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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 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

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