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

Gene ID: 553630, updated on 14-Nov-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
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 ligase activity. Predicted to be involved in innate immune response; positive regulation of type I interferon-mediated signaling pathway; and protein monoubiquitination. Predicted to be located in endoplasmic reticulum membrane. Is expressed in brain; male organism; muscle; ovary; and testis. Orthologous to human TRIM13 (tripartite motif containing 13). [provided by Alliance of Genome Resources, Nov 2024]
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
RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (29643039..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. Metabolic regulation and antihyperglycemic properties of diet-derived PGG through transcriptomic and metabolomic profiling. Zhang AN, et al. Food Funct, 2023 Jun 19. PMID 37232296
  2. 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
  3. 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
  4. 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
  5. 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
  
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: GCF_000002035.6-RS_2024_08

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
    29643039..29649834
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009304742.4 → XP_009303017.1  tripartite motif-containing 13 isoform X1

    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..255154
    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..13883
    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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