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Scn9a sodium channel, voltage-gated, type IX, alpha [ Mus musculus (house mouse) ]

Gene ID: 20274, updated on 29-Jun-2021

Summary

Official Symbol
Scn9aprovided by MGI
Official Full Name
sodium channel, voltage-gated, type IX, alphaprovided by MGI
Primary source
MGI:MGI:107636
See related
Ensembl:ENSMUSG00000075316
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
P; PN1; Nav1.7; mKIAA4197
Expression
Biased expression in CNS E18 (RPKM 4.9), whole brain E14.5 (RPKM 3.0) and 6 other tissues See more
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Genomic context

See Scn9a in Genome Data Viewer
Location:
2 C1.3; 2 39.13 cM
Exon count:
29
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (66310424..66465456, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (66480080..66635114, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (66318137..66473009, complement)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene sodium channel, voltage-gated, type I, alpha Neighboring gene predicted gene 13630 Neighboring gene ribosomal protein L35, pseudogene 1 Neighboring gene predicted gene 13629 Neighboring gene predicted gene, 35265 Neighboring gene sodium channel, voltage-gated, type VII, alpha Neighboring gene predicted gene 13600

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (6)  1 citation
  • Endonuclease-mediated (2) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA4197

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables cation channel activity IEA
Inferred from Electronic Annotation
more info
 
enables ion channel activity IEA
Inferred from Electronic Annotation
more info
 
enables sodium channel activity IEA
Inferred from Electronic Annotation
more info
 
enables sodium ion binding ISO
Inferred from Sequence Orthology
more info
 
enables voltage-gated ion channel activity IEA
Inferred from Electronic Annotation
more info
 
enables voltage-gated sodium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables voltage-gated sodium channel activity ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within behavioral response to pain IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within inflammatory response IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within ion transport IEA
Inferred from Electronic Annotation
more info
 
involved_in ion transport IEA
Inferred from Electronic Annotation
more info
 
involved_in membrane depolarization during action potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in neuronal action potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in neuronal action potential ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within post-embryonic development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within regulation of ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within response to toxic substance IDA
Inferred from Direct Assay
more info
PubMed 
involved_in sensory perception of pain ISO
Inferred from Sequence Orthology
more info
 
involved_in sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in sodium ion transmembrane transport ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within sodium ion transport IEA
Inferred from Electronic Annotation
more info
 
involved_in sodium ion transport IEA
Inferred from Electronic Annotation
more info
 
involved_in transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in axon ISO
Inferred from Sequence Orthology
more info
 
located_in cell projection IEA
Inferred from Electronic Annotation
more info
 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
located_in integral component of plasma membrane ISO
Inferred from Sequence Orthology
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
 
part_of voltage-gated sodium channel complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of voltage-gated sodium channel complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
sodium channel protein type 9 subunit alpha
Names
peripheral sodium channel 1
sodium channel 25
sodium channel, voltage-gated, type IX, alpha polypeptide
voltage-gated sodium channel Nav1.7 variant a
voltage-gated sodium channel Nav1.7 variant b
voltage-gated sodium channel alpha subunit Nav1.7

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_001290674.1NP_001277603.1  sodium channel protein type 9 subunit alpha isoform a

    See identical proteins and their annotated locations for NP_001277603.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AK141871, AL928623, AL928726, BP765553
    Consensus CDS
    CCDS71063.1
    UniProtKB/Swiss-Prot
    Q62205
    Related
    ENSMUSP00000097642.3, ENSMUST00000100064.9
    Conserved Domains (5) summary
    cd13433
    Location:14561508
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12241464
    Ion_trans; Ion transport protein
    pfam06512
    Location:9811185
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:487606
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17801835
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  2. NM_001290675.1NP_001277604.1  sodium channel protein type 9 subunit alpha isoform b

    See identical proteins and their annotated locations for NP_001277604.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon but contains an alternate in-frame exon in the 5' coding region, and also contains an alternate in-frame splice site in the central coding region, compared to variant 1. The resulting isoform (b) is shorter than isoform a.
    Source sequence(s)
    AK141871, AL928623, AL928726, BP765553
    UniProtKB/TrEMBL
    E9PW82
    Related
    ENSMUSP00000131711.2, ENSMUST00000169900.8
    Conserved Domains (5) summary
    cd13433
    Location:14451497
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12131453
    Ion_trans; Ion transport protein
    pfam06512
    Location:9701174
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:487606
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17691824
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated

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_000068.8 Reference GRCm39 C57BL/6J

    Range
    66310424..66465456 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006499033.5XP_006499096.1  sodium channel protein type 9 subunit alpha isoform X1

    Conserved Domains (5) summary
    cd13433
    Location:14561508
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11891464
    Ion_trans; Ion transport protein
    pfam06512
    Location:9811185
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488693
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17801827
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  2. XM_006499035.5XP_006499098.1  sodium channel protein type 9 subunit alpha isoform X2

    See identical proteins and their annotated locations for XP_006499098.1

    UniProtKB/TrEMBL
    B1AYL0
    Related
    ENSMUSP00000107973.2, ENSMUST00000112354.3
    Conserved Domains (5) summary
    cd13433
    Location:14451497
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11781453
    Ion_trans; Ion transport protein
    pfam06512
    Location:9701174
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488682
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17691816
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated

RNA

  1. XR_001781564.3 RNA Sequence

  2. XR_374432.5 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_018852.2: Suppressed sequence

    Description
    NM_018852.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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