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

Gene ID: 287015, updated on 27-Nov-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (140678064..140701150)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (143425371..143448461)
RS_2024_09 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 (19) 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)

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 ubiquitin protein ligase activity IEA
Inferred from Electronic Annotation
more info
  
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_2024_08

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

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Chemical Information
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