Scn1a (sodium voltage-gated channel alpha subunit 1) - Rat Genome Database

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Gene: Scn1a (sodium voltage-gated channel alpha subunit 1) Rattus norvegicus
Analyze
Symbol: Scn1a
Name: sodium voltage-gated channel alpha subunit 1
RGD ID: 69364
Description: Enables voltage-gated sodium channel activity. Involved in neuronal action potential. Is active in presynaptic membrane. 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 human SCN1A (sodium voltage-gated channel alpha subunit 1); INTERACTS WITH 1-bromopropane; 1-naphthyl isothiocyanate; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC102553713; sodium channel protein brain I subunit alpha; sodium channel protein type 1 subunit alpha; sodium channel protein type 1 subunit alpha-like; sodium channel protein type I subunit alpha; sodium channel protein, brain I subunit alpha; sodium channel voltage-gated type I alpha polypeptide; sodium channel, voltage-gated, type 1, alpha polypeptide; sodium channel, voltage-gated, type I, alpha; sodium channel, voltage-gated, type I, alpha polypeptide; sodium channel, voltage-gated, type I, alpha subunit; voltage-gated sodium channel subunit alpha Nav1.1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: Scn1am1Kyo ; Scn1am2Kyo
Genetic Models: F344-Scn1am1Kyo ; F344-Scn1am2Kyo
Is Marker For: Strains:   F344.NER-(D1Mgh6-D1Rat73)(D5Mgh4-D5Rat36)Scn1am1/Kyo
Candidate Gene For: Alc19
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8371,360,840 - 71,479,870 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl371,360,841 - 71,479,791 (-)EnsemblGRCr8
mRatBN7.2350,952,790 - 51,071,804 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl350,952,791 - 51,071,699 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx354,295,423 - 54,414,933 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0362,879,049 - 62,998,545 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0360,659,682 - 60,779,082 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0352,388,811 - 52,533,365 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl352,381,975 - 52,510,507 (-)Ensemblrn6Rnor6.0
Rnor_5.0359,016,641 - 59,135,580 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4348,238,528 - 48,364,143 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera350,540,798 - 50,655,298 (-)NCBICelera
RGSC_v3.1348,134,899 - 48,260,515 (-)NCBI
Cytogenetic Map3q21NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene  (ISO)
1-bromopropane  (EXP)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4,4'-trichlorobiphenyl  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-nitrophenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alpha-Zearalanol  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (EXP)
azathioprine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cypermethrin  (ISO)
D-glucose  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP)
endosulfan  (ISO)
entinostat  (ISO)
ethanol  (ISO)
fulvestrant  (ISO)
glucose  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
nickel atom  (ISO)
PCB138  (EXP,ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (EXP)
phenytoin  (ISO)
quercetin  (ISO)
razoxane  (EXP)
rotenone  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sodium disulfite  (EXP)
sulforaphane  (ISO)
tacrine  (EXP)
trichostatin A  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc atom  (EXP)
zinc sulfate  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Downregulation of neuronal sodium channel subunits Nav1.1 and Nav1.6 in the sinoatrial node from volume-overloaded heart failure rat. Du Y, etal., Pflugers Arch. 2007 Jun;454(3):451-9. Epub 2007 Feb 2.
2. Mutations of SCN1A, encoding a neuronal sodium channel, in two families with GEFS+2. Escayg A, etal., Nat Genet 2000 Apr;24(4):343-5.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Autosomal dominant epilepsy with febrile seizures plus with missense mutations of the (Na+)-channel alpha 1 subunit gene, SCN1A. Ito M, etal., Epilepsy Res 2002 Jan;48(1-2):15-23.
6. A missense mutation of the gene encoding voltage-dependent sodium channel (Nav1.1) confers susceptibility to febrile seizures in rats. Mashimo T, etal., J Neurosci. 2010 Apr 21;30(16):5744-53. doi: 10.1523/JNEUROSCI.3360-09.2010.
7. Molecular diversity of voltage-gated sodium channel alpha subunits expressed in neuronal and non-neuronal excitable cells. Mechaly I, etal., Neuroscience. 2005;130(2):389-96.
8. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
9. Voltage-gated sodium channel alpha-subunits Na(v)1.1, Na(v)1.2, and Na(v)1.6 in the distal mammalian retina. Mojumder DK, etal., Mol Vis. 2007 Nov 27;13:2163-82.
10. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. Structure and function of sodium channel. Noda M and Numa S, J Recept Res 1987;7(1-4):467-97.
12. Existence of distinct sodium channel messenger RNAs in rat brain. Noda M, etal., Nature 1986 Mar 13-19;320(6058):188-92.
13. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
14. Sodium currents in medullary neurons isolated from the pre-Botzinger complex region. Ptak K, etal., J Neurosci. 2005 May 25;25(21):5159-70.
15. GOA pipeline RGD automated data pipeline
16. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
18. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
Additional References at PubMed
PMID:1658739   PMID:10769382   PMID:10827969   PMID:12835125   PMID:15272007   PMID:15746173   PMID:15797713   PMID:15878599   PMID:16921370   PMID:16966585   PMID:17228331   PMID:17322896  
PMID:17537961   PMID:17709186   PMID:17884088   PMID:17928448   PMID:19426735   PMID:19765660   PMID:20483028   PMID:20707984   PMID:20875856   PMID:21714116   PMID:22871113   PMID:22920678  
PMID:22992729   PMID:23219908   PMID:23318929   PMID:23375560   PMID:26259688   PMID:26528804   PMID:26978272   PMID:27207958   PMID:27281198   PMID:29956586   PMID:32318899   PMID:32377688  
PMID:33045260  


Genomics

Comparative Map Data
Scn1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8371,360,840 - 71,479,870 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl371,360,841 - 71,479,791 (-)EnsemblGRCr8
mRatBN7.2350,952,790 - 51,071,804 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl350,952,791 - 51,071,699 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx354,295,423 - 54,414,933 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0362,879,049 - 62,998,545 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0360,659,682 - 60,779,082 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0352,388,811 - 52,533,365 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl352,381,975 - 52,510,507 (-)Ensemblrn6Rnor6.0
Rnor_5.0359,016,641 - 59,135,580 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4348,238,528 - 48,364,143 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera350,540,798 - 50,655,298 (-)NCBICelera
RGSC_v3.1348,134,899 - 48,260,515 (-)NCBI
Cytogenetic Map3q21NCBI
SCN1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382165,984,641 - 166,149,161 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2165,984,641 - 166,182,806 (-)Ensemblhg38GRCh38
GRCh372166,841,151 - 167,005,671 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362166,553,916 - 166,638,395 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm38266,270,781 - 66,440,837 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl266,270,778 - 66,440,840 (-)Ensemblmm10GRCm38
MGSCv37266,108,839 - 66,278,894 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36266,071,621 - 66,241,676 (-)NCBIMGSCv36mm8
Celera267,950,131 - 68,119,920 (-)NCBICelera
Cytogenetic Map2C1.3NCBI
cM Map239.13NCBI
Scn1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554498,160,986 - 8,221,951 (+)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3611,250,750 - 11,390,861 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03611,240,396 - 11,380,203 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493646913,194,769 - 13,345,979 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1572,529,875 - 72,678,066 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11572,529,866 - 72,696,715 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21581,177,412 - 81,188,630 (-)NCBISscrofa10.2Sscrofa10.2susScr3
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247873,767,405 - 3,939,065 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Scn1a
2362 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:99
Count of miRNA genes:71
Interacting mature miRNAs:89
Transcripts:ENSRNOT00000008026
Prediction methods:Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)351490129111359995Rat
634317Bw117Body weight QTL 1173.58abdominal fat pad mass (VT:1000711)abdominal fat pad weight to body weight ratio (CMO:0000095)35986366373704481Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)35986366387321459Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)35365182698651826Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)34887661993876619Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)34887661993876619Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)33540319997383526Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)358601291153936591Rat
631832Sach1Saccharin preference QTL 12.70.02consumption behavior trait (VT:0002069)calculated saccharin drink intake volume (CMO:0001600)34790417292904172Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)349872657138829559Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)35986366387321459Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35109256196092561Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33642511681425116Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)34865774493657744Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)370845569136091483Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)33779691982796919Rat
2302276Bw82Body weight QTL 824.32body mass (VT:0001259)body weight (CMO:0000012)35986366383358329Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)358925062103925062Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)370311536115311536Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)34865774493657744Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)35076614595766145Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)35109256196092561Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)336721849110333156Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)35076614595766145Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)34865774493657744Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)342158111124558371Rat
2325840Bp345Blood pressure QTL 3450.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)33870893183708931Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)34865774493657744Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)33736373482363734Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)33610140381101403Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)34865774493657744Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)342158111124558371Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat

Markers in Region
D3Rat181  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8371,376,555 - 71,376,684 (+)Marker Load Pipeline
mRatBN7.2350,968,507 - 50,968,636 (+)MAPPERmRatBN7.2
Rnor_6.0352,408,191 - 52,408,319NCBIRnor6.0
Rnor_5.0359,034,932 - 59,035,060UniSTSRnor5.0
RGSC_v3.4348,254,475 - 48,254,603UniSTSRGSC3.4
RGSC_v3.4348,254,474 - 48,254,603RGDRGSC3.4
Celera350,556,511 - 50,556,639UniSTS
RGSC_v3.1348,150,760 - 48,150,995RGD
SHRSP x BN Map336.0899UniSTS
SHRSP x BN Map336.0899RGD
Cytogenetic Map3q21UniSTS
SCN1A_3451  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,954,797 - 50,955,708 (+)MAPPERmRatBN7.2
Rnor_6.0352,390,819 - 52,391,729NCBIRnor6.0
Rnor_6.0352,383,990 - 52,384,900NCBIRnor6.0
Rnor_5.0359,011,819 - 59,012,729UniSTSRnor5.0
Rnor_5.0359,018,648 - 59,019,558UniSTSRnor5.0
RGSC_v3.4348,240,535 - 48,241,445UniSTSRGSC3.4
Celera350,542,805 - 50,543,715UniSTS
Cytogenetic Map3q21UniSTS
Scn1a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,432,608 - 50,433,910 (+)MAPPERmRatBN7.2
Rnor_6.0351,817,586 - 51,818,887NCBIRnor6.0
Rnor_5.0358,452,236 - 58,453,537UniSTSRnor5.0
RGSC_v3.4347,718,197 - 47,719,498UniSTSRGSC3.4
Celera350,025,799 - 50,027,100UniSTS
Cytogenetic Map3q21UniSTS
Cytogenetic Map3q24UniSTS
Scn3a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,432,608 - 50,433,887 (+)MAPPERmRatBN7.2
Rnor_6.0351,817,586 - 51,818,864NCBIRnor6.0
Rnor_5.0358,452,236 - 58,453,514UniSTSRnor5.0
RGSC_v3.4347,718,197 - 47,719,475UniSTSRGSC3.4
Celera350,025,799 - 50,027,077UniSTS
Cytogenetic Map7q36UniSTS
Cytogenetic Map3q21UniSTS
Cytogenetic Map8q32UniSTS
Cytogenetic Map3q24UniSTS


Related Rat Strains
The following Strains have been annotated to Scn1a
F344.NER-(D1Mgh6-D1Rat73)(D5Mgh4-D5Rat36)Scn1am1/Kyo    


Genetic Models
This gene Scn1a is modified in the following models/strains:
F344-Scn1am1Kyo     F344-Scn1am2Kyo    


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
10 10 63 145 50 49 21 28 21 6 231 119 10 127 73 85 28 16 16

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_030875 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761923 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761925 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592056 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063284623 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001837049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010064701 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC122968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212107 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M22253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X03638 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000079020   ⟹   ENSRNOP00000068852
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl371,360,841 - 71,479,784 (-)Ensembl
mRatBN7.2 Ensembl350,954,907 - 51,071,699 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000083552   ⟹   ENSRNOP00000074819
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl371,362,692 - 71,479,743 (-)Ensembl
mRatBN7.2 Ensembl350,954,642 - 51,071,699 (-)Ensembl
Rnor_6.0 Ensembl352,381,975 - 52,447,622 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000091259   ⟹   ENSRNOP00000073986
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl371,360,841 - 71,479,743 (-)Ensembl
mRatBN7.2 Ensembl350,952,791 - 51,071,699 (-)Ensembl
Rnor_6.0 Ensembl352,388,812 - 52,510,507 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000098569   ⟹   ENSRNOP00000078175
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl371,360,841 - 71,479,791 (-)Ensembl
RefSeq Acc Id: NM_030875   ⟹   NP_110502
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8371,360,841 - 71,479,743 (-)NCBI
mRatBN7.2350,952,791 - 51,071,699 (-)NCBI
Rnor_6.0352,388,812 - 52,510,507 (-)NCBI
Rnor_5.0359,016,641 - 59,135,580 (-)NCBI
RGSC_v3.4348,238,528 - 48,364,143 (-)RGD
Celera350,540,798 - 50,655,298 (-)RGD
Sequence:
RefSeq Acc Id: XM_063284618   ⟹   XP_063140688
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8371,360,840 - 71,479,870 (-)NCBI
RefSeq Acc Id: XM_063284619   ⟹   XP_063140689
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8371,360,840 - 71,479,870 (-)NCBI
RefSeq Acc Id: XM_063284620   ⟹   XP_063140690
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8371,360,840 - 71,479,870 (-)NCBI
RefSeq Acc Id: XM_063284621   ⟹   XP_063140691
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8371,360,840 - 71,479,870 (-)NCBI
RefSeq Acc Id: XM_063284622   ⟹   XP_063140692
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8371,377,044 - 71,479,870 (-)NCBI
RefSeq Acc Id: XM_063284623   ⟹   XP_063140693
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8371,382,120 - 71,479,870 (-)NCBI
RefSeq Acc Id: XR_010064701
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8371,360,840 - 71,479,870 (-)NCBI
RefSeq Acc Id: NP_110502   ⟸   NM_030875
- UniProtKB: P04774 (UniProtKB/Swiss-Prot),   A0A0G2K6Y2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000073986   ⟸   ENSRNOT00000091259
Ensembl Acc Id: ENSRNOP00000074819   ⟸   ENSRNOT00000083552
Ensembl Acc Id: ENSRNOP00000068852   ⟸   ENSRNOT00000079020
RefSeq Acc Id: XP_063140690   ⟸   XM_063284620
- Peptide Label: isoform X3
- UniProtKB: P04774 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063140689   ⟸   XM_063284619
- Peptide Label: isoform X2
- UniProtKB: P04774 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063140691   ⟸   XM_063284621
- Peptide Label: isoform X4
- UniProtKB: P04774 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063140688   ⟸   XM_063284618
- Peptide Label: isoform X1
- UniProtKB: P04774 (UniProtKB/Swiss-Prot),   A0A0G2K6Y2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140692   ⟸   XM_063284622
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063140693   ⟸   XM_063284623
- Peptide Label: isoform X6
Ensembl Acc Id: ENSRNOP00000078175   ⟸   ENSRNOT00000098569
Protein Domains
Ion transport   IQ   Sodium ion transport-associated   Voltage-gated Na+ ion channel cytoplasmic

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P04774-F1-model_v2 AlphaFold P04774 1-2009 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69364 AgrOrtholog
BioCyc Gene G2FUF-49546 BioCyc
Ensembl Genes ENSRNOG00000053122 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000083552 ENTREZGENE
  ENSRNOT00000091259 ENTREZGENE
  ENSRNOT00000098569 ENTREZGENE
Gene3D-CATH 1.10.287.70 UniProtKB/Swiss-Prot
  1.20.120.350 UniProtKB/Swiss-Prot
  EF-hand UniProtKB/Swiss-Prot
  iswi atpase UniProtKB/Swiss-Prot
InterPro Ion_trans_dom UniProtKB/Swiss-Prot
  Na_channel_a1su UniProtKB/Swiss-Prot
  Na_channel_asu UniProtKB/Swiss-Prot
  Na_chnl_inactivation_gate UniProtKB/Swiss-Prot
  Na_trans_assoc UniProtKB/Swiss-Prot
  Na_trans_cytopl UniProtKB/Swiss-Prot
  VGCC_Ca_Na UniProtKB/Swiss-Prot
  Volt_channel_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:81574 UniProtKB/Swiss-Prot
NCBI Gene 81574 ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot
  SODIUM CHANNEL PROTEIN TYPE 1 SUBUNIT ALPHA UniProtKB/Swiss-Prot
Pfam Ion_trans UniProtKB/Swiss-Prot
  IQ_SCN5A_C UniProtKB/Swiss-Prot
  Na_trans_assoc UniProtKB/Swiss-Prot
  Na_trans_cytopl UniProtKB/Swiss-Prot
PharmGKB SCN1A RGD
PhenoGen Scn1a PhenoGen
PRINTS NACHANNEL UniProtKB/Swiss-Prot
  NACHANNEL1 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000053122 RatGTEx
Superfamily-SCOP Voltage-gated potassium channels UniProtKB/Swiss-Prot
TIGR TC235885
UniProt A0A0G2K6Y2 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K914_RAT UniProtKB/TrEMBL
  A0A8I5ZKG7_RAT UniProtKB/TrEMBL
  A0A8L2R0Q2_RAT UniProtKB/TrEMBL
  P04774 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Scn1a  sodium voltage-gated channel alpha subunit 1  LOC102553713  sodium channel protein type 1 subunit alpha-like  Data merged from RGD:7529469 737654 PROVISIONAL
2016-02-11 Scn1a  sodium voltage-gated channel alpha subunit 1  Scn1a  sodium channel, voltage-gated, type I, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-03-13 Scn1a  sodium channel, voltage-gated, type I, alpha subunit  Scn1a  sodium channel, voltage-gated, type I, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-17 LOC102553713  sodium channel protein type 1 subunit alpha-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-30 Scn1a  sodium channel, voltage-gated, type I, alpha    sodium channel, voltage-gated, type 1, alpha polypeptide  Name updated 1299863 APPROVED
2002-06-10 Scn1a  sodium channel, voltage-gated, type 1, alpha polypeptide      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease mutations of the human homolog are detected in generalized epilepsy with febrile seizures plus (GEFS+) 727292