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    scnm1 sodium channel modifier 1 [ Danio rerio (zebrafish) ]

    Gene ID: 321696, updated on 2-Nov-2024

    Summary

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    Official Symbol
    scnm1provided by ZNC
    Official Full Name
    sodium channel modifier 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-415
    See related
    Ensembl:ENSDARG00000003027 AllianceGenome:ZFIN:ZDB-GENE-030131-415
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    fb30c06; wu:fb30c06; zgc:123015
    Summary
    Predicted to enable metal ion binding activity. Predicted to be involved in alternative mRNA splicing, via spliceosome. Predicted to act upstream of or within mRNA processing. 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]
    Orthologs
    human all
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    Genomic context

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    See scnm1 in Genome Data Viewer
    Location:
    chromosome: 16
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 16 NC_007127.7 (29685557..29690188, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 16 NC_007127.6 (29750934..29755606, complement)

    Chromosome 16 - NC_007127.7Genomic Context describing neighboring genes Neighboring gene vacuolar protein sorting 72 homolog b Neighboring gene uncharacterized LOC137487915 Neighboring gene tropomodulin 4 (muscle) Neighboring gene LysM, putative peptidoglycan-binding, domain containing 1 Neighboring gene tumor necrosis factor, alpha-induced protein 8-like 2b

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. Sreenivasan R, et al. PLoS One, 2008 Mar 12. PMID 18335061, Free PMC Article
    2. Hematopoietic gene expression profile in zebrafish kidney marrow. Song HD, et al. Proc Natl Acad Sci U S A, 2004 Nov 16. PMID 15520368, Free PMC Article
    3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. 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

    Clone Names

    • MGC123015

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in alternative mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear speck ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    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_001001813.1 → NP_001001813.1  sodium channel modifier 1

      See identical proteins and their annotated locations for NP_001001813.1

      Status: PROVISIONAL

      Source sequence(s)
      AY398412
      UniProtKB/Swiss-Prot
      Q2YDS5
      Related
      ENSDARP00000118829.1, ENSDART00000132351.3
      Conserved Domains (2) summary
      pfam15803
      Location:42 → 67
      zf-SCNM1; Zinc-finger of sodium channel modifier 1
      pfam15805
      Location:196 → 241
      SCNM1_acidic; Acidic C-terminal region of sodium channel modifier 1 SCNM1

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007127.7 Reference GRCz11 Primary Assembly

      Range
      29685557..29690188 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005158161.5 → XP_005158218.1  sodium channel modifier 1 isoform X1

      See identical proteins and their annotated locations for XP_005158218.1

      UniProtKB/Swiss-Prot
      Q2YDS5, Q5BJD3, Q6TGU4
      Related
      ENSDARP00000026288.6, ENSDART00000004284.7
      Conserved Domains (2) summary
      pfam15803
      Location:44 → 69
      zf-SCNM1; Zinc-finger of sodium channel modifier 1
      pfam15805
      Location:198 → 243
      SCNM1_acidic; Acidic C-terminal region of sodium channel modifier 1 SCNM1
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2YDS5.1 GenPept UniProtKB/Swiss-Prot:Q2YDS5

    Gene LinkOut

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