SCN1A (sodium voltage-gated channel alpha subunit 1) - Rat Genome Database

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Gene: SCN1A (sodium voltage-gated channel alpha subunit 1) Sus scrofa
Analyze
Symbol: SCN1A
Name: sodium voltage-gated channel alpha subunit 1
RGD ID: 14158613
Description: ENCODES a protein that exhibits sodium ion binding (ortholog); voltage-gated sodium channel activity (ortholog); INVOLVED IN adult walking behavior (ortholog); determination of adult lifespan (ortholog); establishment of localization in cell (ortholog); ASSOCIATED WITH absence epilepsy (ortholog); asphyxiating thoracic dystrophy (ortholog); asphyxiating thoracic dystrophy 1 (ortholog); FOUND IN plasma membrane (ortholog); presynaptic membrane (ortholog); voltage-gated sodium channel complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: sodium channel protein type 1 subunit alpha; sodium channel protein type 1 subunit alpha pseudogene
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1572,529,875 - 72,678,066 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11572,529,866 - 72,696,715 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21581,177,412 - 81,188,630 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
absence epilepsy  (ISO)
asphyxiating thoracic dystrophy  (ISO)
asphyxiating thoracic dystrophy 1  (ISO)
autism spectrum disorder  (ISO)
autistic disorder  (ISO)
Autosomal Dominant Intellectual Developmental Disorder 64  (ISO)
autosomal dominant nocturnal frontal lobe epilepsy  (ISO)
benign epilepsy with centrotemporal spikes  (ISO)
benign familial infantile seizures 3  (ISO)
benign familial neonatal epilepsy  (ISO)
developmental and epileptic encephalopathy  (ISO)
developmental and epileptic encephalopathy 1  (ISO)
developmental and epileptic encephalopathy 11  (ISO)
developmental and epileptic encephalopathy 6B  (ISO)
developmental and epileptic encephalopathy 76  (ISO)
Developmental Disabilities  (ISO)
Dravet syndrome  (ISO)
early infantile epileptic encephalopathy  (ISO)
early myoclonic encephalopathy  (ISO)
epilepsy  (ISO)
epilepsy with generalized tonic-clonic seizures  (ISO)
familial febrile seizures 1  (ISO)
Familial Febrile Seizures 3A  (ISO)
familial hemiplegic migraine  (ISO)
familial hemiplegic migraine 3  (ISO)
Familial Sudden Death  (ISO)
Febrile Seizures  (ISO)
focal epilepsy  (ISO)
Generalized Epilepsy  (ISO)
generalized epilepsy with febrile seizures plus  (ISO)
generalized epilepsy with febrile seizures plus 1  (ISO)
generalized epilepsy with febrile seizures plus 2  (ISO)
generalized epilepsy with febrile seizures plus 7  (ISO)
genetic disease  (ISO)
hereditary sensory and autonomic neuropathy type 2A  (ISO)
hereditary sensory neuropathy  (ISO)
hereditary spastic paraplegia 11  (ISO)
Hip Contracture  (ISO)
Hypertelorism  (ISO)
intellectual disability  (ISO)
Lennox-Gastaut syndrome  (ISO)
microcephaly  (ISO)
movement disease  (ISO)
Muscle Hypotonia  (ISO)
Myoclonic Epilepsies  (ISO)
myoclonic-atonic epilepsy  (ISO)
nephronophthisis  (ISO)
nephronophthisis 1  (ISO)
Nervous System Malformations  (ISO)
Neurodevelopmental Disorders  (ISO)
Plagiocephaly  (ISO)
sudden infant death syndrome  (ISO)
Vision Disorders  (ISO)
West syndrome  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References
Additional References at PubMed
PMID:14681463   PMID:17145712   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
SCN1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1572,529,875 - 72,678,066 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11572,529,866 - 72,696,715 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21581,177,412 - 81,188,630 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCN1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382165,984,641 - 166,149,161 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2165,984,641 - 166,149,214 (-)EnsemblGRCh38hg38GRCh38
GRCh372166,841,151 - 167,005,671 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362166,553,916 - 166,638,395 (-)NCBINCBI36Build 36hg18NCBI36
Build 342166,673,232 - 166,755,638NCBI
Celera2160,455,660 - 160,540,161 (-)NCBICelera
Cytogenetic Map2q24.3NCBI
HuRef2158,727,062 - 158,886,965 (-)NCBIHuRef
CHM1_12166,851,977 - 167,011,835 (-)NCBICHM1_1
T2T-CHM13v2.02166,442,174 - 166,606,734 (-)NCBIT2T-CHM13v2.0
Scn1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39266,101,125 - 66,271,181 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl266,101,122 - 66,271,184 (-)EnsemblGRCm39 Ensembl
GRCm38266,270,781 - 66,440,837 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl266,270,778 - 66,440,840 (-)EnsemblGRCm38mm10GRCm38
MGSCv37266,108,839 - 66,278,894 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36266,071,621 - 66,241,676 (-)NCBIMGSCv36mm8
Celera267,950,131 - 68,119,920 (-)NCBICelera
Cytogenetic Map2C1.3NCBI
cM Map239.13NCBI
Scn1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8371,360,840 - 71,479,870 (-)NCBIGRCr8
mRatBN7.2350,952,790 - 51,071,804 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl350,952,791 - 51,071,699 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx354,295,423 - 54,414,933 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0362,879,049 - 62,998,545 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0360,659,682 - 60,779,082 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0352,388,811 - 52,533,365 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl352,381,975 - 52,510,507 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0359,016,641 - 59,135,580 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4348,238,528 - 48,364,143 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1348,134,899 - 48,260,515 (-)NCBI
Celera350,540,798 - 50,655,298 (-)NCBICelera
Cytogenetic Map3q21NCBI
Scn1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554498,160,986 - 8,221,951 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554498,072,910 - 8,220,763 (+)NCBIChiLan1.0ChiLan1.0
SCN1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21368,644,295 - 68,784,031 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B68,659,272 - 68,799,010 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B53,258,614 - 53,348,131 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B170,736,651 - 170,826,069 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B170,736,651 - 170,822,014 (-)Ensemblpanpan1.1panPan2
SCN1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13611,105,936 - 11,245,978 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3611,108,050 - 11,183,496 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3611,250,750 - 11,390,861 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03611,240,396 - 11,380,203 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3611,240,401 - 11,380,345 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13611,322,130 - 11,462,589 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03611,294,554 - 11,434,591 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03611,407,225 - 11,547,338 (-)NCBIUU_Cfam_GSD_1.0
Scn1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303128,271,735 - 128,421,841 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493646913,256,925 - 13,345,978 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493646913,194,769 - 13,345,979 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11051,490,204 - 51,653,916 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666040147,883,083 - 148,032,547 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scn1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247873,768,120 - 3,908,889 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247873,767,405 - 3,939,065 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SCN1A
3304 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system endocrine system musculoskeletal system nervous system reproductive system
High
Medium 20
Low 2 1 1 1
Below cutoff 8 2 1 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000017323   ⟹   ENSSSCP00000016859
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1572,529,875 - 72,678,066 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000045364   ⟹   ENSSSCP00000057874
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1572,529,875 - 72,678,066 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000053211   ⟹   ENSSSCP00000047835
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1572,529,875 - 72,678,066 (-)Ensembl
RefSeq Acc Id: XM_021076169   ⟹   XP_020931828
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11572,529,866 - 72,696,715 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021076170   ⟹   XP_020931829
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11572,529,868 - 72,678,079 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021076171   ⟹   XP_020931830
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11572,529,868 - 72,676,471 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021076172   ⟹   XP_020931831
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11572,529,866 - 72,696,715 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021076173   ⟹   XP_020931832
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11572,529,866 - 72,678,079 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021076174   ⟹   XP_020931833
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11572,529,868 - 72,696,715 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_020931831   ⟸   XM_021076172
- Peptide Label: isoform X2
- UniProtKB: A0A480KPT1 (UniProtKB/TrEMBL),   A0A4X1VLG4 (UniProtKB/TrEMBL),   A0A287AUP8 (UniProtKB/TrEMBL),   A0A4X1VLH2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020931828   ⟸   XM_021076169
- Peptide Label: isoform X1
- UniProtKB: A0A8D0ZZT5 (UniProtKB/TrEMBL),   A0A287BNX1 (UniProtKB/TrEMBL),   A0A8D1I6X2 (UniProtKB/TrEMBL),   A0A8D1ZD26 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020931832   ⟸   XM_021076173
- Peptide Label: isoform X2
- UniProtKB: A0A480KPT1 (UniProtKB/TrEMBL),   A0A4X1VLG4 (UniProtKB/TrEMBL),   A0A287AUP8 (UniProtKB/TrEMBL),   A0A4X1VLH2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020931833   ⟸   XM_021076174
- Peptide Label: isoform X3
- UniProtKB: A0A287AUP8 (UniProtKB/TrEMBL),   A0A4X1VLH2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020931829   ⟸   XM_021076170
- Peptide Label: isoform X1
- UniProtKB: A0A8D0ZZT5 (UniProtKB/TrEMBL),   A0A287BNX1 (UniProtKB/TrEMBL),   A0A8D1I6X2 (UniProtKB/TrEMBL),   A0A8D1ZD26 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020931830   ⟸   XM_021076171
- Peptide Label: isoform X1
- UniProtKB: A0A8D0ZZT5 (UniProtKB/TrEMBL),   A0A287BNX1 (UniProtKB/TrEMBL),   A0A8D1I6X2 (UniProtKB/TrEMBL),   A0A8D1ZD26 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000057874   ⟸   ENSSSCT00000045364
RefSeq Acc Id: ENSSSCP00000016859   ⟸   ENSSSCT00000017323
RefSeq Acc Id: ENSSSCP00000047835   ⟸   ENSSSCT00000053211
Protein Domains
Ion transport   Sodium ion transport-associated   Voltage-gated Na+ ion channel cytoplasmic


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000024204 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00030002454 UniProtKB/TrEMBL
  ENSSSCG00035045896 UniProtKB/TrEMBL
  ENSSSCG00040045561 UniProtKB/TrEMBL
  ENSSSCG00045025547 UniProtKB/TrEMBL
  ENSSSCG00050040194 UniProtKB/TrEMBL
  ENSSSCG00055026621 UniProtKB/TrEMBL
  ENSSSCG00065055901 UniProtKB/TrEMBL
  ENSSSCG00070025254 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000017323.5 UniProtKB/TrEMBL
  ENSSSCT00000045364 ENTREZGENE
  ENSSSCT00000045364.3 UniProtKB/TrEMBL
  ENSSSCT00000053211 ENTREZGENE
  ENSSSCT00000053211.3 UniProtKB/TrEMBL
  ENSSSCT00030003232.1 UniProtKB/TrEMBL
  ENSSSCT00030003274.1 UniProtKB/TrEMBL
  ENSSSCT00030003307.1 UniProtKB/TrEMBL
  ENSSSCT00035061042.1 UniProtKB/TrEMBL
  ENSSSCT00035061048.1 UniProtKB/TrEMBL
  ENSSSCT00035061056.1 UniProtKB/TrEMBL
  ENSSSCT00040061300.1 UniProtKB/TrEMBL
  ENSSSCT00040061698.1 UniProtKB/TrEMBL
  ENSSSCT00040061849.1 UniProtKB/TrEMBL
  ENSSSCT00040062061.1 UniProtKB/TrEMBL
  ENSSSCT00045043898.1 UniProtKB/TrEMBL
  ENSSSCT00045044206.1 UniProtKB/TrEMBL
  ENSSSCT00045044443.1 UniProtKB/TrEMBL
  ENSSSCT00050054371.1 UniProtKB/TrEMBL
  ENSSSCT00050054375.1 UniProtKB/TrEMBL
  ENSSSCT00050054378.1 UniProtKB/TrEMBL
  ENSSSCT00055052857.1 UniProtKB/TrEMBL
  ENSSSCT00055052964.1 UniProtKB/TrEMBL
  ENSSSCT00055053152.1 UniProtKB/TrEMBL
  ENSSSCT00065076580.1 UniProtKB/TrEMBL
  ENSSSCT00065076589.1 UniProtKB/TrEMBL
  ENSSSCT00065076595.1 UniProtKB/TrEMBL
  ENSSSCT00070050478.1 UniProtKB/TrEMBL
  ENSSSCT00070050481.1 UniProtKB/TrEMBL
  ENSSSCT00070050485.1 UniProtKB/TrEMBL
  ENSSSCT00070050487.1 UniProtKB/TrEMBL
  ENSSSCT00070050492.1 UniProtKB/TrEMBL
  ENSSSCT00070050497.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.70 UniProtKB/TrEMBL
  1.20.120.350 UniProtKB/TrEMBL
  EF-hand UniProtKB/TrEMBL
  iswi atpase UniProtKB/TrEMBL
InterPro Ion_trans_dom UniProtKB/TrEMBL
  Na_channel_a1su UniProtKB/TrEMBL
  Na_channel_asu UniProtKB/TrEMBL
  Na_chnl_inactivation_gate UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/TrEMBL
  Na_trans_cytopl UniProtKB/TrEMBL
  VGCC_Ca_Na UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/TrEMBL
NCBI Gene SCN1A ENTREZGENE
PANTHER PTHR10037 UniProtKB/TrEMBL
  SODIUM CHANNEL PROTEIN TYPE 1 SUBUNIT ALPHA UniProtKB/TrEMBL
Pfam Ion_trans UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/TrEMBL
  Na_trans_cytopl UniProtKB/TrEMBL
PRINTS NACHANNEL UniProtKB/TrEMBL
  NACHANNEL1 UniProtKB/TrEMBL
Superfamily-SCOP Voltage-gated potassium channels UniProtKB/TrEMBL
UniProt A0A287AUP8 ENTREZGENE, UniProtKB/TrEMBL
  A0A287BNX1 ENTREZGENE, UniProtKB/TrEMBL
  A0A480KPT1 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1VL07_PIG UniProtKB/TrEMBL
  A0A4X1VLG4 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1VLH2 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1VLI4_PIG UniProtKB/TrEMBL
  A0A4X1VNR3_PIG UniProtKB/TrEMBL
  A0A8D0V698_PIG UniProtKB/TrEMBL
  A0A8D0V6G6_PIG UniProtKB/TrEMBL
  A0A8D0V6H3_PIG UniProtKB/TrEMBL
  A0A8D0ZZT5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1ERU2_PIG UniProtKB/TrEMBL
  A0A8D1I6X2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1I7A8_PIG UniProtKB/TrEMBL
  A0A8D1IFH6_PIG UniProtKB/TrEMBL
  A0A8D1KCP7_PIG UniProtKB/TrEMBL
  A0A8D1KCU1_PIG UniProtKB/TrEMBL
  A0A8D1ZD26 ENTREZGENE, UniProtKB/TrEMBL
  B2M0Z5_PIG UniProtKB/TrEMBL
  F1RPM7_PIG UniProtKB/TrEMBL
VGNC ID VGNC:95478 ENTREZGENE