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

Gene ID: 316732, updated on 11-Apr-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
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 protein homodimerization activity. Predicted to be involved in inactivation of X chromosome by heterochromatin assembly; nose development; and regulation of double-strand break repair. Predicted to act upstream of or within dosage compensation by inactivation of X chromosome. Predicted to be located in site of double-strand break. Predicted to be active in Barr body. Predicted to colocalize with chromosome, telomeric region. 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, Apr 2022]
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

Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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