hypomorphic Risk Haplotype in TBX6 Causes Congenital Scoliosis. (PMID: 28054739) Takeda K … Ikegawa S (Human mutation 2017) 3 4 58
  4. TBX6 null variants and a common hypomorphic allele in congenital scoliosis. (PMID: 25564734) Wu N … Zhang F (The New England journal of medicine 2015) 3 4 58
  5. Autosomal dominant spondylocostal dysostosis is caused by mutation in TBX6. (PMID: 23335591) Sparrow DB … Dunwoodie SL (Human molecular genetics 2013) 3 4 58

Products for TBX6 Gene

Sources for TBX6 Gene

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