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TRPS1 transcriptional repressor GATA binding 1 [ Homo sapiens (human) ]

Gene ID: 7227, updated on 3-Jun-2018
Official Symbol
TRPS1provided by HGNC
Official Full Name
transcriptional repressor GATA binding 1provided by HGNC
Primary source
HGNC:HGNC:12340
See related
Ensembl:ENSG00000104447 MIM:604386; Vega:OTTHUMG00000142829
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
GC79; LGCR
Summary
This gene encodes a transcription factor that represses GATA-regulated genes and binds to a dynein light chain protein. Binding of the encoded protein to the dynein light chain protein affects binding to GATA consensus sequences and suppresses its transcriptional activity. Defects in this gene are a cause of tricho-rhino-phalangeal syndrome (TRPS) types I-III. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in esophagus (RPKM 4.1), gall bladder (RPKM 3.6) and 24 other tissues See more
Orthologs
See TRPS1 in Genome Data Viewer
Location:
8q23.3
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 8 NC_000008.11 (115408496..115669637, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (116420724..116713299, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene cysteinyl-tRNA synthetase pseudogene 2 Neighboring gene uncharacterized LOC107986901 Neighboring gene VISTA enhancer hs919 Neighboring gene uncharacterized LOC107986968 Neighboring gene uncharacterized LOC107986902

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Trichorhinophalangeal dysplasia type I
MedGen: C0432233 OMIM: 190350 GeneReviews: Trichorhinophalangeal Syndrome
Compare labs
Trichorhinophalangeal syndrome type 3
MedGen: C1860823 OMIM: 190351 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-01-12)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-01-12)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association study (GWAS) for bronchopulmonary dysplasia.
NHGRI GWA Catalog
A mega-analysis of genome-wide association studies for major depressive disorder.
NHGRI GWA Catalog
Biological, clinical and population relevance of 95 loci for blood lipids.
NHGRI GWA Catalog
Discovery and refinement of loci associated with lipid levels.
NHGRI GWA Catalog
Genome-wide association analysis of eating disorder-related symptoms, behaviors, and personality traits.
NHGRI GWA Catalog
Genome-wide association study identifies new susceptibility loci for posttraumatic stress disorder.
NHGRI GWA Catalog
Genome-wide association study of periodontal pathogen colonization.
NHGRI GWA Catalog

Protein interactions

Protein Gene Interaction Pubs
retropepsin gag-pol HIV-1 PR is identified to have a physical interaction with trichorhinophalangeal syndrome I (TRPS1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC134928

Gene Ontology Provided by GOA

Process Evidence Code Pubs
NLS-bearing protein import into nucleus TAS
Traceable Author Statement
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
protein heterooligomerization IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of chondrocyte differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
skeletal system development TAS
Traceable Author Statement
more info
PubMed 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IMP
Inferred from Mutant Phenotype
more info
PubMed 
Preferred Names
zinc finger transcription factor Trps1
Names
tricho-rhino-phalangeal syndrome type I protein
trichorhinophalangeal syndrome I
zinc finger protein GC79

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_012383.3 RefSeqGene

    Range
    4974..265506
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001282902.2NP_001269831.1  zinc finger transcription factor Trps1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate 5' structure which results in the use of an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AF178030, AF183810, AK304046, DC339831, KC877306, KF454923
    Consensus CDS
    CCDS64957.1
    UniProtKB/Swiss-Prot
    Q9UHF7
    Related
    ENSP00000428680.1, OTTHUMP00000227887, ENST00000520276.5, OTTHUMT00000380905
    Conserved Domains (2) summary
    smart00401
    Location:895938
    ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
    cd00202
    Location:899955
    ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
  2. NM_001282903.2NP_001269832.1  zinc finger transcription factor Trps1 isoform 3

    See identical proteins and their annotated locations for NP_001269832.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice in the coding region which results in the use of an alternate start codon, compared to variant 1. The encoded isoform (3) is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AF178030, BC125020, KC877306, KF454923
    UniProtKB/Swiss-Prot
    Q9UHF7
    Conserved Domains (2) summary
    smart00401
    Location:897940
    ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
    cd00202
    Location:901957
    ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
  3. NM_001330599.1NP_001317528.1  zinc finger transcription factor Trps1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AF178030, AF183810, AF264784, KC877306, KF454923
    Consensus CDS
    CCDS83316.1
    UniProtKB/Swiss-Prot
    Q9UHF7
    Related
    ENSP00000220888.5, ENST00000220888.9
  4. NM_014112.4NP_054831.2  zinc finger transcription factor Trps1 isoform 1

    See identical proteins and their annotated locations for NP_054831.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF178030, AF183810, KC877306, KF454923
    Consensus CDS
    CCDS6318.2
    UniProtKB/Swiss-Prot
    Q9UHF7
    Related
    ENSP00000379065.3, OTTHUMP00000183498, ENST00000395715.7, OTTHUMT00000286435
    Conserved Domains (2) summary
    smart00401
    Location:904947
    ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
    cd00202
    Location:908964
    ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p12 Primary Assembly

    Range
    115408496..115669637 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011517266.3XP_011515568.1  zinc finger transcription factor Trps1 isoform X1

    See identical proteins and their annotated locations for XP_011515568.1

    UniProtKB/Swiss-Prot
    Q9UHF7
    Conserved Domains (2) summary
    smart00401
    Location:904947
    ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
    cd00202
    Location:908964
    ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
  2. XM_011517268.2XP_011515570.1  zinc finger transcription factor Trps1 isoform X3

    See identical proteins and their annotated locations for XP_011515570.1

    UniProtKB/Swiss-Prot
    Q9UHF7
    Conserved Domains (2) summary
    smart00401
    Location:891934
    ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
    cd00202
    Location:895951
    ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
  3. XM_011517264.2XP_011515566.1  zinc finger transcription factor Trps1 isoform X1

    See identical proteins and their annotated locations for XP_011515566.1

    UniProtKB/Swiss-Prot
    Q9UHF7
    Conserved Domains (2) summary
    smart00401
    Location:904947
    ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
    cd00202
    Location:908964
    ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
  4. XM_011517267.1XP_011515569.1  zinc finger transcription factor Trps1 isoform X2

    See identical proteins and their annotated locations for XP_011515569.1

    Conserved Domains (2) summary
    smart00401
    Location:897940
    ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
    cd00202
    Location:901957
    ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
  5. XM_006716625.1XP_006716688.1  zinc finger transcription factor Trps1 isoform X1

    See identical proteins and their annotated locations for XP_006716688.1

    UniProtKB/Swiss-Prot
    Q9UHF7
    Conserved Domains (2) summary
    smart00401
    Location:904947
    ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
    cd00202
    Location:908964
    ZnF_GATA; Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
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