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

Gene ID: 558011, updated on 4-Jan-2025

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, Jan 2025]
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
  • 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

Gene LinkOut

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