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

    Gene ID: 69269, updated on 23-Jun-2021

    Summary

    Official Symbol
    Scnm1provided by MGI
    Official Full Name
    sodium channel modifier 1provided by MGI
    Primary source
    MGI:MGI:1341284
    See related
    Ensembl:ENSMUSG00000092607
    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
    Scnm; 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]
    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

    See Scnm1 in Genome Data Viewer
    Location:
    3 F2.1; 3 40.74 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (95037030..95041323, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (95129719..95134050, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 3 NC_000069.5 (94933641..94937934, 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 vacuolar protein sorting 72 Neighboring gene tropomodulin 4 Neighboring gene LysM, putative peptidoglycan-binding, domain containing 1 Neighboring gene microRNA 8099-1 Neighboring gene tumor necrosis factor, alpha-induced protein 8-like 2

    Genomic regions, transcripts, and products

    Expression

    • 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

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    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
    PubMed 
    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 
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    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
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    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_001163573.1NP_001157045.1  sodium channel modifier 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks the exon containing the stop codon compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK013948, BQ032998, BU756175
      Consensus CDS
      CCDS50986.1
      UniProtKB/Swiss-Prot
      Q8K136
      Related
      ENSMUSP00000133769.2, ENSMUST00000173462.3
      Conserved Domains (2) summary
      pfam15803
      Location:4470
      zf-SCNM1; Zinc-finger of sodium channel modifier 1
      pfam15805
      Location:119162
      SCNM1_acidic; Acidic C-terminal region of sodium channel modifier 1 SCNM1
    2. NM_027013.2NP_081289.2  sodium channel modifier 1 isoform 1

      See identical proteins and their annotated locations for NP_081289.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). The C-terminus of this isoform is truncated compared to that of the same variant in mouse strains not derived from C57BL6. This truncated isoform is not able to counteract the deleterious effects of the Scn8amedJ mutation whereas the longer isoform found in non-C57BL6 strains can partially overcome these effects.
      Source sequence(s)
      AK013948, BU756175
      Consensus CDS
      CCDS50987.1
      UniProtKB/Swiss-Prot
      Q8K136
      UniProtKB/TrEMBL
      A0A0R4J262
      Related
      ENSMUSP00000134337.2, ENSMUST00000172572.9
      Conserved Domains (1) summary
      pfam15803
      Location:4470
      zf-SCNM1; Zinc-finger of sodium channel modifier 1

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

    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..95041323 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017319716.3XP_017175205.1  sodium channel modifier 1 isoform X2

      Conserved Domains (1) summary
      pfam15803
      Location:4470
      zf-SCNM1; Zinc-finger of sodium channel modifier 1
    2. XM_017319715.3XP_017175204.1  sodium channel modifier 1 isoform X1

      Conserved Domains (1) summary
      pfam15803
      Location:4470
      zf-SCNM1; Zinc-finger of sodium channel modifier 1
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