Format

Send to:

Choose Destination

TRIM6 tripartite motif containing 6 [ Homo sapiens (human) ]

Gene ID: 117854, updated on 9-Feb-2020

Summary

Official Symbol
TRIM6provided by HGNC
Official Full Name
tripartite motif containing 6provided by HGNC
Primary source
HGNC:HGNC:16277
See related
Ensembl:ENSG00000121236 MIM:607564
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
RNF89
Summary
The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, B-box type 1 and B-box type 2 domain, and a coiled-coil region. The protein localizes to the nucleus, but its specific function has not been identified. This gene is mapped to chromosome 11p15, where it resides within a TRIM gene cluster. Alternative splicing results in multiple transcript variants. A read-through transcript from this gene into the downstream TRIM34 gene has also been observed, which results in a fusion product from these neighboring family members. [provided by RefSeq, Oct 2010]
Expression
Broad expression in kidney (RPKM 10.6), testis (RPKM 6.4) and 15 other tissues See more
Orthologs

Genomic context

See TRIM6 in Genome Data Viewer
Location:
11p15.4
Exon count:
9
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (5596111..5612952)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (5617331..5634188)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 53 Neighboring gene Sharpr-MPRA regulatory region 4920 Neighboring gene olfactory receptor family 52 subfamily B member 6 Neighboring gene TRIM6-TRIM34 readthrough Neighboring gene tripartite motif containing 5 Neighboring gene tripartite motif containing 34 Neighboring gene uncharacterized LOC107984302

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

NHGRI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
capsid gag Human TRIM6 binds in vitro assembled HIV-1 CA-NC complexes PubMed
gag The RING, B-box 2, and coiled-coil domains of TRIM6 can functionally replace the corresponding domains of rhesus monkey TRIM5alpha with respect to inhibition of HIV-1 infection through the binding of the chimeras to HIV-1 capsid complexes PubMed
nucleocapsid gag Human TRIM6 binds in vitro assembled HIV-1 CA-NC complexes PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Readthrough TRIM6-TRIM34

Readthrough gene: TRIM6-TRIM34, Included gene: TRIM34

Homology

Clone Names

  • MGC176399

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding, bridging IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein tyrosine kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
ubiquitin protein ligase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cellular response to interferon-beta IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to virus IEA
Inferred from Electronic Annotation
more info
 
free ubiquitin chain polymerization IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of stem cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
negative regulation of viral genome replication IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cytokine secretion involved in immune response IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of defense response to virus by host IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
positive regulation of peptidyl-serine phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of peptidyl-threonine phosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription regulatory region DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of type I interferon-mediated signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein polyubiquitination IEA
Inferred from Electronic Annotation
more info
 
protein trimerization IDA
Inferred from Direct Assay
more info
PubMed 
NOT regulation of NIK/NF-kappaB signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to lipopolysaccharide IMP
Inferred from Mutant Phenotype
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
tripartite motif-containing protein 6
Names
RING finger protein 89
RING-type E3 ubiquitin transferase TRIM6
NP_001003818.1
NP_001185573.1
NP_001185574.1
NP_477514.1

NCBI Reference Sequences (RefSeq)

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_001003818.3NP_001003818.1  tripartite motif-containing protein 6 isoform 1

    See identical proteins and their annotated locations for NP_001003818.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF220030, AK290172, AK316178, BC047564
    Consensus CDS
    CCDS31389.1
    UniProtKB/Swiss-Prot
    Q9C030
    Related
    ENSP00000369440.3, ENST00000380097.8
    Conserved Domains (4) summary
    smart00336
    Location:121161
    BBOX; B-Box-type zinc finger
    cd15823
    Location:327514
    SPRY_PRY_TRIM6; PRY/SPRY domain in tripartite motif-binding protein 6 (TRIM6), also known as RING finger protein 89 (RNF89)
    cl17238
    Location:4387
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    cl23765
    Location:170287
    iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits
  2. NM_001198644.2NP_001185573.1  tripartite motif-containing protein 6 isoform 3

    See identical proteins and their annotated locations for NP_001185573.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the 5' coding region, and uses a downstream AUG start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Both variants 3 and 4 encode the same isoform.
    Source sequence(s)
    AF220030, AK290172, AK293295, AK298301, AK316178, BC047564, DA401634
    Consensus CDS
    CCDS55738.1
    UniProtKB/Swiss-Prot
    Q9C030
    Related
    ENSP00000421079.1, ENST00000506134.5
    Conserved Domains (1) summary
    cd15823
    Location:124311
    SPRY_PRY_TRIM6; PRY/SPRY domain in tripartite motif-binding protein 6 (TRIM6), also known as RING finger protein 89 (RNF89)
  3. NM_001198645.2NP_001185574.1  tripartite motif-containing protein 6 isoform 3

    See identical proteins and their annotated locations for NP_001185574.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two alternate exons in the 5' coding region, and uses a downstream AUG start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Both variants 3 and 4 encode the same isoform.
    Source sequence(s)
    AF220030, AK290172, AK293295, BC047564, DA401634
    Consensus CDS
    CCDS55738.1
    UniProtKB/Swiss-Prot
    Q9C030
    Related
    ENSP00000421802.1, ENST00000515022.5
    Conserved Domains (1) summary
    cd15823
    Location:124311
    SPRY_PRY_TRIM6; PRY/SPRY domain in tripartite motif-binding protein 6 (TRIM6), also known as RING finger protein 89 (RNF89)
  4. NM_058166.5NP_477514.1  tripartite motif-containing protein 6 isoform 2

    See identical proteins and their annotated locations for NP_477514.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream AUG start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AF220030, AK027664, AK290172, DC354457
    Consensus CDS
    CCDS31390.1
    UniProtKB/Swiss-Prot
    Q9C030
    Related
    ENSP00000278302.5, ENST00000278302.9
    Conserved Domains (4) summary
    smart00336
    Location:93133
    BBOX; B-Box-type zinc finger
    cd15823
    Location:299486
    SPRY_PRY_TRIM6; PRY/SPRY domain in tripartite motif-binding protein 6 (TRIM6), also known as RING finger protein 89 (RNF89)
    cl17238
    Location:1559
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    cl23765
    Location:142259
    iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    5596111..5612952
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center