TBX15 Gene (Protein Coding)

T-Box Transcription Factor 15

GC01M118883
GIFtS:
42
This gene belongs to the T-box family of genes, which encode a phylogenetically conserved family of transcription factors that regulate a variety of developmental processes. All these genes contain a common T-box DNA-binding domain. Mutations in this gene are associated with Cousin syndrome.[provided by RefSeq, Oct 2009] See more...

Aliases for TBX15 Gene

Aliases for TBX15 Gene

  • T-Box Transcription Factor 15 2 3 5
  • T-Box Transcription Factor TBX15 3 4
  • T-Box Transcription Factor TBX14 3 4
  • T-Box Protein 14 3 4
  • T-Box Protein 15 3 4
  • T-Box 14 2 3
  • T-Box 15 2 3
  • TBX14 3 4
  • TBX15 5

External Ids for TBX15 Gene

Previous HGNC Symbols for TBX15 Gene

  • TBX14

Previous GeneCards Identifiers for TBX15 Gene

  • GC01U990165
  • GC01M118264
  • GC01M118572
  • GC01M118772
  • GC01M119137
  • GC01M119227
  • GC01M119425
  • GC01M117285

Summaries for TBX15 Gene

Entrez Gene Summary for TBX15 Gene

  • This gene belongs to the T-box family of genes, which encode a phylogenetically conserved family of transcription factors that regulate a variety of developmental processes. All these genes contain a common T-box DNA-binding domain. Mutations in this gene are associated with Cousin syndrome.[provided by RefSeq, Oct 2009]

GeneCards Summary for TBX15 Gene

TBX15 (T-Box Transcription Factor 15) is a Protein Coding gene. Diseases associated with TBX15 include Cousin Syndrome and Acromegaloid Facial Appearance Syndrome. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and protein heterodimerization activity. An important paralog of this gene is TBX18.

UniProtKB/Swiss-Prot Summary for TBX15 Gene

  • Probable transcriptional regulator involved in the development of the skeleton of the limb, vertebral column and head. Acts by controlling the number of mesenchymal precursor cells and chondrocytes (By similarity).

Additional gene information for TBX15 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TBX15 Gene

Genomics for TBX15 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for TBX15 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
GH01J118981 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 255.5 +3.3 3309 9 ZNF395 VEZF1 CBX8 NRF1 ZBTB33 ZNF589 ZNF148 L3MBTL2 ZNF584 BRD4 TBX15 WARS2 LOC105378933 WARS2-AS1 HSALNG0006456 SPAG17
GH01J119000 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE dbSUPER 250.4 -12.0 -11977 2.5 MCM3 CEBPB ZNF395 VEZF1 GABPA FOSL1 PRDM10 JUND CBX8 ZNF589 ENSG00000239216 LOC105378933 LOC107985191 TBX15 WARS2
GH01J118990 Enhancer 0.5 ENCODE dbSUPER 250.7 -1.4 -1397 0.2 CBX8 EZH2 TBX15 HSALNG0006457 WARS2
GH01J119397 Enhancer 0.4 ENCODE 4.4 -408.6 -408575 1.6 FOXA2 ESRRA HNF4A ZNF740 HAO2 HAO2-IT1 TBX15 HSALNG0006489 lnc-HSD3B2-1 HSD3B2
GH01J119115 Enhancer 0.3 Ensembl 4.5 -126.9 -126945 2.6 SPI1 EZH2 WARS2 WARS2-AS1 TBX15 piR-50852-005 lnc-TBX15-4 RBMX2P3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TBX15 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TBX15

Top Transcription factor binding sites by QIAGEN in the TBX15 gene promoter:
  • AREB6
  • C/EBPalpha
  • CHOP-10
  • Hlf
  • IRF-7A
  • NRSF form 1
  • NRSF form 2
  • p53
  • Sox9
  • Spz1

Genomic Locations for TBX15 Gene

Latest Assembly
chr1:118,883,046-118,989,556
(GRCh38/hg38)
Size:
106,511 bases
Orientation:
Minus strand

Previous Assembly
chr1:119,425,670-119,532,133
(GRCh37/hg19 by Entrez Gene)
Size:
106,464 bases
Orientation:
Minus strand

chr1:119,425,669-119,532,179
(GRCh37/hg19 by Ensembl)
Size:
106,511 bases
Orientation:
Minus strand

Genomic View for TBX15 Gene

Genes around TBX15 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBX15 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBX15 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TBX15 Gene

Proteins for TBX15 Gene

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  • Protein details for TBX15 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96SF7-TBX15_HUMAN
    Recommended name:
    T-box transcription factor TBX15
    Protein Accession:
    Q96SF7
    Secondary Accessions:
    • Q08E76
    • Q5JT54
    • Q5T9S7

    Protein attributes for TBX15 Gene

    Size:
    602 amino acids
    Molecular mass:
    65757 Da
    Quaternary structure:
    • Can form a heterodimer with TBX18.
    Miscellaneous:
    • [Isoform 1]: Gene prediction based on similarity to orthologs.

    Alternative splice isoforms for TBX15 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBX15 Gene

Protein Expression for TBX15 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TBX15 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TBX15 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TBX15 Gene

Domains & Families for TBX15 Gene

Gene Families for TBX15 Gene

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

Protein Domains for TBX15 Gene

InterPro:
Blocks:
  • Transcription factor, T-box
ProtoNet:

Suggested Antigen Peptide Sequences for TBX15 Gene

GenScript: Design optimal peptide antigens:
  • T-box 15 (Q5JT55_HUMAN)
  • T-box transcription factor TBX14 (TBX15_HUMAN)
genes like me logo Genes that share domains with TBX15: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for TBX15 Gene

Function for TBX15 Gene

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  5. Clone products for research
  6. Cell Lines for research

Molecular function for TBX15 Gene

UniProtKB/Swiss-Prot Function:
Probable transcriptional regulator involved in the development of the skeleton of the limb, vertebral column and head. Acts by controlling the number of mesenchymal precursor cells and chondrocytes (By similarity).
GENATLAS Biochemistry:
murine T-box gene Tbx15 (T,brachyury) homolog,expressed in the craniofacial region and in the developing limbs,maybe a candidate gene for acromegaloid facial appearance syndrome

Phenotypes From GWAS Catalog for TBX15 Gene

Gene Ontology (GO) - Molecular Function for TBX15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IEA --
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA,IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IEA --
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with TBX15: view
genes like me logo Genes that share phenotypes with TBX15: view

Human Phenotype Ontology for TBX15 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TBX15 Gene

MGI Knock Outs for TBX15:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBX15

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for TBX15 Gene

Localization for TBX15 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBX15 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 TBX15 gene
Compartment Confidence
nucleus 4
mitochondrion 2
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for TBX15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IEA --
GO:0090571 RNA polymerase II transcription repressor complex IEA --
genes like me logo Genes that share ontologies with TBX15: view

Pathways & Interactions for TBX15 Gene

PathCards logo

SuperPathways for TBX15 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TBX15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0001708 cell fate specification IBA 21873635
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0048701 embryonic cranial skeleton morphogenesis IEA --
genes like me logo Genes that share ontologies with TBX15: view

No data available for Pathways by source and SIGNOR curated interactions for TBX15 Gene

Drugs & Compounds for TBX15 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for TBX15 Gene

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  2. miRNA products for research
  3. Inhibitory RNAs for research
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mRNA/cDNA for TBX15 Gene

2 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBX15

Alternative Splicing Database (ASD) splice patterns (SP) for TBX15 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9
SP1: -
SP2:

Relevant External Links for TBX15 Gene

GeneLoc Exon Structure for
TBX15

Expression for TBX15 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TBX15 Gene

mRNA expression in normal human tissues for TBX15 Gene
mRNA expression by GTEx for TBX15 GenemRNA expression by BioGPS for TBX15 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TBX15 Gene

This gene is overexpressed in Muscle - Skeletal (x23.6), Artery - Tibial (x5.3), and Adipose - Subcutaneous (x5.2).

Protein differential expression in normal tissues from HIPED for TBX15 Gene

This gene is overexpressed in Placenta (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TBX15 Gene



Protein tissue co-expression partners for TBX15 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TBX15

SOURCE GeneReport for Unigene cluster for TBX15 Gene:

Hs.146196

Evidence on tissue expression from TISSUES for TBX15 Gene

  • Muscle(2.5)
  • Liver(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TBX15 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • chin
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • meninges
  • mouth
  • nose
  • outer ear
  • skull
  • tongue
  • tooth
Thorax:
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • kidney
Pelvis:
  • pelvis
  • penis
  • testicle
  • ureter
  • urethra
  • vulva
Limb:
  • arm
  • digit
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • hair
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with TBX15: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt for TBX15 Gene

Orthologs for TBX15 Gene

This gene was present in the common ancestor of animals.

Orthologs for TBX15 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia TBX15 30 31
  • 99.6 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia TBX15 30 31
  • 93.48 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia TBX15 30 31
  • 93.08 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Tbx15 30 17 31
  • 93.01 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia LOC500213 30
  • 92.29 (n)
Oppossum
(Monodelphis domestica)
 Mammalia TBX15 31
  • 79 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves TBX15 30 31
  • 85.12 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia TBX15 31
  • 73 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia tbx15 30
  • 78.11 (n)
Zebrafish
(Danio rerio)
 Actinopterygii tbx15 30 31
  • 75.75 (n)
 OneToOne
Worm
(Caenorhabditis elegans)
 Secernentea mls-1 31
  • 46 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 21 (a)
 OneToMany
Sea Vase
(Ciona intestinalis)
 Ascidiacea Cin.14222 30
Species where no ortholog for TBX15 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • 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)
  • Wheat (Triticum aestivum)

Evolution for TBX15 Gene

ENSEMBL:
Gene Tree for TBX15 (if available)
TreeFam:
Gene Tree for TBX15 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TBX15: view image

Paralogs for TBX15 Gene

Paralogs for TBX15 Gene

(8) SIMAP similar genes for TBX15 Gene using alignment to 2 proteins:

  • TBX15_HUMAN
  • Q5JT55_HUMAN
genes like me logo Genes that share paralogs with TBX15: view

Variants for TBX15 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TBX15 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs140463861 Likely Benign: not provided 118,923,505(-) C/G
NM_001330677.2(TBX15):c.792G>C (p.Gly264=) 		SYNONYMOUS
rs140670116 Benign/Likely Benign: not specified; not provided 118,923,460(-) T/C
NM_001330677.2(TBX15):c.837A>G (p.Thr279=) 		SYNONYMOUS
rs141002143 Likely Benign: not specified; not provided 118,899,072(-) C/T
NM_001330677.2(TBX15):c.980G>A (p.Arg327His) 		MISSENSE
rs143725585 Likely Benign: not provided 118,885,176(-) C/T
NM_001330677.2(TBX15):c.1365G>A (p.Ser455=) 		SYNONYMOUS
rs144291418 Uncertain Significance: Pelviscapular dysplasia; not provided 118,885,216(-) C/T
NM_001330677.2(TBX15):c.1325G>A (p.Arg442Lys) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TBX15 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TBX15 Gene

Variant ID Type Subtype PubMed ID
esv25417 CNV loss 19812545
esv2675423 CNV deletion 23128226
esv3587336 CNV loss 21293372
esv3587338 CNV loss 21293372
nsv160473 CNV deletion 16902084
nsv506958 OTHER sequence alteration 20534489
nsv524681 CNV gain 19592680
nsv831181 CNV gain 17160897
nsv997707 CNV gain 25217958

Variation tolerance for TBX15 Gene

Residual Variation Intolerance Score: 49.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.63; 78.27% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBX15 Gene

Human Gene Mutation Database (HGMD)
TBX15
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBX15

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TBX15 Gene

Disorders for TBX15 Gene

MalaCards: The human disease database

(5) MalaCards diseases for TBX15 Gene - From: OMI, CVR, GTR, ORP, COP, and GCD

Disorder Aliases PubMed IDs
cousin syndrome
  • craniofacial dysmorphism, hypoplasia of scapula and pelvis, and short stature
acromegaloid facial appearance syndrome
  • afa syndrome
ulnar-mammary syndrome
  • ums
brachydactyly
strabismus
  • strabismus, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search TBX15 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TBX15_HUMAN
  • Cousin syndrome (COUSS) [MIM:260660]: Defined as pelviscapular dysplasia with epiphyseal abnormalities, congenital dwarfism and facial dysmorphy (frontal bossing, hypertelorism, narrow palpebral fissures, deep set globes, strabismus, low-set posteriory rotated and unusually formed external ears, dysplasia of conchae, small chin, short neck with redundant skin folds, and a low hairline). Intelligence may vary from normal to moderately impaired. Radiographic features comprise aplasia of the body of the scapula, hypoplasia of the iliac bone, humeroradial synosthosis, dislocation of the femoral heads, and moderate brachydactyly. {ECO:0000269 PubMed:19068278}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for TBX15

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with TBX15: view

No data available for Genatlas for TBX15 Gene

Publications for TBX15 Gene

  1. TBX15 mutations cause craniofacial dysmorphism, hypoplasia of scapula and pelvis, and short stature in Cousin syndrome. (PMID: 19068278) Lausch E … Superti-Furga A (American journal of human genetics 2008) 3 4 74
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  3. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 41
  4. Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. (PMID: 20935629) Heid IM … Lindgren CM (Nature genetics 2010) 3 41
  5. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4

ExternalLinks

View latest publications for TBX15 gene in Mastermind

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