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    TRIM42 tripartite motif containing 42 [ Homo sapiens (human) ]

    Gene ID: 287015, updated on 11-Apr-2024

    Summary

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    Official Symbol
    TRIM42provided by HGNC
    Official Full Name
    tripartite motif containing 42provided by HGNC
    Primary source
    HGNC:HGNC:19014
    See related
    Ensembl:ENSG00000155890 MIM:620334; AllianceGenome:HGNC:19014
    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
    T4A1; PPP1R40
    Summary
    This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, namely a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. [provided by RefSeq, Jul 2008]
    Expression
    Restricted expression toward testis (RPKM 9.8) See more
    Orthologs
    mouse all
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    Genomic context

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    See TRIM42 in Genome Data Viewer
    Location:
    3q23
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (140678064..140701150)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (143425371..143448461)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (140396906..140419992)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene calsyntenin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:140240291-140240792 Neighboring gene CLSTN2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20618 Neighboring gene uncharacterized LOC102724068 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:140307280-140307869 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:140401669-140402169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20620 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:140661115-140661962 Neighboring gene ribosomal protein L23a pseudogene 41 Neighboring gene solute carrier family 25 member 36

    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. Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium. Li Q, et al. Hum Genet, 2015 Feb. PMID 25367360, Free PMC Article
    2. Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2. Winham SJ, et al. Mol Psychiatry, 2014 Sep. PMID 24322204
    3. Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. Baranzini SE, et al. Hum Mol Genet, 2009 Feb 15. PMID 19010793, Free PMC Article
    4. The tripartite motif family identifies cell compartments. Reymond A, et al. EMBO J, 2001 May 1. PMID 11331580, Free PMC Article
    5. Docking motif-guided mapping of the interactome of protein phosphatase-1. Hendrickx A, et al. Chem Biol, 2009 Apr 24. PMID 19389623

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium.
    EBI GWAS Catalog
    Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2.
    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)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of tripartite motif containing 42 (TRIM42) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells 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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    Homology

    Clone Names

    • FLJ40097, MGC163346

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein 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 protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    tripartite motif-containing protein 42
    Names
    protein phosphatase 1, regulatory subunit 40

    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.

    mRNA and Protein(s)

    1. NM_152616.5 → NP_689829.3  tripartite motif-containing protein 42

      See identical proteins and their annotated locations for NP_689829.3

      Status: REVIEWED

      Source sequence(s)
      AC026324, AF521868, BX093220, DC397052
      Consensus CDS
      CCDS3113.1
      UniProtKB/Swiss-Prot
      A1L4B4, A1L4B6, Q8IWZ5, Q8N832, Q8NDL3
      Related
      ENSP00000286349.3, ENST00000286349.4
      Conserved Domains (3) summary
      cd00063
      Location:612 → 698
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00643
      Location:285 → 326
      zf-B_box; B-box zinc finger
      cl23765
      Location:369 → 452
      iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      140678064..140701150
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011512740.4 → XP_011511042.1  tripartite motif-containing protein 42 isoform X1

      Conserved Domains (3) summary
      cd00063
      Location:612 → 692
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam00643
      Location:285 → 326
      zf-B_box; B-box zinc finger
      cl23765
      Location:369 → 452
      iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      143425371..143448461
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346361.1 → XP_054202336.1  tripartite motif-containing protein 42 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IWZ5.2 GenPept UniProtKB/Swiss-Prot:Q8IWZ5

    Gene LinkOut

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

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