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    Mysm1 myb-like, SWIRM and MPN domains 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 298247, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Mysm1provided by RGD
    Official Full Name
    myb-like, SWIRM and MPN domains 1provided by RGD
    Primary source
    RGD:1311787
    See related
    Ensembl:ENSRNOG00000026299 AllianceGenome:RGD:1311787
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1311787
    Summary
    Predicted to enable histone binding activity; peptidase activity; and transcription coactivator activity. Predicted to be involved in several processes, including chromatin remodeling; monoubiquitinated histone H2A deubiquitination; and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within pigmentation; regulation of cell migration; and regulation of hair follicle development. Predicted to be located in nucleolus and nucleoplasm. Predicted to be part of protein-containing complex. Human ortholog(s) of this gene implicated in diabetic retinopathy. Orthologous to human MYSM1 (Myb like, SWIRM and MPN domains 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Lung (RPKM 134.1), Thymus (RPKM 125.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    5q33
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (114877112..114981463, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (109761345..109826652, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (113902115..113939083, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene intraflagellar transport 74 Neighboring gene microRNA 872 Neighboring gene TEK receptor tyrosine kinase Neighboring gene equatorin Neighboring gene small nucleolar RNA SNORA70 Neighboring gene uncharacterized LOC120102921 Neighboring gene Jun proto-oncogene, AP-1 transcription factor subunit

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. An in vivo genetic reversion highlights the crucial role of Myb-Like, SWIRM, and MPN domains 1 (MYSM1) in human hematopoiesis and lymphocyte differentiation. Le Guen T, et al. J Allergy Clin Immunol, 2015 Dec. PMID 26220525
    2. The critical role of histone H2A-deubiquitinase Mysm1 in hematopoiesis and lymphocyte differentiation. Nijnik A, et al. Blood, 2012 Feb 9. PMID 22184403
    3. Genome-wide association study of diabetic retinopathy in a Taiwanese population. Huang YC, et al. Ophthalmology, 2011 Apr. PMID 21310492
    4. H2A-DUBbing the mammalian epigenome: expanding frontiers for histone H2A deubiquitinating enzymes in cell biology and physiology. Belle JI, et al. Int J Biochem Cell Biol, 2014 May. PMID 24647359
    5. A histone H2A deubiquitinase complex coordinating histone acetylation and H1 dissociation in transcriptional regulation. Zhu P, et al. Mol Cell, 2007 Aug 17. PMID 17707232, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2A deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal-dependent deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription coactivator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within pigmentation ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of cell migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of hair follicle development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of hemopoiesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    histone H2A deubiquitinase MYSM1; deubiquitinase MYSM1
    XP_006238471.1
    XP_008762133.1
    XP_008762134.1
    XP_008762135.1
    XP_008762136.1
    XP_038967035.1
    XP_038967037.1
    XP_038967038.1
    XP_063144649.1
    XP_063144650.1
    XP_063144651.1
    XP_063144652.1
    XP_063144653.1

    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_001428926.1 → NP_001415855.1  histone H2A deubiquitinase MYSM1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005

    2. NM_001428927.1 → NP_001415856.1  histone H2A deubiquitinase MYSM1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      114877112..114981463 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039111107.2 → XP_038967035.1  deubiquitinase MYSM1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6B5I6, D4A7T9
      Related
      ENSRNOP00000030043.4
      Conserved Domains (3) summary
      cd08067
      Location:554 → 736
      MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase
      pfam00249
      Location:116 → 160
      Myb_DNA-binding; Myb-like DNA-binding domain
      pfam04433
      Location:365 → 444
      SWIRM; SWIRM domain

    2. XM_063288579.1 → XP_063144649.1  deubiquitinase MYSM1 isoform X1

      UniProtKB/TrEMBL
      D4A7T9

    3. XM_008763911.4 → XP_008762133.1  deubiquitinase MYSM1 isoform X1

      See identical proteins and their annotated locations for XP_008762133.1

      UniProtKB/TrEMBL
      A0A8I6B5I6, D4A7T9
      Conserved Domains (3) summary
      cd08067
      Location:554 → 736
      MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase
      pfam00249
      Location:116 → 160
      Myb_DNA-binding; Myb-like DNA-binding domain
      pfam04433
      Location:365 → 444
      SWIRM; SWIRM domain

    4. XM_063288581.1 → XP_063144651.1  deubiquitinase MYSM1 isoform X6

    5. XM_008763914.3 → XP_008762136.1  deubiquitinase MYSM1 isoform X5

      See identical proteins and their annotated locations for XP_008762136.1

      UniProtKB/TrEMBL
      A0A8I6A9L8, A0A8I6B5I6
      Related
      ENSRNOP00000089875.1, ENSRNOT00000102038.1
      Conserved Domains (4) summary
      cd08067
      Location:546 → 728
      MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase
      smart00717
      Location:109 → 153
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      pfam00249
      Location:109 → 151
      Myb_DNA-binding; Myb-like DNA-binding domain
      pfam04433
      Location:357 → 436
      SWIRM; SWIRM domain

    6. XM_039111109.1 → XP_038967037.1  deubiquitinase MYSM1 isoform X4

      UniProtKB/TrEMBL
      A0A8I6B5I6
      Conserved Domains (3) summary
      cd08067
      Location:554 → 733
      MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase
      pfam00249
      Location:116 → 160
      Myb_DNA-binding; Myb-like DNA-binding domain
      pfam04433
      Location:365 → 444
      SWIRM; SWIRM domain

    7. XM_008763913.3 → XP_008762135.1  deubiquitinase MYSM1 isoform X3

      See identical proteins and their annotated locations for XP_008762135.1

      UniProtKB/TrEMBL
      A0A8I6B5I6
      Conserved Domains (4) summary
      cd08067
      Location:554 → 733
      MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase
      smart00717
      Location:117 → 161
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      pfam00249
      Location:117 → 159
      Myb_DNA-binding; Myb-like DNA-binding domain
      pfam04433
      Location:365 → 444
      SWIRM; SWIRM domain

    8. XM_008763912.3 → XP_008762134.1  deubiquitinase MYSM1 isoform X2

      See identical proteins and their annotated locations for XP_008762134.1

      UniProtKB/TrEMBL
      A0A8I6B5I6
      Conserved Domains (4) summary
      cd08067
      Location:554 → 736
      MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase
      smart00717
      Location:117 → 161
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      pfam00249
      Location:117 → 159
      Myb_DNA-binding; Myb-like DNA-binding domain
      pfam04433
      Location:365 → 444
      SWIRM; SWIRM domain

    9. XM_063288580.1 → XP_063144650.1  deubiquitinase MYSM1 isoform X1

      UniProtKB/TrEMBL
      D4A7T9

    10. XM_006238409.5 → XP_006238471.1  deubiquitinase MYSM1 isoform X7

      See identical proteins and their annotated locations for XP_006238471.1

      UniProtKB/TrEMBL
      A0A8I6B5I6
      Conserved Domains (4) summary
      cd08067
      Location:539 → 721
      MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase
      smart00717
      Location:102 → 146
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      pfam00249
      Location:102 → 144
      Myb_DNA-binding; Myb-like DNA-binding domain
      pfam04433
      Location:350 → 429
      SWIRM; SWIRM domain

    11. XM_063288582.1 → XP_063144652.1  deubiquitinase MYSM1 isoform X8

    12. XM_039111110.2 → XP_038967038.1  deubiquitinase MYSM1 isoform X9

      UniProtKB/TrEMBL
      A0A8I6B5I6
      Conserved Domains (3) summary
      cd08067
      Location:475 → 657
      MPN_2A_DUB; Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase
      pfam00249
      Location:37 → 81
      Myb_DNA-binding; Myb-like DNA-binding domain
      pfam04433
      Location:286 → 365
      SWIRM; SWIRM domain

    13. XM_063288583.1 → XP_063144653.1  deubiquitinase MYSM1 isoform X10

    Nucleotide Protein Strain
    Heading Accession and Version

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