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

    Gene ID: 7227, updated on 27-Nov-2024

    Summary

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    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
    mouse all
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    Genomic context

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    See TRPS1 in Genome Data Viewer
    Location:
    8q23.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (115408496..115668975, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (116535995..116796128, complement)
    RS_2024_09 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Trps1 regulates biliary epithelial-mesenchymal transition and has roles during biliary fibrosis in liver grafts: a preliminary study. Zhe C, et al. PLoS One, 2015. PMID 25886207, Free PMC Article
    2. Somatic mosaicism in trichorhinophalangeal syndrome: a lesson for genetic counseling. Corsini C, et al. Eur J Hum Genet, 2014 Jan. PMID 23572024, Free PMC Article
    3. Prognostic value of the trichorhinophalangeal syndrome-1 (TRPS-1), a GATA family transcription factor, in early-stage breast cancer. Chen JQ, et al. Ann Oncol, 2013 Oct. PMID 23729783, Free PMC Article
    4. Increased expression of TRPS1 affects tumor progression and correlates with patients' prognosis of colon cancer. Hong J, et al. Biomed Res Int, 2013. PMID 23762846, Free PMC Article
    5. Co-segregation of trichorhinophalangeal syndrome with a t(8;13)(q23.3;q21.31) familial translocation that appears to increase TRPS1 gene expression. David D, et al. Hum Genet, 2013 Nov. PMID 23835950

    See all (168) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Analysis of the function, mechanism and clinical application prospect of TRPS1, a new marker for breast cancer.
      Title: Analysis of the function, mechanism and clinical application prospect of TRPS1, a new marker for breast cancer.
    2. Single-cell exome sequencing reveals polyclonal seeding and TRPS1 mutations in colon cancer metastasis.
      Title: Single-cell exome sequencing reveals polyclonal seeding and TRPS1 mutations in colon cancer metastasis.
    3. UVB-induced TRPS1 regulates MITF transcription activity to promote skin pigmentation.
      Title: UVB-induced TRPS1 regulates MITF transcription activity to promote skin pigmentation.
    4. Clinical presentation and genetics of tricho-rhino-phalangeal syndrome (TRPS) type 1: A single-center case series of 15 patients and seven novel TRPS1 variants.
      Title: Clinical presentation and genetics of tricho-rhino-phalangeal syndrome (TRPS) type 1: A single-center case series of 15 patients and seven novel TRPS1 variants.
    5. TRPS1 modulates chromatin accessibility to regulate estrogen receptor alpha (ER) binding and ER target gene expression in luminal breast cancer cells.
      Title: TRPS1 modulates chromatin accessibility to regulate estrogen receptor alpha (ER) binding and ER target gene expression in luminal breast cancer cells.
    6. TRPS1 and GATA3 Expression in Invasive Breast Carcinoma With Apocrine Differentiation.
      Title: TRPS1 and GATA3 Expression in Invasive Breast Carcinoma With Apocrine Differentiation.
    7. Molecular Genetic Analysis and Growth Hormone Treatment in a Three-Generation Chinese Family with Tricho-Rhino-Phalangeal Syndrome I.
      Title: Molecular Genetic Analysis and Growth Hormone Treatment in a Three-Generation Chinese Family with Tricho-Rhino-Phalangeal Syndrome I.
    8. Mucinous cystadenocarcinoma of the breast harbours TRPS1 expressions and PIK3CA alterations.
      Title: Mucinous cystadenocarcinoma of the breast harbours TRPS1 expressions and PIK3CA alterations.
    9. Novel TRPS1 frameshift variant in tricho-rhino-phalangeal syndrome type I accompanied by zinc deficiency.
      Title: Novel TRPS1 frameshift variant in tricho-rhino-phalangeal syndrome type I accompanied by zinc deficiency.
    10. [TRPS1 expression in salivary gland-type breast carcinoma and its clinical application].
      Title: [TRPS1 expression in salivary gland-type breast carcinoma and its clinical application].
    Submit: New GeneRIF Correction See all GeneRIFs (91)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    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

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC134928

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    located_in 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

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    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)

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    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_001282902.3 → NP_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:895 → 938
      ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
      cd00202
      Location:899 → 955
      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_001282903.3 → NP_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:897 → 940
      ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
      cd00202
      Location:901 → 957
      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_001330599.2 → NP_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_014112.5 → NP_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:904 → 947
      ZnF_GATA; zinc finger binding to DNA consensus sequence [AT]GATA[AG]
      cd00202
      Location:908 → 964
      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_2024_08

    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)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UHF7.2 GenPept UniProtKB/Swiss-Prot:Q9UHF7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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