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

    Gene ID: 81844, updated on 9-Dec-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 ubiquitin protein ligase activity. Involved in defense response to virus; positive regulation of signal transduction; and protein monoubiquitination. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in spleen (RPKM 9.3), ovary (RPKM 7.5) and 25 other tissues See more
    Orthologs
    NEW
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (101085481..101097967)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (102408287..102420773)
    RS_2024_09 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
     
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    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)

    NEW Try the new Transcript table

    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_2024_08

    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