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TBX5 T-box 5 [ Homo sapiens (human) ]

Gene ID: 6910, updated on 13-Feb-2019

Summary

Official Symbol
TBX5provided by HGNC
Official Full Name
T-box 5provided by HGNC
Primary source
HGNC:HGNC:11604
See related
Ensembl:ENSG00000089225 MIM:601620
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HOS
Summary
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. This gene is closely linked to related family member T-box 3 (ulnar mammary syndrome) on human chromosome 12. The encoded protein may play a role in heart development and specification of limb identity. Mutations in this gene have been associated with Holt-Oram syndrome, a developmental disorder affecting the heart and upper limbs. Several transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]
Expression
Biased expression in heart (RPKM 12.5), placenta (RPKM 8.8) and 6 other tissues See more
Orthologs

Genomic context

See TBX5 in Genome Data Viewer
Location:
12q24.21
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (114353911..114408708, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (114791735..114846247, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2459 Neighboring gene CRE9 enhancer downstream of TBX5 Neighboring gene uncharacterized LOC105369998 Neighboring gene CRE16 enhancer upstream of TBX5 Neighboring gene TBX5 antisense RNA 1 Neighboring gene RN7SK pseudogene 216

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Holt-Oram syndrome
MedGen: C0265264 OMIM: 142900 GeneReviews: Holt-Oram Syndrome
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-02-23)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-02-23)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis.
NHGRI GWA Catalog
Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction.
NHGRI GWA Catalog
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
NHGRI GWA Catalog
Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction.
NHGRI GWA Catalog
Genome-wide association studies of the PR interval in African Americans.
NHGRI GWA Catalog
Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.
NHGRI GWA Catalog
Genome-wide association study identifies three susceptibility loci for laryngeal squamous cell carcinoma in the Chinese population.
NHGRI GWA Catalog
Genome-wide association study of blood pressure and hypertension.
NHGRI GWA Catalog
Genome-wide association study of PR interval.
NHGRI GWA Catalog
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
NHGRI GWA Catalog
Identification of a novel percent mammographic density locus at 12q24.
NHGRI GWA Catalog
Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog
Novel loci associated with PR interval in a genome-wide association study of 10 African American cohorts.
NHGRI GWA Catalog
Several common variants modulate heart rate, PR interval and QRS duration.
NHGRI GWA Catalog

Pathways from BioSystems

  • Cardiac Progenitor Differentiation, organism-specific biosystem (from WikiPathways)
    Cardiac Progenitor Differentiation, organism-specific biosystemFactors involved in the induction of cardiac differentiation in vitro and in vivo. This model was based on the below two review articles.
  • Cardiac conduction, organism-specific biosystem (from REACTOME)
    Cardiac conduction, organism-specific biosystemThe normal sequence of contraction of atria and ventricles of the heart require activation of groups of cardiac cells. The mechanism must elicit rapid changes in heart rate and respond to changes in ...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • Heart Development, organism-specific biosystem (from WikiPathways)
    Heart Development, organism-specific biosystemThis pathway has been largely adapted from an article by Deepak Srivastava, Cell. 2006 Sep 22;126(6):1037-48. In this pathway are known transcription factors, miRNAs and regulatory proteins that impa...
  • Muscle contraction, organism-specific biosystem (from REACTOME)
    Muscle contraction, organism-specific biosystemIn this module, the processes by which calcium binding triggers actin - myosin interactions and force generation in smooth and striated muscle tissues are annotated.
  • Physiological factors, organism-specific biosystem (from REACTOME)
    Physiological factors, organism-specific biosystemCardiovascular homeostasis can be regulated by natriuretic peptides (Pandey 2014).
  • YAP1- and WWTR1 (TAZ)-stimulated gene expression, organism-specific biosystem (from REACTOME)
    YAP1- and WWTR1 (TAZ)-stimulated gene expression, organism-specific biosystemYAP1 and WWTR1 (TAZ) are transcriptional co-activators, both homologues of the Drosophila Yorkie protein. They both interact with members of the TEAD family of transcription factors, and WWTR1 intera...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
atrial septum morphogenesis IEA
Inferred from Electronic Annotation
more info
 
atrioventricular valve morphogenesis IEA
Inferred from Electronic Annotation
more info
 
bundle of His development IEA
Inferred from Electronic Annotation
more info
 
cardiac left ventricle formation ISS
Inferred from Sequence or Structural Similarity
more info
 
cardiac muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
cell migration involved in coronary vasculogenesis TAS
Traceable Author Statement
more info
PubMed 
cell-cell signaling IDA
Inferred from Direct Assay
more info
PubMed 
embryonic forelimb morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
embryonic limb morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
endocardial cushion development IEA
Inferred from Electronic Annotation
more info
 
forelimb morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
heart development IDA
Inferred from Direct Assay
more info
PubMed 
heart development IMP
Inferred from Mutant Phenotype
more info
PubMed 
lung development IEA
Inferred from Electronic Annotation
more info
 
morphogenesis of an epithelium IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cardiac muscle cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of epithelial to mesenchymal transition TAS
Traceable Author Statement
more info
PubMed 
pattern specification process IEA
Inferred from Electronic Annotation
more info
 
pericardium development IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cardiac muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cardioblast differentiation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of secondary heart field cardioblast proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
ventricular septum development ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-DNA complex IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
T-box transcription factor TBX5
Names
T-box protein 5

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007373.1 RefSeqGene

    Range
    5001..59513
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_670

mRNA and Protein(s)

  1. NM_000192.3NP_000183.2  T-box transcription factor TBX5 isoform 1

    See identical proteins and their annotated locations for NP_000183.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 4 both encode the same isoform (1).
    Source sequence(s)
    AC009260, AF221714, BC027942, DA863182
    Consensus CDS
    CCDS9173.1
    UniProtKB/Swiss-Prot
    Q99593
    Related
    ENSP00000309913.4, ENST00000310346.8
    Conserved Domains (1) summary
    cd00182
    Location:53241
    TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...
  2. NM_080717.2NP_542448.1  T-box transcription factor TBX5 isoform 3

    See identical proteins and their annotated locations for NP_542448.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks the exon containing the translation start site compared to transcript variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AB051068, AC009260, AF221714, BC027942
    Consensus CDS
    CCDS9174.1
    UniProtKB/Swiss-Prot
    Q99593
    Related
    ENSP00000337723.5, ENST00000349716.9
    Conserved Domains (1) summary
    cd00182
    Location:3191
    TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...
  3. NM_181486.2NP_852259.1  T-box transcription factor TBX5 isoform 1

    See identical proteins and their annotated locations for NP_852259.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1 and 4 both encode the same isoform (1).
    Source sequence(s)
    AC009260, BC027942, CB960757
    Consensus CDS
    CCDS9173.1
    UniProtKB/Swiss-Prot
    Q99593
    Related
    ENSP00000384152.2, ENST00000405440.6
    Conserved Domains (1) summary
    cd00182
    Location:53241
    TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    114353911..114408708 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017019912.1XP_016875401.1  T-box transcription factor TBX5 isoform X1

    Conserved Domains (1) summary
    cd00182
    Location:69257
    TBOX; T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA ...

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_080718.1: Suppressed sequence

    Description
    NM_080718.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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