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    YOD1 YOD1 deubiquitinase [ Homo sapiens (human) ]

    Gene ID: 55432, updated on 27-Nov-2024

    Summary

    Official Symbol
    YOD1provided by HGNC
    Official Full Name
    YOD1 deubiquitinaseprovided by HGNC
    Primary source
    HGNC:HGNC:25035
    See related
    Ensembl:ENSG00000180667 MIM:612023; AllianceGenome:HGNC:25035
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DUBA8; OTUD2; PRO0907
    Summary
    Protein ubiquitination controls many intracellular processes, including cell cycle progression, transcriptional activation, and signal transduction. This dynamic process, involving ubiquitin conjugating enzymes and deubiquitinating enzymes, adds and removes ubiquitin. Deubiquitinating enzymes are cysteine proteases that specifically cleave ubiquitin from ubiquitin-conjugated protein substrates. The protein encoded by this gene belongs to a DUB subfamily characterized by an ovarian tumor (OTU) domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]
    Expression
    Broad expression in bone marrow (RPKM 24.5), esophagus (RPKM 15.7) and 23 other tissues See more
    Orthologs
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    Genomic context

    See YOD1 in Genome Data Viewer
    Location:
    1q32.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (207043849..207053116, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (206309040..206318351, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (207217194..207226461, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:207192892-207194091 Neighboring gene chromosome 1 open reading frame 116 Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory region 4428 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:207224117-207224687 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:207225911-207226550 Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:207240869-207241100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2439 Neighboring gene complement component 4 binding protein beta Neighboring gene uncharacterized LOC107985251 Neighboring gene complement component 4 binding protein alpha

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • DKFZp451J1719

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables K48-linked deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables K63-linked deubiquitinase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables cysteine-type deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cysteine-type deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables deubiquitinase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ERAD pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endoplasmic reticulum unfolded protein response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in endoplasmic reticulum unfolded protein response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in macroautophagy IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of retrograde protein transport, ER to cytosol IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein K11-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein K11-linked deubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein K27-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein K29-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein K33-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein K48-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein K48-linked deubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein K63-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein K63-linked deubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    ubiquitin thioesterase OTU1
    Names
    DUBA-8
    HIN-7
    HIV-1-induced protease 7
    OTU domain containing 2
    OTU domain-containing protein 2
    YOD1 OTU deubiquinating enzyme 1 homolog ( yeast)
    hsHIN7
    NP_001263249.1
    NP_061036.3
    XP_047280403.1
    XP_054193502.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001276320.2NP_001263249.1  ubiquitin thioesterase OTU1 isoform 2

      See identical proteins and their annotated locations for NP_001263249.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains alternate exons in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AL445493
      Consensus CDS
      CCDS60402.1
      UniProtKB/Swiss-Prot
      Q5VVQ6
      Related
      ENSP00000356051.1, ENST00000367084.1
      Conserved Domains (1) summary
      COG5539
      Location:47303
      COG5539; Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
    2. NM_018566.4NP_061036.3  ubiquitin thioesterase OTU1 isoform 1

      See identical proteins and their annotated locations for NP_061036.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AL445493
      Consensus CDS
      CCDS31002.1
      UniProtKB/Swiss-Prot
      B2RNX3, Q5VVQ5, Q5VVQ6, Q6ZRS6, Q86T63, Q9P1L8
      Related
      ENSP00000326813.4, ENST00000315927.9
      Conserved Domains (1) summary
      COG5539
      Location:91347
      COG5539; Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      207043849..207053116 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047424447.1XP_047280403.1  ubiquitin thioesterase OTU1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      206309040..206318351 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337527.1XP_054193502.1  ubiquitin thioesterase OTU1 isoform X1