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    TRIM13 tripartite motif containing 13 [ Homo sapiens (human) ]

    Gene ID: 10206, updated on 7-Dec-2018

    Summary

    Official Symbol
    TRIM13provided by HGNC
    Official Full Name
    tripartite motif containing 13provided by HGNC
    Primary source
    HGNC:HGNC:9976
    See related
    Ensembl:ENSG00000204977 MIM:605661
    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
    CAR; LEU5; RFP2; DLEU5; RNF77
    Summary
    This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This gene is located on chromosome 13 within the minimal deletion region for B-cell chronic lymphocytic leukemia. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in testis (RPKM 17.7), bone marrow (RPKM 8.8) and 25 other tissues See more
    Orthologs

    Genomic context

    See TRIM13 in Genome Data Viewer
    Location:
    13q14.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 13 NC_000013.11 (49997007..50018467)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (50571143..50592603)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene SPRY domain containing 7 Neighboring gene deleted in lymphocytic leukemia 2 Neighboring gene microRNA 3613 Neighboring gene potassium channel regulator Neighboring gene microRNA 16-1 Neighboring gene microRNA 15a

    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 FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    NHGRI GWA Catalog

    Pathways from BioSystems

    • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
      Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
    • Calnexin/calreticulin cycle, organism-specific biosystem (from REACTOME)
      Calnexin/calreticulin cycle, organism-specific biosystemThe unfolded protein is recognized by a chaperon protein (calnexin or calreticulin) and the folding process starts. The binding of these protein requires a mono-glucosylated glycan (Caramelo JJ and P...
    • ER Quality Control Compartment (ERQC), organism-specific biosystem (from REACTOME)
      ER Quality Control Compartment (ERQC), organism-specific biosystemProteins that are released from the CNX or CRT complex with folding defects accumulate in a compartment of the ER called ERQC (Kamhi-Nesher et al. 2001). Here, the enzymes UGGG1 or UGGG2 are able to ...
    • Metabolism of proteins, organism-specific biosystem (from REACTOME)
      Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
    • N-glycan trimming in the ER and Calnexin/Calreticulin cycle, organism-specific biosystem (from REACTOME)
      N-glycan trimming in the ER and Calnexin/Calreticulin cycle, organism-specific biosystemAfter being synthesized in the ER membrane the 14-sugars lipid-linked oligosaccharide is co-translationally transferred to an unfolded protein, as described in the previous steps. After this point th...
    • Post-translational protein modification, organism-specific biosystem (from REACTOME)
      Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    ubiquitin protein ligase activity TAS
    Traceable Author Statement
    more info
     
    ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    endoplasmic reticulum quality control compartment IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    perinuclear endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    E3 ubiquitin-protein ligase TRIM13
    Names
    B-cell chronic lymphocytic leukemia tumor suppressor Leu5
    CLL-associated RING finger
    RING finger protein 77
    RING-type E3 ubiquitin transferase TRIM13
    leukemia-associated protein 5
    putative tumor suppressor RFP2
    ret finger protein 2
    tripartite motif protein 13
    tripartite motif-containing protein 13
    NP_001007279.1
    NP_005789.2
    NP_434698.1
    NP_998755.1

    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_001007278.2NP_001007279.1  E3 ubiquitin-protein ligase TRIM13 isoform 2

      See identical proteins and their annotated locations for NP_001007279.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an additional internal exon, which contains an upstream in-frame AUG start codon compared to variant 1. The encoded protein (isoform 2) has a longer N-terminus, as compared to isoform 1.
      Source sequence(s)
      AL832695, AY455758, AY764035, BI668033, KF455768
      Consensus CDS
      CCDS41888.1
      UniProtKB/Swiss-Prot
      O60858
      UniProtKB/TrEMBL
      L7MTJ6
      Related
      ENSP00000348299.4, ENST00000356017.8
      Conserved Domains (2) summary
      smart00336
      Location:93134
      BBOX; B-Box-type zinc finger
      cd00162
      Location:1264
      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 ...
    2. NM_005798.4NP_005789.2  E3 ubiquitin-protein ligase TRIM13 isoform 1

      See identical proteins and their annotated locations for NP_005789.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shortest transcript and encodes the same protein (isoform 1) as variants 2 and 3.
      Source sequence(s)
      AF241850, AL832695, AY455758, BI668033, KF455768
      Consensus CDS
      CCDS9423.1
      UniProtKB/Swiss-Prot
      O60858
      UniProtKB/TrEMBL
      A0A024RDU3, L7MTJ6
      Related
      ENSP00000412943.2, ENST00000420995.6
      Conserved Domains (3) summary
      smart00336
      Location:90131
      BBOX; B-Box-type zinc finger
      pfam12252
      Location:163234
      SidE; Dot/Icm substrate protein
      cd16762
      Location:561
      RING-HC_TRIM13_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins
    3. NM_052811.3NP_434698.1  E3 ubiquitin-protein ligase TRIM13 isoform 1

      See identical proteins and their annotated locations for NP_434698.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared variant 1. Variants 1, 2 and 3 encode the same protein (isoform 1).
      Source sequence(s)
      AL832695, AY191002, AY455758, BI668033, KF455768
      Consensus CDS
      CCDS9423.1
      UniProtKB/Swiss-Prot
      O60858
      UniProtKB/TrEMBL
      A0A024RDU3, L7MTJ6
      Related
      ENSP00000399206.2, ENST00000457662.2
      Conserved Domains (3) summary
      smart00336
      Location:90131
      BBOX; B-Box-type zinc finger
      pfam12252
      Location:163234
      SidE; Dot/Icm substrate protein
      cd16762
      Location:561
      RING-HC_TRIM13_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins
    4. NM_213590.3NP_998755.1  E3 ubiquitin-protein ligase TRIM13 isoform 1

      See identical proteins and their annotated locations for NP_998755.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein (isoform 1).
      Source sequence(s)
      AL832695, AY455758, KF455768
      Consensus CDS
      CCDS9423.1
      UniProtKB/Swiss-Prot
      O60858
      UniProtKB/TrEMBL
      A0A024RDU3, L7MTJ6
      Related
      ENSP00000367424.3, ENST00000378182.3
      Conserved Domains (3) summary
      smart00336
      Location:90131
      BBOX; B-Box-type zinc finger
      pfam12252
      Location:163234
      SidE; Dot/Icm substrate protein
      cd16762
      Location:561
      RING-HC_TRIM13_C-V; RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p12 Primary Assembly

      Range
      49997007..50018467
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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