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

Gene ID: 298247, updated on 2-Nov-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
EnsemblRapid: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 deubiquitinase activity; histone binding activity; and transcription coactivator activity. Predicted to be involved in chromatin remodeling; positive regulation of transcription by RNA polymerase II; and regulation of hemopoiesis. 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, Nov 2024]
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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See Mysm1 in Genome Data Viewer
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 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 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
    UniProtKB/TrEMBL
    D4A7T9

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

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000005
    UniProtKB/TrEMBL
    A0A8I6A9L8

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
    ENSRNOP00000030043.5, ENSRNOT00000039554.8
    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
    ENSRNOP00000097255.2, ENSRNOT00000119743.2
    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

  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
    Related
    ENSRNOP00000112470.1, ENSRNOT00000124137.1
    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
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