U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    scn1laa sodium channel, voltage-gated, type I-like, alpha [ Danio rerio (zebrafish) ]

    Gene ID: 393101, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    scn1laaprovided by ZNC
    Official Full Name
    sodium channel, voltage-gated, type I-like, alphaprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-751
    See related
    Ensembl:ENSDARG00000086819 AllianceGenome:ZFIN:ZDB-GENE-040426-751
    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
    scn1a; zscn8; Nav1.1; zgc:55600; unm_sa1674; zgc:158596
    Summary
    Contributes to voltage-gated sodium channel activity. Predicted to be involved in membrane depolarization during action potential; neuronal action potential; and sodium ion transmembrane transport. Predicted to act upstream of or within monoatomic ion transmembrane transport and sodium ion transport. Predicted to be located in plasma membrane. Predicted to be part of voltage-gated sodium channel complex. Predicted to be active in axon. Is expressed in heart; nervous system; and neural tube. Used to study Dravet syndrome. Human ortholog(s) of this gene implicated in Dravet syndrome; developmental and epileptic encephalopathy 6B; familial hemiplegic migraine 3; generalized epilepsy with febrile seizures plus; and generalized epilepsy with febrile seizures plus 2. Orthologous to several human genes including SCN7A (sodium voltage-gated channel alpha subunit 7). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See scn1laa in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (49905467..50001472, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (50208642..50304215, complement)

    Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene tetratricopeptide repeat domain 21B Neighboring gene uncharacterized LOC137496435 Neighboring gene solute carrier family 38 member 11 Neighboring gene cordon-bleu WH2 repeat protein-like 1b Neighboring gene growth factor receptor-bound protein 14

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. SCN1A overexpression, associated with a genomic region marked by a risk variant for a common epilepsy, raises seizure susceptibility. Silvennoinen K, et al. Acta Neuropathol, 2022 Jul. PMID 35551471, Free PMC Article
    2. Genetic and Functional Differences between Duplicated Zebrafish Genes for Human SCN1A. Weuring WJ, et al. Cells, 2022 Jan 28. PMID 35159264, Free PMC Article
    3. Developmental, molecular, and genetic dissection of INa in vivo in embryonic zebrafish sensory neurons. Pineda RH, et al. J Neurophysiol, 2005 Jun. PMID 15673553
    4. Molecular components underlying nongenomic thyroid hormone signaling in embryonic zebrafish neurons. Yonkers MA, et al. Neural Dev, 2009 Jun 8. PMID 19505305, Free PMC Article
    5. CRISPRa-Mediated Upregulation of scn1laa During Early Development Causes Epileptiform Activity and dCas9-Associated Toxicity. Weuring WJ, et al. CRISPR J, 2021 Aug. PMID 34406040

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SCN1A overexpression, associated with a genomic region marked by a risk variant for a common epilepsy, raises seizure susceptibility.
      Title: SCN1A overexpression, associated with a genomic region marked by a risk variant for a common epilepsy, raises seizure susceptibility.
    2. Genetic and Functional Differences between Duplicated Zebrafish Genes for Human SCN1A.
      Title: Genetic and Functional Differences between Duplicated Zebrafish Genes for Human SCN1A.
    Submit: New GeneRIF Correction

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC55600

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables monoatomic cation channel activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables monoatomic ion channel activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sodium channel activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables voltage-gated sodium channel activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    contributes_to voltage-gated sodium channel activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in membrane depolarization during action potential IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within monoatomic ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within monoatomic ion transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuronal action potential IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sodium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within sodium ion transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within 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
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of monoatomic ion channel complex 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
    		  
    part_of voltage-gated sodium channel complex IC
    Inferred by Curator
    more info
    		 PubMed 
    part_of voltage-gated sodium channel complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    sodium channel, voltage-gated, type I-like, alpha
    Names
    sodium channel, voltage-gated, type I, alpha subunit
    voltage-gated sodium channel type I alpha subunit Nav1.1La

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_200132.2 → NP_956426.2  sodium channel, voltage-gated, type I-like, alpha

      See identical proteins and their annotated locations for NP_956426.2

      Status: PROVISIONAL

      Source sequence(s)
      DQ149503
      UniProtKB/TrEMBL
      Q20JQ9
      Related
      ENSDARP00000138437.2, ENSDART00000170814.2
      Conserved Domains (5) summary
      cd13433
      Location:1430 → 1482
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:1184 → 1438
      Ion_trans; Ion transport protein
      pfam06512
      Location:972 → 1161
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:483 → 594
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:1752 → 1801
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated

    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_007120.7 Reference GRCz11 Primary Assembly

      Range
      49905467..50001472 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068223345.1 → XP_068079446.1  sodium channel, voltage-gated, type I-like, alpha isoform X2

    2. XM_017357661.3 → XP_017213150.1  sodium channel, voltage-gated, type I-like, alpha isoform X1

      UniProtKB/TrEMBL
      A0A0R4IQT2, A0A0R4IUM7, A0A8M6Z2I4
      Related
      ENSDARP00000137025.2, ENSDART00000161648.3
      Conserved Domains (5) summary
      cd13433
      Location:1430 → 1482
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:1184 → 1438
      Ion_trans; Ion transport protein
      pfam06512
      Location:972 → 1161
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:483 → 594
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:1752 → 1801
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.