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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
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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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