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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
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Genomic context

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See MINDY1 in Genome Data Viewer
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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