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    trim13 tripartite motif containing 13 [ Danio rerio (zebrafish) ]

    Gene ID: 553630, updated on 13-Jun-2024

    Summary

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    Official Symbol
    trim13provided by ZNC
    Official Full Name
    tripartite motif containing 13provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-050522-516
    See related
    Ensembl:ENSDARG00000010010 AllianceGenome:ZFIN:ZDB-GENE-050522-516
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    zgc:110578
    Summary
    Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in positive regulation of transcription, DNA-templated. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. Predicted to be active in chromatin and nucleoplasm. Is expressed in brain; male organism; muscle; ovary; and testis. Orthologous to human TRIM13 (tripartite motif containing 13). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See trim13 in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (29643019..29649834)
    105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (29832290..29839088)

    Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene mcf.2 cell line derived transforming sequence-like b Neighboring gene PHD finger protein 11 Neighboring gene SPRY domain containing 7b Neighboring gene microRNA 15a-2 Neighboring gene microRNA 16c

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. The 13q and 11q B-cell chronic lymphocytic leukaemia-associated regions derive from a common ancestral region in the zebrafish. Auer RL, et al. Br J Haematol, 2007 Jun. PMID 17488487
    2. Origin and evolution of TRIM proteins: new insights from the complete TRIM repertoire of zebrafish and pufferfish. Boudinot P, et al. PLoS One, 2011. PMID 21789205, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC110578

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in innate immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of type I interferon-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein monoubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    tripartite motif-containing 13

    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_001020603.2 → NP_001018439.1  tripartite motif-containing 13

      See identical proteins and their annotated locations for NP_001018439.1

      Status: VALIDATED

      Source sequence(s)
      CU855930
      UniProtKB/Swiss-Prot
      F1R8C7, Q503I2
      Conserved Domains (3) summary
      cd00162
      Location:9 → 59
      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 ...
      pfam00643
      Location:87 → 129
      zf-B_box; B-box zinc finger
      cl12013
      Location:154 → 242
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007120.7 Reference GRCz11 Primary Assembly

      Range
      29643019..29649834
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005167703.2 → XP_005167760.1  tripartite motif-containing 13 isoform X1

      UniProtKB/TrEMBL
      A0A8M2BF46, H9KUW1
      Related
      ENSDARP00000013495.8, ENSDART00000023210.10
      Conserved Domains (3) summary
      cd00162
      Location:19 → 69
      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 ...
      pfam00643
      Location:97 → 139
      zf-B_box; B-box zinc finger
      cl12013
      Location:164 → 252
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    2. XM_009304742.3 → XP_009303017.1  tripartite motif-containing 13 isoform X2

      See identical proteins and their annotated locations for XP_009303017.1

      UniProtKB/Swiss-Prot
      F1R8C7, Q503I2
      Conserved Domains (3) summary
      cd00162
      Location:9 → 59
      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 ...
      pfam00643
      Location:87 → 129
      zf-B_box; B-box zinc finger
      cl12013
      Location:154 → 242
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394759.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      248852..253960
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCz11 ALT_DRER_TU_2

    Genomic

    1. NW_018395285.1 Reference GRCz11 ALT_DRER_TU_2

      Range
      7091..12689
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q503I2.1 GenPept UniProtKB/Swiss-Prot:Q503I2

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