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TRIM56 tripartite motif containing 56 [ Homo sapiens (human) ]

Gene ID: 81844, updated on 5-Mar-2024

Summary

Official Symbol
TRIM56provided by HGNC
Official Full Name
tripartite motif containing 56provided by HGNC
Primary source
HGNC:HGNC:19028
See related
Ensembl:ENSG00000169871 MIM:616996; AllianceGenome:HGNC:19028
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RNF109
Summary
Enables RNA binding activity. Predicted to be involved in several processes, including defense response to other organism; positive regulation of macromolecule metabolic process; and protein K63-linked ubiquitination. Predicted to be located in cytoplasm. Predicted to be active in chromatin and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in spleen (RPKM 9.3), ovary (RPKM 7.5) and 25 other tissues See more
Orthologs
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Genomic context

See TRIM56 in Genome Data Viewer
Location:
7q22.1
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (101085481..101097967)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (102408287..102420773)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (100728762..100741248)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene mucin 12, cell surface associated Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100658552-100659220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26396 Neighboring gene Sharpr-MPRA regulatory region 8701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26397 Neighboring gene MUC12 antisense RNA 1 Neighboring gene mucin 17, cell surface associated Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100709117-100709986 Neighboring gene RN7SK pseudogene 54 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:100727119-100727619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100730454-100731094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100731095-100731734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100742673-100743380 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100743381-100744088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100751090-100752040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100752041-100752991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100755193-100755694 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100760705-100761406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100765023-100765642 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:100766263-100766880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100769261-100770040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100770821-100771600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100771601-100772380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100778603-100779104 Neighboring gene serpin family E member 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100781393-100782168 Neighboring gene negCOR silencer S6 Neighboring gene Sharpr-MPRA regulatory region 5920 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:100798163-100798663 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:100799642-100800841 Neighboring gene microRNA 4653 Neighboring gene adaptor related protein complex 1 subunit sigma 1

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?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of tripartite motif containing 56 (TRIM56) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ35608, DKFZp667O116

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables ubiquitin protein ligase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables ubiquitin-protein transferase activity TAS
Traceable Author Statement
more info
 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
E3 ubiquitin-protein ligase TRIM56
Names
RING finger protein 109
RING-type E3 ubiquitin transferase TRIM56
tripartite motif-containing protein 56
NP_112223.1
XP_011514891.1
XP_054215089.1

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_030961.3NP_112223.1  E3 ubiquitin-protein ligase TRIM56

    See identical proteins and their annotated locations for NP_112223.1

    Status: VALIDATED

    Source sequence(s)
    AC105446, BC005847, BC048194
    Consensus CDS
    CCDS43625.1
    UniProtKB/Swiss-Prot
    Q6PJS5, Q86VT6, Q8N2H8, Q8NAC0, Q9BRZ2, Q9H031
    Related
    ENSP00000305161.6, ENST00000306085.11
    Conserved Domains (6) summary
    cd00021
    Location:169205
    BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
    cd05819
    Location:598626
    NHL; NHL repeat [structural motif]
    sd00039
    Location:593627
    7WD40; WD40 repeat [structural motif]
    cl18310
    Location:521748
    NHL; NHL repeat unit of beta-propeller proteins
    cd16584
    Location:1960
    RING-HC_TRIM56_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar proteins
    cl28410
    Location:8214
    RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    101085481..101097967
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011516589.4XP_011514891.1  E3 ubiquitin-protein ligase TRIM56 isoform X1

    See identical proteins and their annotated locations for XP_011514891.1

    UniProtKB/Swiss-Prot
    Q6PJS5, Q86VT6, Q8N2H8, Q8NAC0, Q9BRZ2, Q9H031
    Conserved Domains (6) summary
    cd00021
    Location:169205
    BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
    cd05819
    Location:598626
    NHL; NHL repeat [structural motif]
    sd00039
    Location:593627
    7WD40; WD40 repeat [structural motif]
    cl18310
    Location:521748
    NHL; NHL repeat unit of beta-propeller proteins
    cd16584
    Location:1960
    RING-HC_TRIM56_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar proteins
    cl28410
    Location:8214
    RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    102408287..102420773
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054359114.1XP_054215089.1  E3 ubiquitin-protein ligase TRIM56 isoform X1

    UniProtKB/Swiss-Prot
    Q6PJS5, Q86VT6, Q8N2H8, Q8NAC0, Q9BRZ2, Q9H031