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    Mindy3 MINDY lysine 48 deubiquitinase 3 [ Mus musculus (house mouse) ]

    Gene ID: 66960, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Mindy3provided by MGI
    Official Full Name
    MINDY lysine 48 deubiquitinase 3provided by MGI
    Primary source
    MGI:MGI:1914210
    See related
    Ensembl:ENSMUSG00000026767 AllianceGenome:MGI:1914210
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Fam188a; 1810041E18Rik; 2310047O13Rik; 5830410F13Rik
    Summary
    Predicted to enable K48-linked deubiquitinase activity and cysteine-type deubiquitinase activity. Predicted to be involved in apoptotic process; protein K48-linked deubiquitination; and proteolysis. Predicted to be located in nuclear membrane and nucleoplasm. Is expressed in cranial ganglion; dorsal root ganglion; heart; neural retina; and telencephalon. Orthologous to human MINDY3 (MINDY lysine 48 deubiquitinase 3). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in CNS E18 (RPKM 3.8), CNS E14 (RPKM 3.4) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Mindy3 in Genome Data Viewer
    Location:
    2 A1; 2 9.27 cM
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (12352074..12424298, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (12347263..12419489, complement)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_03684 Neighboring gene STARR-seq mESC enhancer starr_03685 Neighboring gene karyopherin (importin) alpha 2 pseudogene Neighboring gene STARR-seq mESC enhancer starr_03686 Neighboring gene STARR-seq mESC enhancer starr_03687 Neighboring gene integrin alpha 8 Neighboring gene STARR-seq mESC enhancer starr_03688 Neighboring gene STARR-seq mESC enhancer starr_03689 Neighboring gene RIKEN cDNA E030013I19 gene Neighboring gene STARR-seq mESC enhancer starr_03690 Neighboring gene STARR-positive B cell enhancer ABC_E5886 Neighboring gene STARR-seq mESC enhancer starr_03692 Neighboring gene STARR-seq mESC enhancer starr_03694 Neighboring gene predicted gene 13321 Neighboring gene STARR-seq mESC enhancer starr_03695 Neighboring gene STARR-seq mESC enhancer starr_03696 Neighboring gene STARR-seq mESC enhancer starr_03697 Neighboring gene STARR-positive B cell enhancer ABC_E4415 Neighboring gene phosphotriesterase related Neighboring gene predicted gene, 52597

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells. Kole C, et al. PLoS One, 2016. PMID 26985665, Free PMC Article
    2. A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart. Kalsotra A, et al. Proc Natl Acad Sci U S A, 2008 Dec 23. PMID 19075228, Free PMC Article
    3. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article
    4. A large-scale, gene-driven mutagenesis approach for the functional analysis of the mouse genome. Hansen J, et al. Proc Natl Acad Sci U S A, 2003 Aug 19. PMID 12904583, Free PMC Article
    5. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Stryke D, et al. Nucleic Acids Res, 2003 Jan 1. PMID 12520002, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (4) 

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables K48-linked deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables K48-linked deubiquitinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables K48-linked deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type deubiquitinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cysteine-type deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    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
    caspase recruitment domain containing protein
    deubiquitinating enzyme MINDY-3
    family with sequence similarity 188, member A
    protein FAM188A
    ubiquitin carboxyl-terminal hydrolase FAM188A
    NP_001342464.1
    NP_001342465.1
    NP_001342466.1
    NP_001342467.1
    NP_001342468.1
    NP_077147.2
    XP_006497585.1
    XP_006497586.1
    XP_006497587.1
    XP_006497588.1
    XP_006497589.1
    XP_006497592.1
    XP_030107834.1
    XP_036018396.1
    XP_036018397.1
    XP_036018398.1

    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_001355535.1 → NP_001342464.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform b

      Status: VALIDATED

      Source sequence(s)
      AK143250, AL772342
      Related
      ENSMUST00000130225.7
      Conserved Domains (1) summary
      pfam13898
      Location:29 → 314
      DUF4205; Domain of unknown function (DUF4205)

    2. NM_001355536.1 → NP_001342465.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform c precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3), as well as variant 4, encodes isoform c.
      Source sequence(s)
      AL772342, AL845533
      Conserved Domains (1) summary
      pfam13898
      Location:6 → 142
      DUF4205; Domain of unknown function (DUF4205)

    3. NM_001355537.1 → NP_001342466.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform c precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4), as well as variant 3, encodes isoform c.
      Source sequence(s)
      AL772342, AL845533
      Conserved Domains (1) summary
      pfam13898
      Location:6 → 142
      DUF4205; Domain of unknown function (DUF4205)

    4. NM_001355538.1 → NP_001342467.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform d precursor

      Status: VALIDATED

      Source sequence(s)
      AK075792, AL772342, AL845533
      Conserved Domains (1) summary
      pfam13898
      Location:6 → 142
      DUF4205; Domain of unknown function (DUF4205)

    5. NM_001355539.1 → NP_001342468.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform e

      Status: VALIDATED

      Source sequence(s)
      AL845533, FO708924
      Conserved Domains (1) summary
      pfam13898
      Location:30 → 103
      DUF4205; Domain of unknown function (DUF4205)

    6. NM_024185.4 → NP_077147.2  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform a

      See identical proteins and their annotated locations for NP_077147.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AK009891, BY297479
      Consensus CDS
      CCDS15690.1
      UniProtKB/Swiss-Prot
      Q3UPS0, Q9CV28, Q9DCC9
      Related
      ENSMUSP00000028105.7, ENSMUST00000028105.13
      Conserved Domains (1) summary
      pfam13898
      Location:29 → 314
      DUF4205; Domain of unknown function (DUF4205)

    RNA

    1. NR_149730.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL772342, AL845533
      Related
      ENSMUST00000194533.6

    2. NR_149731.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL772342, AL845533

    3. NR_149732.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL772342, AL845533
      Related
      ENSMUST00000129489.8

    4. NR_149745.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL772342, AL845533
      Related
      ENSMUST00000144645.8

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      12352074..12424298 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036162503.1 → XP_036018396.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X3

      Conserved Domains (1) summary
      pfam13898
      Location:29 → 266
      DUF4205; Domain of unknown function (DUF4205)

    2. XM_006497523.5 → XP_006497586.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X2

      Conserved Domains (1) summary
      pfam13898
      Location:29 → 266
      DUF4205; Domain of unknown function (DUF4205)

    3. XM_006497522.5 → XP_006497585.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X1

      Conserved Domains (1) summary
      pfam13898
      Location:29 → 314
      DUF4205; Domain of unknown function (DUF4205)

    4. XM_030251974.2 → XP_030107834.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X7

      Conserved Domains (1) summary
      pfam13898
      Location:6 → 142
      DUF4205; Domain of unknown function (DUF4205)

    5. XM_036162504.1 → XP_036018397.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X5

      Conserved Domains (1) summary
      pfam13898
      Location:54 → 190
      DUF4205; Domain of unknown function (DUF4205)

    6. XM_006497524.3 → XP_006497587.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X4

      Conserved Domains (1) summary
      pfam13898
      Location:29 → 257
      DUF4205; Domain of unknown function (DUF4205)

    7. XM_006497529.3 → XP_006497592.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X9

      Conserved Domains (1) summary
      pfam13898
      Location:30 → 103
      DUF4205; Domain of unknown function (DUF4205)

    8. XM_006497525.3 → XP_006497588.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X6

      UniProtKB/TrEMBL
      D6REU0
      Related
      ENSMUSP00000117457.3, ENSMUST00000124603.8
      Conserved Domains (1) summary
      pfam13898
      Location:80 → 150
      DUF4205; Domain of unknown function (DUF4205)

    9. XM_036162505.1 → XP_036018398.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X8

      Conserved Domains (1) summary
      pfam13898
      Location:6 → 142
      DUF4205; Domain of unknown function (DUF4205)

    10. XM_006497526.5 → XP_006497589.1  ubiquitin carboxyl-terminal hydrolase MINDY-3 isoform X7

      See identical proteins and their annotated locations for XP_006497589.1

      Conserved Domains (1) summary
      pfam13898
      Location:6 → 142
      DUF4205; Domain of unknown function (DUF4205)

    RNA

    1. XR_004940709.1 RNA Sequence

    2. XR_001783166.3 RNA Sequence

    3. XR_003953695.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9CV28.2 GenPept UniProtKB/Swiss-Prot:Q9CV28

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