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    Mindy3 MINDY lysine 48 deubiquitinase 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 291320, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Mindy3provided by RGD
    Official Full Name
    MINDY lysine 48 deubiquitinase 3provided by RGD
    Primary source
    RGD:1309605
    See related
    EnsemblRapid:ENSRNOG00000016955 AllianceGenome:RGD:1309605
    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
    Fam188a; RGD1309605
    Summary
    Predicted to enable K48-linked deubiquitinase activity and cysteine-type deubiquitinase activity. Predicted to be involved in protein K48-linked deubiquitination and proteolysis. Predicted to be located in nuclear membrane and nucleoplasm. Orthologous to human MINDY3 (MINDY lysine 48 deubiquitinase 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Liver (RPKM 178.9), Kidney (RPKM 159.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Mindy3 in Genome Data Viewer
    Location:
    17q12.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (80454404..80532999, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (75545286..75623884, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (79720534..79798470, complement)

    Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene integrin subunit alpha 8 Neighboring gene uncharacterized LOC120097958 Neighboring gene U7 small nuclear RNA Neighboring gene uncharacterized LOC103694135 Neighboring gene uncharacterized LOC134482608 Neighboring gene Sec61 translocon subunit gamma like 2 Neighboring gene U7 small nuclear RNA

    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. MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes. Abdul Rehman SA, et al. Mol Cell, 2016 Jul 7. PMID 27292798, Free PMC Article
    2. 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 K48-linked deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables K48-linked deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in protein K48-linked deubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase MINDY-3
    Names
    family with sequence similarity 188, member A
    protein FAM188A
    NP_001099592.1
    XP_017455984.1
    XP_017455985.1
    XP_038951473.1
    XP_038951477.1
    XP_063132316.1
    XP_063132317.1
    XP_063132318.1

    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_001106122.1 → NP_001099592.1  ubiquitin carboxyl-terminal hydrolase MINDY-3

      See identical proteins and their annotated locations for NP_001099592.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473990
      UniProtKB/TrEMBL
      A6JM32, D3Z916
      Related
      ENSRNOP00000022986.5, ENSRNOT00000022986.7
      Conserved Domains (1) summary
      pfam13898
      Location:29 → 314
      DUF4205; Domain of unknown function (DUF4205)

    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_086035.1 Reference GRCr8

      Range
      80454404..80532999 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063276246.1 → XP_063132316.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X2

    2. XM_017600496.2 → XP_017455985.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X4

      Related
      ENSRNOP00000107442.1, ENSRNOT00000154944.1

    3. XM_063276247.1 → XP_063132317.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X3

    4. XM_017600495.2 → XP_017455984.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X1

    5. XM_039095549.1 → XP_038951477.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X6

      Conserved Domains (1) summary
      pfam13898
      Location:3 → 51
      DUF4205; Domain of unknown function (DUF4205)

    6. XM_063276248.1 → XP_063132318.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X6

    7. XM_039095545.1 → XP_038951473.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X5

      Conserved Domains (1) summary
      pfam13898
      Location:6 → 120
      DUF4205; Domain of unknown function (DUF4205)

    RNA

    1. XR_010058840.1 RNA Sequence

    2. XR_010058841.1 RNA Sequence

    3. XR_010058842.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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