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Yod1 YOD1 deubiquitinase [ Rattus norvegicus (Norway rat) ]

Gene ID: 363982, updated on 2-Nov-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, Nov 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 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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