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    Scnm1 sodium channel modifier 1 [ Mus musculus (house mouse) ]

    Gene ID: 69269, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Scnm1provided by MGI
    Official Full Name
    sodium channel modifier 1provided by MGI
    Primary source
    MGI:MGI:1341284
    See related
    AllianceGenome:MGI:1341284
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Scnm1-ps; 3110001I17Rik
    Summary
    Mutations in the voltage-gated sodium channel gene Scn8a lead to neurological problems in mice. For one particular mutation, Scn8amedJ, mice live to adulthood but have tremors and muscle weakness, among other problems, in all strains except those derived from C57BL6 mice. In these strains, the product of the Scnm1 gene (229 aa) partially overcomes the effects of the Scn8amedJ mutation. However, in C57BL6-derived mice, a one nt change in the penultimate exon creates a premature stop codon, truncating the Scnm1 protein at 186 aa. This truncated protein lacks the ability to overcome the effects of the Scn8amedJ mutation, and these mice suffer paralysis and juvenile death. [provided by RefSeq, Jul 2009]
    Annotation information
    Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 24.1), CNS E14 (RPKM 23.1) and 28 other tissues See more
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    Genomic context

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    See Scnm1 in Genome Data Viewer
    Location:
    3 F2.1; 3 40.74 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (95037030..95041285, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (95129719..95134050, complement)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol-4-phosphate 5-kinase, type 1 alpha Neighboring gene predicted gene, 22301 Neighboring gene STARR-seq mESC enhancer starr_08367 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:94914795-94915038 Neighboring gene vacuolar protein sorting 72 Neighboring gene tropomodulin 4 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:94937828-94938011 Neighboring gene LysM, putative peptidoglycan-binding, domain containing 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:94945477-94945712 Neighboring gene microRNA 8099-1 Neighboring gene tumor necrosis factor, alpha-induced protein 8-like 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Molecular and pathological effects of a modifier gene on deficiency of the sodium channel Scn8a (Na(v)1.6). Kearney JA, et al. Hum Mol Genet, 2002 Oct 15. PMID 12374766
    2. High-resolution mapping of the sodium channel modifier Scnm1 on mouse chromosome 3 and identification of a 1.3-kb recombination hot spot. Buchner DA, et al. Genomics, 2003 Oct. PMID 13679025
    3. A targeted deleterious allele of the splicing factor SCNM1 in the mouse. Howell VM, et al. Genetics, 2008 Nov. PMID 18791226, Free PMC Article
    4. Behavioral audiograms of homozygous med(J) mutant mice with sodium channel deficiency and unaffected controls. Koay G, et al. Hear Res, 2002 Sep. PMID 12204355
    5. SCNM1, a putative RNA splicing factor that modifies disease severity in mice. Buchner DA, et al. Science, 2003 Aug 15. PMID 12920299

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables enzyme binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA splicing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within RNA splicing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in alternative mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    sodium channel modifier 1
    Names
    sodium channel modifier 1, pseudogene

    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_001409852.1 → NP_001396781.1  sodium channel modifier 1

      Status: VALIDATED

      Source sequence(s)
      BC028867
      UniProtKB/Swiss-Prot
      Q8K136, Q9CXV5

    RNA

    1. NR_176904.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC131769

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000069.7 Reference GRCm39 C57BL/6J

      Range
      95037030..95041285 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001163573.1: Suppressed sequence

      Description
      NM_001163573.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

    2. NM_001406472.1: Suppressed sequence

      Description
      NM_001406472.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

    3. NM_001406473.1: Suppressed sequence

      Description
      NM_001406473.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

    4. NM_001406474.1: Suppressed sequence

      Description
      NM_001406474.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

    5. NM_001406475.1: Suppressed sequence

      Description
      NM_001406475.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

    6. NM_001406476.1: Suppressed sequence

      Description
      NM_001406476.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

    7. NM_001406486.1: Suppressed sequence

      Description
      NM_001406486.1: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.

    8. NM_027013.3: Suppressed sequence

      Description
      NM_027013.3: This RefSeq was removed because it is now thought that this gene is a polymorphic pseudogene.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8K136.1 GenPept UniProtKB/Swiss-Prot:Q8K136

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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