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    LOC4326194 ubiquitin carboxyl-terminal hydrolase 6 [ Oryza sativa Japonica Group (Japanese rice) ]

    Gene ID: 4326194, updated on 12-Jul-2024

    Summary

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    Gene symbol
    LOC4326194
    Gene description
    ubiquitin carboxyl-terminal hydrolase 6
    Locus tag
    OSNPB_010550100
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Oryza sativa Japonica Group
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
    Expression
    Ubiquitous expression in leaves after flowering (RPKM 50.1), flower buds (RPKM 49.3) and 6 other tissues See more
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    Genomic context

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    See LOC4326194 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_06 current ASM3414082v1 (GCF_034140825.1) 1 NC_089035.1 (21151615..21159515, complement)
    102 previous assembly IRGSP-1.0 (GCF_001433935.1) 1 NC_029256.1 (20581637..20589602, complement)

    Chromosome 1 - NC_089035.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC136355170 Neighboring gene DEAD-box ATP-dependent RNA helicase 15-like Neighboring gene F-box protein SKIP8 Neighboring gene B2 protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Transcriptome profiling of various organs at different developmental stages in rice Transcriptome profiling of various organs at different developmental stages in rice
    • Description: Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds
    • BioProject: PRJNA243371
    • Publication: PMID 26387578
    • Analysis date: Fri Dec 15 20:02:59 2017

    Bibliography

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    Related articles in PubMed

    1. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Rice Full-Length cDNA Consortium, et al. Science, 2003 Jul 18. PMID 12869764
    2. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Burge S, et al. Database (Oxford), 2012. PMID 22301074, Free PMC Article
    3. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. Tang H, et al. Bioinformatics, 2019 Feb 1. PMID 30032202, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables cysteine-type deubiquitinase activity IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables proteasome binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables protein binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in protein deubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    involved_in regulation of proteasomal protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 6
    Names
    B1156H12.24
    OSJNBa0024F24.9
    Os01g0550100
    putative ubiquitin-specific protease 6

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: GCF_034140825.1-RS_2024_06

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

    Reference ASM3414082v1 Primary Assembly

    Genomic

    1. NC_089035.1 Reference ASM3414082v1 Primary Assembly

      Range
      21151615..21159515 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015766868.3 → XP_015622354.1  ubiquitin carboxyl-terminal hydrolase 6

      UniProtKB/TrEMBL
      A0A0P0V3V8, B9EXH0, Q0JM15, Q5JK78
      Conserved Domains (2) summary
      cd02657
      Location:105 → 470
      Peptidase_C19A; 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 hydrolyse bonds involving the carboxyl ...
      cd16104
      Location:1 → 75
      Ubl_USP14_like; ubiquitin-like (Ubl) domain found in ubiquitin carboxyl-terminal hydrolase 14 (USP14) and similar proteins
    Nucleotide Protein
    Heading Accession and Version

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    Research Materials