Scn1b sodium voltage-gated channel beta subunit 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Scn1bprovided by RGD
Official Full Name: sodium voltage-gated channel beta subunit 1provided by RGD
Primary source: RGD:3631
See related: EnsemblRapid:ENSRNOG00000021102 AllianceGenome:RGD:3631
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables sodium channel regulator activity. Involved in regulation of voltage-gated sodium channel activity and response to pyrethroid. Located in node of Ranvier and plasma membrane. Part of voltage-gated sodium channel complex. Biomarker of type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in Brugada syndrome 5; developmental and epileptic encephalopathy 52; familial atrial fibrillation; and generalized epilepsy with febrile seizures plus 1. Orthologous to human SCN1B (sodium voltage-gated channel beta subunit 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Muscle (RPKM 1959.3), Brain (RPKM 716.3) and 2 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q21

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (95481298..95491211, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (86353917..86363820, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (89550738..89560469, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The relationship between miRNA-210 and SCN1B in fetal rats with hypoxic-ischemic brain injury.
Title: The relationship between miRNA-210 and SCN1B in fetal rats with hypoxic-ischemic brain injury.
Nav1.1 and Nav1.2 are highly expressed in axon terminals in central hilus compared to stratum radiatum and in dendrites and spines in stratum radiatum compared to central hilus
Title: Sodium channel subtypes are differentially localized to pre- and post-synaptic sites in rat hippocampus.
the role of the intracellular IFM motif of rNav1.4 (skeletal muscle isoform of the rat Na(+) channel) on the alpha-beta1 functional interaction
Title: Characterization of specific allosteric effects of the Na(+) channel β1 subunit on the Na(v)1.4 isoform.
the presences of Nav1.1, Nav1.6, Navbeta1 and Navbeta3 mRNA and their reduced levels in rat SAN during aging.
Title: Age-dependent alterations of voltage-gated Na(+) channel isoforms in rat sinoatrial node.
The beta1 subunit silencing reduced the expression of Nav1.1, Nav1.3 and Nav1.6 isoforms, whereas the Nav 1.2 isoform expression remained unaltered.
Title: Antisense-mediated post-transcriptional silencing of SCN1B gene modulates sodium channel functional expression.
the existence of the putative disulfide bridge in the Ig-like extracellular domain of the beta1 subunit and its disruption in the epileptogenic C121W mutant was demonstrated.
Title: Identification of an intra-molecular disulfide bond in the sodium channel β1-subunit.
Wild-type (WT) NaVbeta1 subunit is protective against increased channel excitability of seizure-causing mechanism induced by elevated temperature; protection is lost in the absence of WT beta1 subunit or with expression of beta1 (Cys121Trp) mutation.
Title: A thermoprotective role of the sodium channel β1 subunit is lost with the β1 (C121W) mutation.
Gene silencing also produces a reduction in potassiun channel interacting protein 2(KChIP2) messenger RNA and protein as well as potassium channels.
Title: Post-transcriptional gene silencing of KChIP2 and Navbeta1 in neonatal rat cardiac myocytes reveals a functional association between Na and Ito currents.
that sodium channel Na(v)1.1, Na(v)1.3 and beta(1) subunit up-regulation at the mRNA and protein levels of SER hippocampus might contribute to the generation of epileptiform activity and underlie the observed seizure phenotype in SER.
Title: Voltage-gated sodium channel Nav1.1, Nav1.3 and beta1 subunit were up-regulated in the hippocampus of spontaneously epileptic rat.
Sodium channel beta1 subunits promote neurite outgrowth in cerebellar granule neurons
Title: Sodium channel beta1 subunits promote neurite outgrowth in cerebellar granule neurons.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Scn1b (e-PCR), detects polymorphism
- UniSTS:516637

Scn1b (e-PCR), detects polymorphism
- UniSTS:472869

PMC15797P1 (e-PCR)
- UniSTS:271432

U85786 (e-PCR)
- UniSTS:159622

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sodium channel inhibitor activity	IBA Inferred from Biological aspect of Ancestor more info
enables sodium channel inhibitor activity	IEA Inferred from Electronic Annotation more info
enables sodium channel inhibitor activity	ISO Inferred from Sequence Orthology more info
enables sodium channel regulator activity	IDA Inferred from Direct Assay more info	PubMed
NOT enables sodium channel regulator activity	ISO Inferred from Sequence Orthology more info
enables sodium channel regulator activity	ISO Inferred from Sequence Orthology more info
enables transmembrane transporter binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within axon guidance	ISO Inferred from Sequence Orthology more info
involved_in cardiac conduction	ISO Inferred from Sequence Orthology more info
involved_in cardiac muscle cell action potential involved in contraction	IBA Inferred from Biological aspect of Ancestor more info
involved_in cardiac muscle cell action potential involved in contraction	IEA Inferred from Electronic Annotation more info
involved_in cardiac muscle cell action potential involved in contraction	ISO Inferred from Sequence Orthology more info
involved_in cardiac muscle contraction	ISO Inferred from Sequence Orthology more info
involved_in corticospinal neuron axon guidance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within corticospinal neuron axon guidance	ISO Inferred from Sequence Orthology more info
involved_in locomotion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within locomotion	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during Purkinje myocyte cell action potential	IEA Inferred from Electronic Annotation more info
involved_in membrane depolarization during Purkinje myocyte cell action potential	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during action potential	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during cardiac muscle cell action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in membrane depolarization during cardiac muscle cell action potential	ISO Inferred from Sequence Orthology more info
acts_upstream_of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in neuronal action potential propagation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuronal action potential propagation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron projection development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of sodium ion transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of sodium ion transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of voltage-gated sodium channel activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of voltage-gated sodium channel activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of atrial cardiac muscle cell membrane depolarization	IEA Inferred from Electronic Annotation more info
involved_in regulation of atrial cardiac muscle cell membrane depolarization	ISO Inferred from Sequence Orthology more info
involved_in regulation of heart rate by cardiac conduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of heart rate by cardiac conduction	IEA Inferred from Electronic Annotation more info
involved_in regulation of heart rate by cardiac conduction	ISO Inferred from Sequence Orthology more info
involved_in regulation of sodium ion transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in regulation of sodium ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of sodium ion transport	ISO Inferred from Sequence Orthology more info
involved_in regulation of ventricular cardiac muscle cell membrane repolarization	IEA Inferred from Electronic Annotation more info
involved_in regulation of ventricular cardiac muscle cell membrane repolarization	ISO Inferred from Sequence Orthology more info
involved_in regulation of voltage-gated sodium channel activity	IDA Inferred from Direct Assay more info	PubMed
involved_in response to pyrethroid	IDA Inferred from Direct Assay more info	PubMed
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in sodium ion transmembrane transport	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in T-tubule	IEA Inferred from Electronic Annotation more info
located_in T-tubule	ISO Inferred from Sequence Orthology more info
located_in intercalated disc	IEA Inferred from Electronic Annotation more info
located_in intercalated disc	ISO Inferred from Sequence Orthology more info
located_in node of Ranvier	IDA Inferred from Direct Assay more info	PubMed
located_in node of Ranvier	IEA Inferred from Electronic Annotation more info
located_in node of Ranvier	ISO Inferred from Sequence Orthology more info
located_in perikaryon	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	TAS Traceable Author Statement more info
part_of sodium channel complex	ISO Inferred from Sequence Orthology 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	IDA Inferred from Direct Assay more info	PubMed
part_of voltage-gated sodium channel complex	IEA Inferred from Electronic Annotation more info
part_of voltage-gated sodium channel complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: sodium channel regulatory subunit beta-1; sodium channel subunit beta-1

Names: sodium channel, voltage-gated, type 1, beta polypeptide; sodium channel, voltage-gated, type I, beta polypeptide; sodium channel, voltage-gated, type I, beta subunit

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_001271045.2 → NP_001257974.1 sodium channel regulatory subunit beta-1 isoform 1 precursor

See identical proteins and their annotated locations for NP_001257974.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) and variant 2 encode the longer isoform (1).

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

Q00954, Q505J0

UniProtKB/TrEMBL

A0A0G2JXY6, A6JA73

Conserved Domains (2) summary

pfam07686
Location:23 → 147

V-set; Immunoglobulin V-set domain

cd00096
Location:26 → 32

Ig; Ig strand A' [structural motif]
NM_001271046.2 → NP_001257975.1 sodium channel regulatory subunit beta-1 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (3) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A0A0G2JXY6

Related

ENSRNOP00000070450.2, ENSRNOT00000092133.3

Conserved Domains (2) summary

cd00096
Location:22 → 25

Ig; Ig strand C [structural motif]

pfam07686
Location:8 → 114

V-set; Immunoglobulin V-set domain
NM_017288.3 → NP_058984.1 sodium channel regulatory subunit beta-1 isoform 1 precursor

See identical proteins and their annotated locations for NP_058984.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an internal segment in the 3' UTR, compared to variant 1. Both variants 1 and 2 encode the same isoform (1).

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

Q00954, Q505J0

UniProtKB/TrEMBL

A0A0G2JXY6, A6JA73

Related

ENSRNOP00000028653.2, ENSRNOT00000028653.7

Conserved Domains (2) summary

pfam07686
Location:23 → 147

V-set; Immunoglobulin V-set domain

cd00096
Location:26 → 32

Ig; Ig strand A' [structural motif]