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    usp16 ubiquitin specific peptidase 16 [ Danio rerio (zebrafish) ]

    Gene ID: 569700, updated on 14-Nov-2024

    Summary

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    Official Symbol
    usp16provided by ZNC
    Official Full Name
    ubiquitin specific peptidase 16provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-4153
    See related
    Ensembl:ENSDARG00000060633 AllianceGenome:ZFIN:ZDB-GENE-030131-4153
    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:fc76b02; wu:fc76b08; si:dkey-121n8.2; si:ch211-238e22.5
    Summary
    Predicted to enable several functions, including peptidase activity; transcription coactivator activity; and zinc ion binding activity. Predicted to be involved in DNA damage response; positive regulation of macromolecule biosynthetic process; and protein homotetramerization. Predicted to act upstream of or within several processes, including chromatin organization; protein deubiquitination; and proteolysis. Predicted to be located in nucleus. Orthologous to human USP16 (ubiquitin specific peptidase 16). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See usp16 in Genome Data Viewer
    Location:
    chromosome: 15
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 15 NC_007126.7 (41290948..41311305, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 15 NC_007126.6 (41333552..41353915, complement)

    Chromosome 15 - NC_007126.7Genomic Context describing neighboring genes Neighboring gene si:dkey-75b17.1 Neighboring gene single-pass membrane protein with coiled-coil domains 4 Neighboring gene si:dkey-121n8.8 Neighboring gene si:dkey-121n8.7

    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. 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
    2. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article
    3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, 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

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    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 IEA
    Inferred from Electronic Annotation
    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 histone H2A deubiquitinase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables histone binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone binding ISS
    Inferred from Sequence or Structural Similarity
    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 transcription coactivator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coactivator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables ubiquitin binding 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
    		  
    enables zinc ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitotic nuclear division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of translational elongation 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 homotetramerization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein homotetramerization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of cell cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 16
    Names
    ubiquitin specific protease 16
    ubiquitin thiolesterase 16
    NP_001139569.1
    XP_009290187.1
    XP_009290190.1
    XP_021337123.1
    XP_021337124.1
    XP_068069677.1

    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_001146097.1 → NP_001139569.1  ubiquitin carboxyl-terminal hydrolase 16

      See identical proteins and their annotated locations for NP_001139569.1

      Status: PROVISIONAL

      Source sequence(s)
      CR854897
      UniProtKB/Swiss-Prot
      A8HAL1
      UniProtKB/TrEMBL
      A0A8M9QC36
      Related
      ENSDARP00000080080.4, ENSDART00000085645.6
      Conserved Domains (4) summary
      cd02667
      Location:624 → 812
      Peptidase_C19K; 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 ...
      pfam02148
      Location:68 → 124
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
      cl02553
      Location:209 → 406
      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 ...
      cl28246
      Location:482 → 614
      DnaJ; DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]

    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_007126.7 Reference GRCz11 Primary Assembly

      Range
      41290948..41311305 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068213576.1 → XP_068069677.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X3

    2. XM_009291915.4 → XP_009290190.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X2

      UniProtKB/TrEMBL
      A0A8M3AQ52
      Conserved Domains (4) summary
      cd02667
      Location:624 → 811
      Peptidase_C19K; 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 ...
      cl02553
      Location:209 → 406
      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 ...
      pfam00443
      Location:603 → 810
      UCH; Ubiquitin carboxyl-terminal hydrolase
      pfam02148
      Location:68 → 124
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

    3. XM_009291912.4 → XP_009290187.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X1

      See identical proteins and their annotated locations for XP_009290187.1

      UniProtKB/Swiss-Prot
      A8HAL1
      UniProtKB/TrEMBL
      A0A8M9QC36
      Conserved Domains (4) summary
      cd02667
      Location:624 → 812
      Peptidase_C19K; 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 ...
      pfam02148
      Location:68 → 124
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
      cl02553
      Location:209 → 406
      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 ...
      cl28246
      Location:482 → 614
      DnaJ; DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]

    4. XM_021481449.2 → XP_021337124.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X3

      UniProtKB/TrEMBL
      A0A8M9QHB9
      Conserved Domains (4) summary
      cd02667
      Location:550 → 738
      Peptidase_C19K; 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 ...
      pfam02148
      Location:1 → 50
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
      cl02553
      Location:135 → 332
      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 ...
      cl28246
      Location:408 → 540
      DnaJ; DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]

    5. XM_021481448.2 → XP_021337123.1  ubiquitin carboxyl-terminal hydrolase 16 isoform X1

      UniProtKB/Swiss-Prot
      A8HAL1
      UniProtKB/TrEMBL
      A0A8M9QC36
      Conserved Domains (4) summary
      cd02667
      Location:624 → 812
      Peptidase_C19K; 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 ...
      pfam02148
      Location:68 → 124
      zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
      cl02553
      Location:209 → 406
      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 ...
      cl28246
      Location:482 → 614
      DnaJ; DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A8HAL1.1 GenPept UniProtKB/Swiss-Prot:A8HAL1

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