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    usp25 ubiquitin specific peptidase 25 [ Danio rerio (zebrafish) ]

    Gene ID: 406790, updated on 11-Apr-2024

    Summary

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    Official Symbol
    usp25provided by ZNC
    Official Full Name
    ubiquitin specific peptidase 25provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-2847
    See related
    Ensembl:ENSDARG00000012314 AllianceGenome:ZFIN:ZDB-GENE-040426-2847
    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
    zgc:55791; wu:fi33c05; wu:fo67e06; wu:fp97a04
    Summary
    Predicted to enable cysteine-type endopeptidase activity and thiol-dependent deubiquitinase. Acts upstream of or within cranial skeletal system development and dorsal/ventral pattern formation. Predicted to be active in cytosol and nucleus. Orthologous to human USP25 (ubiquitin specific peptidase 25). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See usp25 in Genome Data Viewer
    Location:
    chromosome: 10
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 10 NC_007121.7 (38170462..38243618, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 10 NC_007121.6 (38226710..38299857, complement)

    Chromosome 10 - NC_007121.7Genomic Context describing neighboring genes Neighboring gene microRNA 99-2 Neighboring gene microRNA let7c-2 Neighboring gene nuclear receptor interacting protein 1b Neighboring gene SAM domain, SH3 domain and nuclear localisation signals 1b

    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. Zebrafish transforming growth factor-β-stimulated clone 22 domain 3 (TSC22D3) plays critical roles in Bmp-dependent dorsoventral patterning via two deubiquitylating enzymes Usp15 and Otud4. Tse WK, et al. Biochim Biophys Acta, 2013 Oct. PMID 23665588
    2. Importance of deubiquitinases in zebrafish craniofacial development. Tse WKF. Biochem Biophys Res Commun, 2017 Jun 10. PMID 28450118
    3. Patterns of alternative splicing in response to cold acclimation in fish. Healy TM, et al. J Exp Biol, 2019 Mar 7. PMID 30692167
    4. 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
    5. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    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 hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cranial skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within dorsal/ventral pattern formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein deubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within proteolysis IEA
    Inferred from Electronic Annotation
    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 25
    Names
    ubiquitin specific protease 25
    NP_001001886.1
    XP_005169213.1
    XP_005169214.1
    XP_005169218.1
    XP_009303832.1
    XP_009303833.1
    XP_009303834.1
    XP_009303835.1
    XP_021334826.1

    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_001001886.1 → NP_001001886.1  ubiquitin carboxyl-terminal hydrolase 25

      See identical proteins and their annotated locations for NP_001001886.1

      Status: PROVISIONAL

      Source sequence(s)
      BC045454
      UniProtKB/TrEMBL
      Q7ZVQ4
      Related
      ENSDARP00000123830.1, ENSDART00000150159.3
      Conserved Domains (3) summary
      cd02665
      Location:169 → 657
      Peptidase_C19I; 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 ...
      cd14354
      Location:14 → 59
      UBA_UBP25; UBA domain found in ubiquitin carboxyl-terminal hydrolase 25 (UBP25) and similar proteins
      pfam00443
      Location:167 → 408
      UCH; Ubiquitin carboxyl-terminal hydrolase

    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_007121.7 Reference GRCz11 Primary Assembly

      Range
      38170462..38243618 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009305557.3 → XP_009303832.1  ubiquitin carboxyl-terminal hydrolase 25 isoform X1

      UniProtKB/TrEMBL
      A0A8M3B6G9
      Conserved Domains (3) summary
      cd02665
      Location:169 → 657
      Peptidase_C19I; 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 ...
      cd14354
      Location:14 → 59
      UBA_UBP25; UBA domain found in ubiquitin carboxyl-terminal hydrolase 25 (UBP25) and similar proteins
      pfam00443
      Location:167 → 408
      UCH; Ubiquitin carboxyl-terminal hydrolase

    2. XM_005169161.4 → XP_005169218.1  ubiquitin carboxyl-terminal hydrolase 25 isoform X8

      UniProtKB/TrEMBL
      A0A8M2BGH6
      Conserved Domains (3) summary
      cd02665
      Location:169 → 657
      Peptidase_C19I; 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 ...
      cd14354
      Location:14 → 59
      UBA_UBP25; UBA domain found in ubiquitin carboxyl-terminal hydrolase 25 (UBP25) and similar proteins
      pfam00443
      Location:167 → 408
      UCH; Ubiquitin carboxyl-terminal hydrolase

    3. XM_009305560.3 → XP_009303835.1  ubiquitin carboxyl-terminal hydrolase 25 isoform X7

      UniProtKB/TrEMBL
      A0A8M3BD95
      Conserved Domains (3) summary
      cd02665
      Location:169 → 657
      Peptidase_C19I; 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 ...
      cd14354
      Location:14 → 59
      UBA_UBP25; UBA domain found in ubiquitin carboxyl-terminal hydrolase 25 (UBP25) and similar proteins
      pfam00443
      Location:167 → 408
      UCH; Ubiquitin carboxyl-terminal hydrolase

    4. XM_009305558.3 → XP_009303833.1  ubiquitin carboxyl-terminal hydrolase 25 isoform X2

      UniProtKB/TrEMBL
      A0A8M3B3I3
      Conserved Domains (3) summary
      cd02665
      Location:169 → 656
      Peptidase_C19I; 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 ...
      cd14354
      Location:14 → 59
      UBA_UBP25; UBA domain found in ubiquitin carboxyl-terminal hydrolase 25 (UBP25) and similar proteins
      pfam00443
      Location:167 → 407
      UCH; Ubiquitin carboxyl-terminal hydrolase

    5. XM_009305559.3 → XP_009303834.1  ubiquitin carboxyl-terminal hydrolase 25 isoform X3

      UniProtKB/TrEMBL
      A0A8M3AX40
      Conserved Domains (3) summary
      cd02665
      Location:169 → 657
      Peptidase_C19I; 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 ...
      cd14354
      Location:14 → 59
      UBA_UBP25; UBA domain found in ubiquitin carboxyl-terminal hydrolase 25 (UBP25) and similar proteins
      pfam00443
      Location:167 → 408
      UCH; Ubiquitin carboxyl-terminal hydrolase

    6. XM_005169156.4 → XP_005169213.1  ubiquitin carboxyl-terminal hydrolase 25 isoform X4

      UniProtKB/TrEMBL
      A0A8M2BGE7
      Conserved Domains (3) summary
      cd02665
      Location:169 → 657
      Peptidase_C19I; 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 ...
      cd14354
      Location:14 → 59
      UBA_UBP25; UBA domain found in ubiquitin carboxyl-terminal hydrolase 25 (UBP25) and similar proteins
      pfam00443
      Location:167 → 408
      UCH; Ubiquitin carboxyl-terminal hydrolase

    7. XM_005169157.4 → XP_005169214.1  ubiquitin carboxyl-terminal hydrolase 25 isoform X5

      UniProtKB/TrEMBL
      A0A0R4IQS2, A0A8M2BGJ5
      Related
      ENSDARP00000138813.1, ENSDART00000166108.2
      Conserved Domains (3) summary
      cd02665
      Location:169 → 657
      Peptidase_C19I; 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 ...
      cd14354
      Location:14 → 59
      UBA_UBP25; UBA domain found in ubiquitin carboxyl-terminal hydrolase 25 (UBP25) and similar proteins
      pfam00443
      Location:167 → 408
      UCH; Ubiquitin carboxyl-terminal hydrolase

    8. XM_021479151.1 → XP_021334826.1  ubiquitin carboxyl-terminal hydrolase 25 isoform X6

      UniProtKB/TrEMBL
      A0A8M9QGK5
      Conserved Domains (3) summary
      cd02665
      Location:169 → 657
      Peptidase_C19I; 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 ...
      cd14354
      Location:14 → 59
      UBA_UBP25; UBA domain found in ubiquitin carboxyl-terminal hydrolase 25 (UBP25) and similar proteins
      cl02553
      Location:154 → 297
      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 ...
    Nucleotide Protein Strain
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