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

Gene ID: 310662, updated on 2-Nov-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
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 RNA splicing. Predicted to be located in nuclear speck. Predicted to be part of spliceosomal complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in orofaciodigital syndrome XIX. Orthologous to human SCNM1 (sodium channel modifier 1). [provided by Alliance of Genome Resources, Nov 2024]
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 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
    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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