U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 114803, updated on 26-Nov-2024

    Summary

    Go to the top of the page Help
    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 deubiquitinase activity; histone binding activity; and transcription coactivator activity. Involved in chromatin remodeling; positive regulation of transcription by RNA polymerase II; and regulation of hemopoiesis. Located in nucleolus and nucleoplasm. Part of protein-containing complex. Implicated in diabetic retinopathy. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 8.9), lymph node (RPKM 7.4) and 25 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See MYSM1 in Genome Data Viewer
    Location:
    1p32.1
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (58654743..58700062, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (58532658..58578032, complement)
    RS_2024_09 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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. MYSM1 attenuates DNA damage signals triggered by physiologic and genotoxic DNA breaks. Mathias B, et al. J Allergy Clin Immunol, 2024 Apr. PMID 38065233, Free PMC Article
    2. Structural and functional differences of SWIRM domain subtypes. Yoneyama M, et al. J Mol Biol, 2007 May 25. PMID 17428495
    3. 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
    4. 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
    5. [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

    See all (40) 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

    Go to the top of the page Help

    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
    		Compare labs

    EBI GWAS Catalog

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

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    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

    Go to the top of the page Help
    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)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_2024_08

    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.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous