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    Scnm1 sodium channel modifier 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 310662, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Scnm1provided by RGD
    Official Full Name
    sodium channel modifier 1provided by RGD
    Primary source
    RGD:1308968
    See related
    Ensembl:ENSRNOG00000021092 AllianceGenome:RGD:1308968
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable enzyme binding activity. Predicted to be involved in alternative mRNA splicing, via spliceosome. Predicted to be located in nuclear speck. Predicted to be active in nucleus. Orthologous to human SCNM1 (sodium channel modifier 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Kidney (RPKM 110.8), Muscle (RPKM 76.7) and 9 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Scnm1 in Genome Data Viewer
    Location:
    2q34
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (185389892..185394126, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (182700883..182705119, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (196300239..196304419, complement)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene vacuolar protein sorting 72 homolog Neighboring gene tropomodulin 4 Neighboring gene LysM domain containing 1 Neighboring gene TNF alpha induced protein 8 like 2 Neighboring gene semaphorin 6C Neighboring gene uncharacterized LOC120100877

    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. SCNM1, a putative RNA splicing factor that modifies disease severity in mice. Buchner DA, et al. Science, 2003 Aug 15. PMID 12920299
    2. Evidence for a direct role of the disease modifier SCNM1 in splicing. Howell VM, et al. Hum Mol Genet, 2007 Oct 15. PMID 17656373
    3. A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex. Armour SM, et al. Mol Cell Biol, 2013 Apr. PMID 23382074, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    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
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    sodium channel modifier 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_001107696.1 → NP_001101166.1  sodium channel modifier 1

      See identical proteins and their annotated locations for NP_001101166.1

      Status: PROVISIONAL

      Source sequence(s)
      CH474015
      UniProtKB/TrEMBL
      A0A8I5ZU22, A6K2U8, A6K2U9, D3ZSG1
      Related
      ENSRNOP00000028639.5, ENSRNOT00000028639.6
      Conserved Domains (2) summary
      pfam15803
      Location:44 → 70
      zf-SCNM1; Zinc-finger of sodium channel modifier 1
      pfam15805
      Location:182 → 227
      SCNM1_acidic; Acidic C-terminal region of sodium channel modifier 1 SCNM1

    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_086020.1 Reference GRCr8

      Range
      185389892..185394126 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006232882.5 → XP_006232944.1  sodium channel modifier 1 isoform X1

      See identical proteins and their annotated locations for XP_006232944.1

      Conserved Domains (2) summary
      pfam15803
      Location:9 → 35
      zf-SCNM1; Zinc-finger of sodium channel modifier 1
      pfam15805
      Location:147 → 192
      SCNM1_acidic; Acidic C-terminal region of sodium channel modifier 1 SCNM1

    2. XM_006232883.5 → XP_006232945.1  sodium channel modifier 1 isoform X1

      See identical proteins and their annotated locations for XP_006232945.1

      Conserved Domains (2) summary
      pfam15803
      Location:9 → 35
      zf-SCNM1; Zinc-finger of sodium channel modifier 1
      pfam15805
      Location:147 → 192
      SCNM1_acidic; Acidic C-terminal region of sodium channel modifier 1 SCNM1
    Nucleotide Protein Strain
    Heading Accession and Version

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