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    Otud6b OTU deubiquitinase 6B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 297911, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Otud6bprovided by RGD
    Official Full Name
    OTU deubiquitinase 6Bprovided by RGD
    Primary source
    RGD:1310024
    See related
    EnsemblRapid:ENSRNOG00000006636 AllianceGenome:RGD:1310024
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1310024
    Summary
    Predicted to enable cysteine-type deubiquitinase activity. Predicted to be involved in several processes, including proteasome assembly; protein deubiquitination; and regulation of translation. Predicted to be part of eukaryotic translation initiation factor 4F complex. Orthologous to human OTUD6B (OTU deubiquitinase 6B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Muscle (RPKM 147.4), Brain (RPKM 142.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Otud6b in Genome Data Viewer
    Location:
    5q13
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (32979190..33011781, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (28181992..28214486, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (28333019..28350093, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene solute carrier family 26 member 7 Neighboring gene leucine rich repeat containing 69 Neighboring gene phosphatidylinositol-4,5-bisphosphate 4-phosphatase 2 Neighboring gene similar to human chromosome 8 open reading frame 88

    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. Biallelic Variants in OTUD6B Cause an Intellectual Disability Syndrome Associated with Seizures and Dysmorphic Features. Santiago-Sim T, et al. Am J Hum Genet, 2017 Apr 6. PMID 28343629, Free PMC Article
    2. Evidence for OTUD-6B participation in B lymphocytes cell cycle after cytokine stimulation. Xu Z, et al. PLoS One, 2011 Jan 18. PMID 21267069, Free PMC Article
    3. Deubiquitinase OTUD6B Isoforms Are Important Regulators of Growth and Proliferation. Sobol A, et al. Mol Cancer Res, 2017 Feb. PMID 27864334, Free PMC Article
    4. 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

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    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
    		  
    Process Evidence Code Pubs
    involved_in cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in proteasome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of eukaryotic translation initiation factor 4F complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    deubiquitinase OTUD6B
    Names
    OTU domain containing 6B
    OTU domain-containing protein 6B
    NP_001100109.1
    XP_006237976.1
    XP_038965351.1
    XP_063143363.1
    XP_063143364.1

    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_001106639.1 → NP_001100109.1  deubiquitinase OTUD6B

      See identical proteins and their annotated locations for NP_001100109.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473962
      UniProtKB/TrEMBL
      A0A1W2Q6D9, A6II95
      Conserved Domains (3) summary
      COG5539
      Location:43 → 311
      COG5539; Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
      pfam02338
      Location:184 → 309
      OTU; OTU-like cysteine protease
      cl19511
      Location:36 → 101
      DUF2317; Uncharacterized protein conserved in bacteria (DUF2317)

    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_086023.1 Reference GRCr8

      Range
      32979190..33011781 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039109423.2 → XP_038965351.1  deubiquitinase OTUD6B isoform X1

      UniProtKB/TrEMBL
      A0A1W2Q6D9, A0A1W2Q6I2
      Related
      ENSRNOP00000076236.3, ENSRNOT00000093698.3
      Conserved Domains (2) summary
      COG5539
      Location:43 → 311
      COG5539; Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
      pfam02338
      Location:184 → 309
      OTU; OTU-like cysteine protease

    2. XM_063287293.1 → XP_063143363.1  deubiquitinase OTUD6B isoform X3

    3. XM_006237914.5 → XP_006237976.1  deubiquitinase OTUD6B isoform X2

      UniProtKB/TrEMBL
      A0A1W2Q6D9, D3ZGY2
      Related
      ENSRNOP00000008726.7, ENSRNOT00000008725.9
      Conserved Domains (3) summary
      COG5539
      Location:43 → 311
      COG5539; Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
      pfam02338
      Location:184 → 309
      OTU; OTU-like cysteine protease
      cl19511
      Location:36 → 101
      DUF2317; Uncharacterized protein conserved in bacteria (DUF2317)

    4. XM_063287294.1 → XP_063143364.1  deubiquitinase OTUD6B isoform X4

    Nucleotide Protein Strain
    Heading Accession and Version

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