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    Yod1 YOD1 deubiquitinase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363982, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Yod1provided by RGD
    Official Full Name
    YOD1 deubiquitinaseprovided by RGD
    Primary source
    RGD:1359726
    See related
    AllianceGenome:RGD:1359726
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    hshin7
    Summary
    Predicted to enable K48-linked deubiquitinase activity; cysteine-type deubiquitinase activity; and ubiquitin protein ligase binding activity. Predicted to be involved in several processes, including ERAD pathway; negative regulation of retrograde protein transport, ER to cytosol; and protein deubiquitination. Predicted to be located in cytoplasm. Orthologous to human YOD1 (YOD1 deubiquitinase). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 249.2), Testes (RPKM 124.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Yod1 in Genome Data Viewer
    Location:
    13q13
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (44727319..44733933)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (42175047..42181661)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (47441296..47443013)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated like 1 Neighboring gene complement component 4 binding protein, beta Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 Neighboring gene similar to human chromosome 1 open reading frame 116 Neighboring gene Fc alpha and mu receptor

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. TRIM54 alleviates inflammation and apoptosis by stabilizing YOD1 in rat tendon-derived stem cells. Chen H, et al. J Biol Chem, 2024 Jan. PMID 38042492, Free PMC Article
    2. The otubain YOD1 is a deubiquitinating enzyme that associates with p97 to facilitate protein dislocation from the ER. Ernst R, et al. Mol Cell, 2009 Oct 9. PMID 19818707, Free PMC Article
    3. A deubiquitinase negatively regulates retro-translocation of nonubiquitinated substrates. Bernardi KM, et al. Mol Biol Cell, 2013 Nov. PMID 24068323, Free PMC Article
    4. VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy. Papadopoulos C, et al. EMBO J, 2017 Jan 17. PMID 27753622, Free PMC Article
    5. PARIS (ZNF746) repression of PGC-1α contributes to neurodegeneration in Parkinson's disease. Shin JH, et al. Cell, 2011 Mar 4. PMID 21376232, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TRIM54 alleviates inflammation and apoptosis by stabilizing YOD1 in rat tendon-derived stem cells.
      Title: TRIM54 alleviates inflammation and apoptosis by stabilizing YOD1 in rat tendon-derived stem cells.
    Submit: New GeneRIF Correction

    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

    • MGC124915

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables K48-linked deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cysteine-type deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type deubiquitinase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin protein ligase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ERAD pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ERAD pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in endoplasmic reticulum unfolded protein response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endoplasmic reticulum unfolded protein response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endoplasmic reticulum unfolded protein response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in macroautophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in macroautophagy ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of retrograde protein transport, ER to cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K11-linked deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K11-linked deubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein K27-linked deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K27-linked deubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein K29-linked deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K29-linked deubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein K33-linked deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K33-linked deubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein K48-linked deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K48-linked deubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein K63-linked deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K63-linked deubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin thioesterase OTU1
    Names
    HIV-induced protein-7-like protease
    YOD1 OTU deubiquinating enzyme 1 homolog
    YOD1 OTU deubiquitinating enzyme 1 homologue
    NP_001008889.2

    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_001008889.2 → NP_001008889.2  ubiquitin thioesterase OTU1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/Swiss-Prot
      Q32Q05, Q6IE74

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086031.1 Reference GRCr8

      Range
      44727319..44733933
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q32Q05.1 GenPept UniProtKB/Swiss-Prot:Q32Q05

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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