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    usp13 ubiquitin specific peptidase 13 [ Danio rerio (zebrafish) ]

    Gene ID: 558011, updated on 2-Nov-2024

    Summary

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    Official Symbol
    usp13provided by ZNC
    Official Full Name
    ubiquitin specific peptidase 13provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-080724-7
    See related
    Ensembl:ENSDARG00000079198 AllianceGenome:ZFIN:ZDB-GENE-080724-7
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    wu:fc61g08
    Summary
    Predicted to enable cysteine-type deubiquitinase activity; cysteine-type endopeptidase activity; and ubiquitin binding activity. Predicted to be involved in several processes, including protein K63-linked deubiquitination; protein stabilization; and regulation of autophagy. Predicted to act upstream of or within autophagy; protein deubiquitination; and proteolysis. Predicted to be active in cytosol and nucleus. Orthologous to human USP13 (ubiquitin specific peptidase 13). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See usp13 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 6 NC_007117.7 (29411152..29469205)
    105 previous assembly GRCz10 (GCF_000002035.5) 6 NC_007117.6 (29419763..29478646)

    Chromosome 6 - NC_007117.7Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L47 Neighboring gene NADH:ubiquinone oxidoreductase subunit B5 Neighboring gene peroxisomal biogenesis factor 5-like a Neighboring gene phosphodiesterase 6D, cGMP-specific, rod, delta

    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 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. Prioritizing causal disease genes using unbiased genomic features. Deo RC, et al. Genome Biol, 2014 Dec 3. PMID 25633252, Free PMC Article
    2. Structure-toxicity relationship of cefoperazone and its impurities to developing zebrafish by transcriptome and Raman analysis. Han Y, et al. Toxicol Appl Pharmacol, 2017 Jul 15. PMID 28465218
    3. Expansion of transducin subunit gene families in early vertebrate tetraploidizations. Lagman D, et al. Genomics, 2012 Oct. PMID 22814267
    4. New classes of mind bomb-interacting proteins identified from yeast two-hybrid screens. Tseng LC, et al. PLoS One, 2014. PMID 24714733, Free PMC Article
    5. Genome-wide loss-of-function analysis of deubiquitylating enzymes for zebrafish development. Tse WK, et al. BMC Genomics, 2009 Dec 30. PMID 20040115, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC163140

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables cysteine-type deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cysteine-type deubiquitinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cysteine-type deubiquitinase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables cysteine-type endopeptidase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables cysteine-type peptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell population proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein K63-linked deubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within protein deubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein stabilization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of autophagy ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of protein stability IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 13
    Names
    deubiquitinating enzyme 13
    ubiquitin specific peptidase 13 (isopeptidase T-3)
    ubiquitin thioesterase 13
    ubiquitin-specific-processing protease 13
    NP_001091856.1
    XP_005165987.1
    XP_021332553.1
    XP_021332554.1

    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_001098386.1 → NP_001091856.1  ubiquitin carboxyl-terminal hydrolase 13

      See identical proteins and their annotated locations for NP_001091856.1

      Status: PROVISIONAL

      Source sequence(s)
      BC141800
      UniProtKB/Swiss-Prot
      A5D8T1, F1QFS9
      UniProtKB/TrEMBL
      A0A2R8Q3R9
      Related
      ENSDARP00000065292.5, ENSDART00000065293.7
      Conserved Domains (5) summary
      COG5207
      Location:13 → 857
      UBP14; Uncharacterized Zn-finger protein, UBP-type [General function prediction only]
      cd02658
      Location:319 → 855
      Peptidase_C19B; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
      cd14384
      Location:635 → 683
      UBA1_UBP13; UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13)
      cd14386
      Location:711 → 752
      UBA2_UBP5; UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5)
      pfam02148
      Location:192 → 264
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    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_007117.7 Reference GRCz11 Primary Assembly

      Range
      29411152..29469205
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005165930.5 → XP_005165987.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X1

      UniProtKB/Swiss-Prot
      A5D8T1, F1QFS9
      UniProtKB/TrEMBL
      A0A8M2BD89
      Conserved Domains (5) summary
      COG5207
      Location:13 → 856
      UBP14; Uncharacterized Zn-finger protein, UBP-type [General function prediction only]
      cd02658
      Location:319 → 854
      Peptidase_C19B; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
      cd14384
      Location:634 → 682
      UBA1_UBP13; UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13)
      cd14387
      Location:712 → 746
      UBA2_UBP13; UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13)
      pfam02148
      Location:192 → 264
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    2. XM_021476878.2 → XP_021332553.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X2

      UniProtKB/Swiss-Prot
      A5D8T1, F1QFS9
      UniProtKB/TrEMBL
      A0A8M9PZR8
      Conserved Domains (1) summary
      cl02553
      Location:13 → 850
      Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...

    3. XM_021476879.2 → XP_021332554.1  ubiquitin carboxyl-terminal hydrolase 13 isoform X3

      UniProtKB/Swiss-Prot
      A5D8T1, F1QFS9
      UniProtKB/TrEMBL
      A0A8M9Q650
      Conserved Domains (1) summary
      cl02553
      Location:13 → 849
      Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394647.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      131336..185592
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    F1QFS9.1 GenPept UniProtKB/Swiss-Prot:F1QFS9

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