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    MINDY2 MINDY lysine 48 deubiquitinase 2 [ Homo sapiens (human) ]

    Gene ID: 54629, updated on 2-Nov-2024

    Summary

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    Official Symbol
    MINDY2provided by HGNC
    Official Full Name
    MINDY lysine 48 deubiquitinase 2provided by HGNC
    Primary source
    HGNC:HGNC:26954
    See related
    Ensembl:ENSG00000128923 MIM:618408; AllianceGenome:HGNC:26954
    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
    FAM63B
    Summary
    Enables peptidase activity and polyubiquitin modification-dependent protein binding activity. Predicted to be involved in protein K48-linked deubiquitination. Located in nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in brain (RPKM 6.3), fat (RPKM 6.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See MINDY2 in Genome Data Viewer
    Location:
    15q21.3-q22.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (58771302..58861900)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (56573291..56663918)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (59063501..59154099)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA, C/D box 3 pseudogene 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:59062438-59063363 Neighboring gene MINDY2 divergent transcript Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:59125759-59126526 Neighboring gene zinc finger protein 444 pseudogene 1 Neighboring gene ribosomal protein L21 pseudogene 14

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Hypomethylation of FAM63B in bipolar disorder patients. Starnawska A, et al. Clin Epigenetics, 2016. PMID 27175219, Free PMC Article
    2. Exosomal circFAM63Bsuppresses bone regeneration of postmenopausal osteoporosis via regulating miR-578/HMGA2 axis. Li F, et al. J Orthop Res, 2024 Jun. PMID 38151824
    3. Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2. Abdul Rehman SA, et al. Mol Cell, 2021 Oct 21. PMID 34529927, Free PMC Article
    4. 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
    5. A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains. Kristariyanto YA, et al. EMBO Rep, 2017 Mar. PMID 28082312, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Exosomal circFAM63Bsuppresses bone regeneration of postmenopausal osteoporosis via regulating miR-578/HMGA2 axis.
      Title: Exosomal circFAM63Bsuppresses bone regeneration of postmenopausal osteoporosis via regulating miR-578/HMGA2 axis.
    2. Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2.
      Title: Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2.
    3. Results identified FAM63B hypomethylation in bipolar disorder patients and data support that FAM63B is a shared epigenetic risk gene for bipolar disorder and schizophrenia.
      Title: Hypomethylation of FAM63B in bipolar disorder patients.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1164

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables K11-linked polyubiquitin modification-dependent protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables K48-linked deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables K48-linked deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables K48-linked polyubiquitin modification-dependent protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables K6-linked polyubiquitin modification-dependent protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables K63-linked polyubiquitin modification-dependent protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cysteine-type carboxypeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cysteine-type carboxypeptidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cysteine-type deubiquitinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase MINDY-2
    Names
    MINDY deubiquitinase 2
    deubiquitinating enzyme MINDY-2
    family with sequence similarity 63 member B
    protein FAM63B
    NP_001035540.1
    NP_001035543.1
    XP_011519989.1
    XP_011519990.1
    XP_011519991.1
    XP_011519992.1
    XP_016877821.1
    XP_016877822.1
    XP_016877823.1
    XP_016877824.1
    XP_024305732.1
    XP_047288655.1
    XP_047288656.1
    XP_054234205.1
    XP_054234206.1
    XP_054234207.1
    XP_054234208.1
    XP_054234209.1
    XP_054234210.1
    XP_054234211.1
    XP_054234212.1
    XP_054234213.1
    XP_054234214.1
    XP_054234215.1

    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_001040450.3 → NP_001035540.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform a

      See identical proteins and their annotated locations for NP_001035540.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AC090515, AK075319, CB321913
      Consensus CDS
      CCDS42046.1
      UniProtKB/Swiss-Prot
      B2RTT8, Q8NBR6, Q9ULQ6
      UniProtKB/TrEMBL
      B4DM49
      Related
      ENSP00000452885.1, ENST00000559228.6
      Conserved Domains (1) summary
      pfam04424
      Location:279 → 390
      DUF544; Protein of unknown function (DUF544)

    2. NM_001040453.3 → NP_001035543.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform b

      See identical proteins and their annotated locations for NP_001035543.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the terminal coding exon, compared to variant 1, and encodes a shorter isoform (b), compared to isoform a.
      Source sequence(s)
      AC090515, BC144616, CB321913
      Consensus CDS
      CCDS45268.1
      UniProtKB/TrEMBL
      B4DM49
      Related
      ENSP00000393231.2, ENST00000450403.3
      Conserved Domains (1) summary
      pfam04424
      Location:279 → 390
      DUF544; Protein of unknown function (DUF544)

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      58771302..58861900
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521687.3 → XP_011519989.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X1

      UniProtKB/TrEMBL
      B4DM49
      Conserved Domains (1) summary
      pfam04424
      Location:279 → 408
      DUF544; Protein of unknown function (DUF544)

    2. XM_011521688.3 → XP_011519990.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X2

      UniProtKB/TrEMBL
      B4DM49
      Conserved Domains (1) summary
      pfam04424
      Location:279 → 408
      DUF544; Protein of unknown function (DUF544)

    3. XM_017022332.3 → XP_016877821.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X7

      UniProtKB/TrEMBL
      B4DM49

    4. XM_047432700.1 → XP_047288656.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X8

    5. XM_011521689.3 → XP_011519991.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X3

      UniProtKB/TrEMBL
      B4DM49
      Conserved Domains (1) summary
      pfam04424
      Location:279 → 374
      DUF544; Protein of unknown function (DUF544)

    6. XM_047432699.1 → XP_047288655.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X4

    7. XM_017022333.3 → XP_016877822.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X9

      UniProtKB/TrEMBL
      B4DM49
      Conserved Domains (1) summary
      PRK07003
      Location:19 → 209
      PRK07003; DNA polymerase III subunit gamma/tau

    8. XM_017022334.3 → XP_016877823.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X10

      UniProtKB/TrEMBL
      B4DM49

    9. XM_011521690.3 → XP_011519992.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X5

      UniProtKB/TrEMBL
      B4DM49
      Conserved Domains (1) summary
      pfam04424
      Location:279 → 356
      DUF544; Protein of unknown function (DUF544)

    10. XM_024449964.2 → XP_024305732.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X6

      UniProtKB/TrEMBL
      B4DM49
      Conserved Domains (2) summary
      pfam04424
      Location:279 → 356
      DUF544; Protein of unknown function (DUF544)
      cl26386
      Location:19 → 209
      DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

    11. XM_017022335.3 → XP_016877824.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X11

      UniProtKB/TrEMBL
      J3KNL7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      56573291..56663918
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378230.1 → XP_054234205.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X1

    2. XM_054378231.1 → XP_054234206.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X2

    3. XM_054378236.1 → XP_054234211.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X7

    4. XM_054378237.1 → XP_054234212.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X8

    5. XM_054378232.1 → XP_054234207.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X3

    6. XM_054378233.1 → XP_054234208.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X4

    7. XM_054378238.1 → XP_054234213.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X9

    8. XM_054378239.1 → XP_054234214.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X10

    9. XM_054378234.1 → XP_054234209.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X5

    10. XM_054378235.1 → XP_054234210.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X6

    11. XM_054378240.1 → XP_054234215.1  ubiquitin carboxyl-terminal hydrolase MINDY-2 isoform X11

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_019092.1: Suppressed sequence

      Description
      NM_019092.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NBR6.2 GenPept UniProtKB/Swiss-Prot:Q8NBR6

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