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    Smchd1 structural maintenance of chromosomes flexible hinge domain containing 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 316732, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Smchd1provided by RGD
    Official Full Name
    structural maintenance of chromosomes flexible hinge domain containing 1provided by RGD
    Primary source
    RGD:1307234
    See related
    EnsemblRapid:ENSRNOG00000014319 AllianceGenome:RGD:1307234
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1307234
    Summary
    Predicted to enable ATP hydrolysis activity and protein homodimerization activity. Predicted to be involved in dosage compensation by inactivation of X chromosome; nose development; and regulation of double-strand break repair. Predicted to act upstream of or within inactivation of paternal X chromosome by genomic imprinting. Predicted to be located in chromosome, telomeric region and site of double-strand break. Predicted to be active in Barr body. Human ortholog(s) of this gene implicated in facioscapulohumeral muscular dystrophy 2. Orthologous to human SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 308.0), Spleen (RPKM 300.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Smchd1 in Genome Data Viewer
    Location:
    9q38
    Exon count:
    48
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (118690050..118837281, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (111243445..111387272, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (119675750..119818620, complement)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene lipin 2 Neighboring gene U7 small nuclear RNA Neighboring gene elastin microfibril interfacer 2 Neighboring gene Y box binding protein 1, pseudogene 8 Neighboring gene uncharacterized LOC134480432 Neighboring gene NDC80 kinetochore complex component Neighboring gene methyltransferase 4, N6-adenosine

    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. De novo mutations in SMCHD1 cause Bosma arhinia microphthalmia syndrome and abrogate nasal development. Gordon CT, et al. Nat Genet, 2017 Feb. PMID 28067911
    2. The epigenetic regulator Smchd1 contains a functional GHKL-type ATPase domain. Chen K, et al. Biochem J, 2016 Jun 15. PMID 27059856
    3. SMCHD1 accumulates at DNA damage sites and facilitates the repair of DNA double-strand breaks. Coker H, et al. J Cell Sci, 2014 May 1. PMID 24790221, Free PMC Article
    4. SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome. Shaw ND, et al. Nat Genet, 2017 Feb. PMID 28067909, Free PMC Article
    5. Structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) promotes non-homologous end joining and inhibits homologous recombination repair upon DNA damage. Tang M, et al. J Biol Chem, 2014 Dec 5. PMID 25294876, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein homodimerization 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 chromosome organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dosage compensation by inactivation of X chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within inactivation of paternal X chromosome by genomic imprinting ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of double-strand break repair via homologous recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nose development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Barr body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Barr body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromosome, telomeric region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    structural maintenance of chromosomes flexible hinge domain-containing protein 1

    NCBI Reference Sequences (RefSeq)

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    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_086027.1 Reference GRCr8

      Range
      118690050..118837281 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063267939.1 → XP_063124009.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1

      Related
      ENSRNOP00000083499.2, ENSRNOT00000102031.2
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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