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MYSM1 Myb like, SWIRM and MPN domains 1 [ Homo sapiens (human) ]

Gene ID: 114803, updated on 22-Apr-2024

Summary

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Official Symbol
MYSM1provided by HGNC
Official Full Name
Myb like, SWIRM and MPN domains 1provided by HGNC
Primary source
HGNC:HGNC:29401
See related
Ensembl:ENSG00000162601 MIM:612176; AllianceGenome:HGNC:29401
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
2ADUB; BMFS4; 2A-DUB
Summary
Enables histone binding activity; peptidase activity; and transcription coactivator activity. Involved in several processes, including chromatin remodeling; monoubiquitinated histone H2A deubiquitination; and positive regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. Part of protein-containing complex. Implicated in diabetic retinopathy. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 8.9), lymph node (RPKM 7.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1p32.1
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (58654743..58700062, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (58532658..58578032, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (59120415..59165734, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:59041692-59042387 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:59042388-59043082 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:59049763-59050962 Neighboring gene Sharpr-MPRA regulatory region 6655 Neighboring gene tumor associated calcium signal transducer 2 Neighboring gene Sharpr-MPRA regulatory region 14294 Neighboring gene adenylate kinase 2 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 3519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1087 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:59169902-59170744 Neighboring gene uncharacterized LOC112268263 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:59192522-59193721 Neighboring gene uncharacterized LOC124904191 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:59215043-59215253 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:59220674-59221873 Neighboring gene uncharacterized LOC105378751

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. [Deubiquitinase MYSM1 Regulates Differentiation of Human B Cells to Plasma Cells]. Zhong KL, et al. Zhongguo Shi Yan Xue Ye Xue Za Zhi, 2019 Oct. PMID 31607324
  2. Expression of MYSM1 is associated with tumor progression in colorectal cancer. Li Y, et al. PLoS One, 2017. PMID 28498834, Free PMC Article
  3. Myb-like, SWIRM, and MPN domains 1 (MYSM1) deficiency: Genotoxic stress-associated bone marrow failure and developmental aberrations. Bahrami E, et al. J Allergy Clin Immunol, 2017 Oct. PMID 28115216
  4. MYSM1 is mutated in a family with transient transfusion-dependent anemia, mild thrombocytopenia, and low NK- and B-cell counts. Alsultan A, et al. Blood, 2013 Nov 28. PMID 24288411
  5. Structural and functional differences of SWIRM domain subtypes. Yoneyama M, et al. J Mol Biol, 2007 May 25. PMID 17428495

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. MYSM1 attenuates DNA damage signals triggered by physiologic and genotoxic DNA breaks.
    Title: MYSM1 attenuates DNA damage signals triggered by physiologic and genotoxic DNA breaks.
  2. Deubiquitinase catalytic activity of MYSM1 is essential in vivo for hematopoiesis and immune cell development.
    Title: Deubiquitinase catalytic activity of MYSM1 is essential in vivo for hematopoiesis and immune cell development.
  3. MYSM1 inhibits human colorectal cancer tumorigenesis by activating miR-200 family members/CDH1 and blocking PI3K/AKT signaling.
    Title: MYSM1 inhibits human colorectal cancer tumorigenesis by activating miR-200 family members/CDH1 and blocking PI3K/AKT signaling.
  4. MYSM1 Represses Innate Immunity and Autoimmunity through Suppressing the cGAS-STING Pathway.
    Title: MYSM1 Represses Innate Immunity and Autoimmunity through Suppressing the cGAS-STING Pathway.
  5. Interaction of Deubiquitinase 2A-DUB/MYSM1 with DNA Repair and Replication Factors.
    Title: Interaction of Deubiquitinase 2A-DUB/MYSM1 with DNA Repair and Replication Factors.
  6. MYSM1-AR complex-mediated repression of Akt/c-Raf/GSK-3beta signaling impedes castration-resistant prostate cancer growth.
    Title: MYSM1-AR complex-mediated repression of Akt/c-Raf/GSK-3β signaling impedes castration-resistant prostate cancer growth.
  7. differentiation of B cells to plasma cells was inhibited after the overexpression of MYSM1
    Title: [Deubiquitinase MYSM1 Regulates Differentiation of Human B Cells to Plasma Cells].
  8. Data indicate a pathway MYSM1/miR-150/FLT3 that inhibits proliferation of B1a cells, which may be involved in the pathogenesis of systemic lupus erythematosus (SLE).
    Title: MYSM1/miR-150/FLT3 inhibits B1a cell proliferation.
  9. this study shows that MYSM1 deficiency is associated with developmental aberrations, progressive bone marrow failure with myelodysplastic features, and increased susceptibility to genotoxic stress
    Title: Myb-like, SWIRM, and MPN domains 1 (MYSM1) deficiency: Genotoxic stress-associated bone marrow failure and developmental aberrations.
  10. data suggested that expression of MYSM1 was associated with the progression of CRC and might be a potential biomarker for clinical prognosis
    Title: Expression of MYSM1 is associated with tumor progression in colorectal cancer.
Submit: New GeneRIF Correction See all GeneRIFs (14)

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

Associated conditions

Description Tests
Bone marrow failure syndrome 4
MedGen: C4748257 OMIM: 618116 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide association study of diabetic retinopathy in a Taiwanese population.
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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1915, DKFZp779J1554, DKFZp779J1721

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables histone H2A deubiquitinase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables metal-dependent deubiquitinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transcription coactivator activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in immune system process IEA
Inferred from Electronic Annotation
more info
  
involved_in pigmentation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cell migration IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of hair follicle development IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of hemopoiesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of protein-containing complex IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
deubiquitinase MYSM1
Names
histone H2A deubiquitinase MYSM1
myb-like, SWIRM and MPN domain-containing protein 1
NP_001078956.1
XP_006710377.1
XP_011538875.1
XP_011538876.1
XP_047299673.1
XP_047299674.1
XP_047299675.1
XP_047299676.1
XP_054190070.1
XP_054190071.1
XP_054190072.1
XP_054190073.1
XP_054190074.1
XP_054190075.1
XP_054190076.1

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.

Genomic

  1. NG_065323.2 RefSeqGene

    Range
    5016..50335
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1411

mRNA and Protein(s)

  1. NM_001085487.3 → NP_001078956.1  deubiquitinase MYSM1

    See identical proteins and their annotated locations for NP_001078956.1

    Status: VALIDATED

    Source sequence(s)
    AL035411, AL450024
    Consensus CDS
    CCDS41343.1
    UniProtKB/Swiss-Prot
    A8KA54, B3KX65, Q5VVJ2, Q68DD3, Q6AI53, Q7Z3G8, Q96PX3
    UniProtKB/TrEMBL
    A0A8V8TKW8
    Related
    ENSP00000418734.1, ENST00000472487.6
    Conserved Domains (4) summary
    cd08067
    Location:571 → 753
    MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase
    smart00717
    Location:120 → 164
    SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
    pfam00249
    Location:120 → 162
    Myb_DNA-binding; Myb-like DNA-binding domain
    pfam04433
    Location:382 → 461
    SWIRM; SWIRM domain

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
    58654743..58700062 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006710314.4 → XP_006710377.1  deubiquitinase MYSM1 isoform X1

    UniProtKB/TrEMBL
    A0A8V8TKW8
    Conserved Domains (4) summary
    cd08067
    Location:571 → 753
    MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase
    smart00717
    Location:120 → 164
    SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
    pfam00249
    Location:120 → 162
    Myb_DNA-binding; Myb-like DNA-binding domain
    pfam04433
    Location:382 → 461
    SWIRM; SWIRM domain

  2. XM_011540573.4 → XP_011538875.1  deubiquitinase MYSM1 isoform X2

    UniProtKB/TrEMBL
    A0A8V8TKW8
    Conserved Domains (4) summary
    cd08067
    Location:504 → 686
    MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase
    smart00717
    Location:53 → 97
    SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
    pfam00249
    Location:53 → 95
    Myb_DNA-binding; Myb-like DNA-binding domain
    pfam04433
    Location:315 → 394
    SWIRM; SWIRM domain

  3. XM_047443719.1 → XP_047299675.1  deubiquitinase MYSM1 isoform X4

  4. XM_047443717.1 → XP_047299673.1  deubiquitinase MYSM1 isoform X4

    Related
    ENST00000493821.6

  5. XM_011540574.3 → XP_011538876.1  deubiquitinase MYSM1 isoform X3

    UniProtKB/TrEMBL
    A0A8V8TKW8
    Conserved Domains (4) summary
    cd08067
    Location:482 → 664
    MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase
    smart00717
    Location:31 → 75
    SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
    pfam00249
    Location:31 → 73
    Myb_DNA-binding; Myb-like DNA-binding domain
    pfam04433
    Location:293 → 372
    SWIRM; SWIRM domain

  6. XM_047443718.1 → XP_047299674.1  deubiquitinase MYSM1 isoform X4

  7. XM_047443720.1 → XP_047299676.1  deubiquitinase MYSM1 isoform X5

    UniProtKB/TrEMBL
    A0A590UJW2
    Related
    ENSP00000499586.1, ENST00000665648.1

RNA

  1. XR_946533.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    58532658..58578032 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334095.1 → XP_054190070.1  deubiquitinase MYSM1 isoform X1

  2. XM_054334096.1 → XP_054190071.1  deubiquitinase MYSM1 isoform X2

  3. XM_054334100.1 → XP_054190075.1  deubiquitinase MYSM1 isoform X4

  4. XM_054334098.1 → XP_054190073.1  deubiquitinase MYSM1 isoform X4

  5. XM_054334097.1 → XP_054190072.1  deubiquitinase MYSM1 isoform X3

  6. XM_054334099.1 → XP_054190074.1  deubiquitinase MYSM1 isoform X4

  7. XM_054334101.1 → XP_054190076.1  deubiquitinase MYSM1 isoform X5

    UniProtKB/TrEMBL
    A0A590UJW2

RNA

  1. XR_008485893.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VVJ2.1 GenPept UniProtKB/Swiss-Prot:Q5VVJ2

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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