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

Summary

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
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Genomic context

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_007120.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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

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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

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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)

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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)

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

NC_007120.7 Reference GRCz11 Primary Assembly

Range

49905467..50001472 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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