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

    Gene ID: 7227, updated on 10-Mar-2024

    Summary

    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; AllianceGenome:HGNC:12340
    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
    NEW
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    Genomic context

    Location:
    8q23.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (115408496..115668975, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (116535995..116796128, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (116420724..116681202, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene cysteinyl-tRNA synthetase 1 pseudogene 2 Neighboring gene NANOG hESC enhancer GRCh37_chr8:115914616-115915205 Neighboring gene uncharacterized LOC107986901 Neighboring gene NANOG hESC enhancer GRCh37_chr8:116088942-116089443 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:116170487-116171394 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:116221425-116221969 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:116224145-116224754 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:116224755-116225364 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:116229053-116229886 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:116229887-116230719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27819 Neighboring gene VISTA enhancer hs919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27821 Neighboring gene TRPS1 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr8:116577104-116577660 Neighboring gene Sharpr-MPRA regulatory region 6921 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27824 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:116680959-116681500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:116765634-116766245 Neighboring gene uncharacterized LOC107986968 Neighboring gene uncharacterized LOC107986902

    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 Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-07-08)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-07-08)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

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

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC134928

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of chondrocyte differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 

    General protein information

    Preferred Names
    zinc finger transcription factor Trps1
    Names
    tricho-rhino-phalangeal syndrome type I protein
    trichorhinophalangeal syndrome I
    zinc finger protein GC79

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      5027..265506
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001282902.3NP_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/TrEMBL
      E5RFF3
      Related
      ENSP00000428680.1, ENST00000520276.5
      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_001282903.3NP_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/TrEMBL
      E5RFF3
      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_001330599.2NP_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
      B4E1Z5, Q08AU2, Q9NWE1, Q9UHF7, Q9UHH6
      UniProtKB/TrEMBL
      E5RFF3
      Related
      ENSP00000220888.5, ENST00000220888.9
    4. NM_014112.5NP_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, ENST00000395715.8
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      115408496..115668975 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      116535995..116796128 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)