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    MINDY1 MINDY lysine 48 deubiquitinase 1 [ Homo sapiens (human) ]

    Gene ID: 55793, updated on 7-Apr-2024

    Summary

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    Official Symbol
    MINDY1provided by HGNC
    Official Full Name
    MINDY lysine 48 deubiquitinase 1provided by HGNC
    Primary source
    HGNC:HGNC:25648
    See related
    Ensembl:ENSG00000143409 MIM:618407; AllianceGenome:HGNC:25648
    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
    FAM63A; MINDY-1
    Summary
    Enables K48-linked polyubiquitin modification-dependent protein binding activity; Lys48-specific deubiquitinase activity; and cysteine-type carboxypeptidase activity. Predicted to be involved in protein K48-linked deubiquitination. Located in nuclear body. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 17.7), testis (RPKM 8.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1q21.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (150996536..151008393, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150120231..150132083, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (150969012..150980869, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150937964 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150945529-150946460 Neighboring gene ceramide synthase 2 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 1:150946490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1308 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:150949461-150949964 and GRCh37_chr1:150949965-150950466 Neighboring gene uncharacterized LOC105371438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150955292-150956153 Neighboring gene annexin A9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1700 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:150970021-150970520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150980776-150981318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150981319-150981859 Neighboring gene prune exopolyphosphatase 1 Neighboring gene RNA, U6 small nuclear 884, pseudogene Neighboring gene BCL2 interacting protein like

    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
    • 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. MINDY1 promotes breast cancer cell proliferation by stabilizing estrogen receptor α. Tang J, et al. Cell Death Dis, 2021 Oct 13. PMID 34645792, Free PMC Article
    2. MINDY1 promotes bladder cancer progression by stabilizing YAP. Luo Y, et al. Cancer Cell Int, 2021 Jul 27. PMID 34315490, Free PMC Article
    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 (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MINDY1 promotes breast cancer cell proliferation by stabilizing estrogen receptor alpha.
      Title: MINDY1 promotes breast cancer cell proliferation by stabilizing estrogen receptor α.
    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. MINDY-1 prefers cleaving long polyubiquitin chains and works by trimming chains from the distal end.
      Title: MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies genetic risk underlying primary rhegmatogenous retinal detachment.
    EBI GWAS Catalog
    New loci associated with kidney function and chronic kidney disease.
    EBI GWAS Catalog

    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

    • FLJ11280, FLJ43504

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 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
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in protein K48-linked deubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase MINDY-1
    Names
    MINDY deubiquitinase 1
    MIU-containing novel DUB family member 1
    deubiquitinating enzyme MINDY-1
    family with sequence similarity 63 member A
    motif interacting with Ub-containing novel DUB
    protein FAM63A
    NP_001035307.2
    NP_001156730.3
    NP_001156731.2
    NP_001156732.2
    NP_001306927.2
    NP_001363593.1
    NP_001363594.1
    NP_001363595.1
    NP_001363596.1
    NP_001363597.1
    NP_001363598.1
    NP_001363599.1
    NP_001363600.1
    NP_001363601.1
    NP_001363602.1
    NP_001363603.1
    NP_060849.3
    XP_005245382.1
    XP_016857266.1
    XP_047281081.1
    XP_047281082.1
    XP_047281084.1
    XP_047281089.1
    XP_047281090.1
    XP_047281091.1
    XP_047281094.1
    XP_054193608.1
    XP_054193609.1
    XP_054193610.1
    XP_054193611.1
    XP_054193612.1
    XP_054193613.1
    XP_054193614.1
    XP_054193615.1
    XP_054193616.1
    XP_054193617.1
    XP_054193618.1
    XP_054193619.1

    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_001040217.3 → NP_001035307.2  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR, uses an alternate splice site in the 5' coding region, and uses a downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1. Both variants 2 and 5 encode the same isoform.
      Source sequence(s)
      AL590133
      Consensus CDS
      CCDS30854.1
      Related
      ENSP00000310923.5, ENST00000312210.9
      Conserved Domains (1) summary
      pfam04424
      Location:2 → 119
      MINDY_DUB; MINDY deubiquitinase

    2. NM_001163258.3 → NP_001156730.3  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 3, 6 and 8 encode the same isoform (1).
      Source sequence(s)
      AL590133
      Consensus CDS
      CCDS976.1
      UniProtKB/Swiss-Prot
      B3KWP4, B3KWV8, B4DXF2, B4E1S4, D3DV09, J3KP53, Q5SZF0, Q8N5J2, Q9NUL9, Q9P2F7
      Related
      ENSP00000354669.7, ENST00000361738.12
      Conserved Domains (1) summary
      pfam04424
      Location:144 → 261
      MINDY_DUB; MINDY deubiquitinase

    3. NM_001163259.2 → NP_001156731.2  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the 5' coding region and a downstream start codon, compared to variant 1. The promoter and extent of the 5' UTR for this variant have not been characterized. The resulting isoform (4) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK303962, AL590133, AW072847, BC032321, DA292825
      Consensus CDS
      CCDS55635.1
      Related
      ENSP00000437174.2, ENST00000493834.2
      Conserved Domains (1) summary
      pfam04424
      Location:49 → 166
      MINDY_DUB; MINDY deubiquitinase

    4. NM_001163260.2 → NP_001156732.2  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in the 5' coding region and a downstream start codon, compared to variant 1. The promoter and extent of the 5' UTR for this variant have not been characterized. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1. Both variants 2 and 5 encode the same isoform.
      Source sequence(s)
      AK002142, AK125493, AL590133, AW072847, DA292825
      Consensus CDS
      CCDS30854.1
      Conserved Domains (1) summary
      pfam04424
      Location:2 → 119
      MINDY_DUB; MINDY deubiquitinase

    5. NM_001319998.2 → NP_001306927.2  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, compared to variant 1. Variants 1, 3, 6 and 8 encode the same isoform (1).
      Source sequence(s)
      AL590133
      Consensus CDS
      CCDS976.1
      UniProtKB/Swiss-Prot
      B3KWP4, B3KWV8, B4DXF2, B4E1S4, D3DV09, J3KP53, Q5SZF0, Q8N5J2, Q9NUL9, Q9P2F7
      Conserved Domains (1) summary
      pfam04424
      Location:144 → 261
      MINDY_DUB; MINDY deubiquitinase

    6. NM_001376664.1 → NP_001363593.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL590133
      Conserved Domains (1) summary
      pfam04424
      Location:144 → 262
      MINDY_DUB; MINDY deubiquitinase

    7. NM_001376665.1 → NP_001363594.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR, compared to variant 1. Variants 1, 3, 6 and 8 encode the same isoform (1).
      Source sequence(s)
      AL590133
      Consensus CDS
      CCDS976.1
      UniProtKB/Swiss-Prot
      B3KWP4, B3KWV8, B4DXF2, B4E1S4, D3DV09, J3KP53, Q5SZF0, Q8N5J2, Q9NUL9, Q9P2F7
      Related
      ENSP00000507359.1, ENST00000683666.2
      Conserved Domains (1) summary
      pfam04424
      Location:144 → 261
      MINDY_DUB; MINDY deubiquitinase

    8. NM_001376666.1 → NP_001363595.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AL590133
      Conserved Domains (1) summary
      pfam04424
      Location:144 → 262
      MINDY_DUB; MINDY deubiquitinase

    9. NM_001376667.1 → NP_001363596.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AL590133
      Conserved Domains (1) summary
      pfam04424
      Location:144 → 261
      MINDY_DUB; MINDY deubiquitinase

    10. NM_001376668.1 → NP_001363597.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AL590133
      Conserved Domains (1) summary
      pfam04424
      Location:144 → 261
      MINDY_DUB; MINDY deubiquitinase

    11. NM_001376669.1 → NP_001363598.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AL590133
      Conserved Domains (1) summary
      pfam04424
      Location:144 → 208
      MINDY_DUB; MINDY deubiquitinase

    12. NM_001376670.1 → NP_001363599.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AL590133
      Conserved Domains (1) summary
      pfam04424
      Location:144 → 208
      MINDY_DUB; MINDY deubiquitinase

    13. NM_001376671.1 → NP_001363600.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 11

      Status: VALIDATED

      Source sequence(s)
      AL590133
      Conserved Domains (1) summary
      pfam04424
      Location:1 → 96
      MINDY_DUB; MINDY deubiquitinase

    14. NM_001376672.1 → NP_001363601.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 12

      Status: VALIDATED

      Source sequence(s)
      AL590133
      Conserved Domains (1) summary
      pfam04424
      Location:1 → 95
      MINDY_DUB; MINDY deubiquitinase

    15. NM_001376673.1 → NP_001363602.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 12

      Status: VALIDATED

      Source sequence(s)
      AL590133
      Conserved Domains (1) summary
      pfam04424
      Location:1 → 95
      MINDY_DUB; MINDY deubiquitinase

    16. NM_001376674.1 → NP_001363603.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 13

      Status: VALIDATED

      Source sequence(s)
      AL590133
      Conserved Domains (1) summary
      pfam04424
      Location:1 → 95
      MINDY_DUB; MINDY deubiquitinase

    17. NM_018379.5 → NP_060849.3  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1. Variants 1, 3, 6 and 8 encode the same isoform (1).
      Source sequence(s)
      AL590133
      Consensus CDS
      CCDS976.1
      UniProtKB/Swiss-Prot
      B3KWP4, B3KWV8, B4DXF2, B4E1S4, D3DV09, J3KP53, Q5SZF0, Q8N5J2, Q9NUL9, Q9P2F7
      Related
      ENSP00000354814.5, ENST00000361936.9
      Conserved Domains (1) summary
      pfam04424
      Location:144 → 261
      MINDY_DUB; MINDY deubiquitinase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      150996536..151008393 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047425135.1 → XP_047281091.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X6

    2. XM_047425134.1 → XP_047281090.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X5

    3. XM_047425133.1 → XP_047281089.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X4

    4. XM_047425126.1 → XP_047281082.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X2

    5. XM_047425128.1 → XP_047281084.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X3

    6. XM_047425125.1 → XP_047281081.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X1

    7. XM_047425138.1 → XP_047281094.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X8

    8. XM_005245325.5 → XP_005245382.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X7

      Conserved Domains (1) summary
      pfam04424
      Location:2 → 120
      DUF544; Protein of unknown function (DUF544)

    9. XM_017001777.2 → XP_016857266.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X9

      UniProtKB/Swiss-Prot
      Q8N5J2
      Conserved Domains (1) summary
      pfam04424
      Location:192 → 309
      MINDY_DUB; MINDY deubiquitinase

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      150120231..150132083 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337640.1 → XP_054193615.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X6

    2. XM_054337635.1 → XP_054193610.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X3

    3. XM_054337639.1 → XP_054193614.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X5

    4. XM_054337636.1 → XP_054193611.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X4

    5. XM_054337633.1 → XP_054193608.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X1

    6. XM_054337634.1 → XP_054193609.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X2

    7. XM_054337643.1 → XP_054193618.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X8

    8. XM_054337642.1 → XP_054193617.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X7

    9. XM_054337641.1 → XP_054193616.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X12

    10. XM_054337638.1 → XP_054193613.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X11

    11. XM_054337637.1 → XP_054193612.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X10

    12. XM_054337644.1 → XP_054193619.1  ubiquitin carboxyl-terminal hydrolase MINDY-1 isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N5J2.2 GenPept UniProtKB/Swiss-Prot:Q8N5J2

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