Scn9a (sodium voltage-gated channel alpha subunit 9) - Rat Genome Database

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Gene: Scn9a (sodium voltage-gated channel alpha subunit 9) Rattus norvegicus
Analyze
Symbol: Scn9a
Name: sodium voltage-gated channel alpha subunit 9
RGD ID: 69368
Description: Enables sodium ion binding activity and voltage-gated sodium channel activity. Involved in behavioral response to formalin induced pain; negative regulation of action potential; and neuronal action potential. Located in axon. Part of voltage-gated sodium channel complex. Human ortholog(s) of this gene implicated in erythromelalgia and paroxysmal extreme pain disorder. Orthologous to human SCN9A (sodium voltage-gated channel alpha subunit 9); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Nav1.7; peripheral sodium channel 1; PN1; Scn2a; sodium channel protein type 9 subunit alpha; sodium channel protein type IX subunit alpha; sodium channel type IX alpha polypeptide; sodium channel voltage-gated type IX alpha polypeptide; sodium channel, voltage-gated, type 9, alpha polypeptide; sodium channel, voltage-gated, type IX, alpha; sodium channel, voltage-gated, type IX, alpha polypeptide; sodium channel, voltage-gated, type IX, alpha subunit; voltage-gated sodium channel subunit alpha Nav1.7
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Scn9a*tm1Amgn  
Genetic Models: SD-Scn9a*tm1Amgn/Crl
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2351,145,148 - 51,293,342 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl351,145,146 - 51,293,516 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx354,489,348 - 54,634,230 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0363,072,952 - 63,217,828 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0360,852,549 - 60,997,783 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0352,583,953 - 52,664,209 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl352,583,951 - 52,664,209 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0359,207,264 - 59,286,961 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4348,438,725 - 48,518,893NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera350,729,098 - 50,808,151 (-)NCBICelera
Cytogenetic Map3q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat NaV1.7 loss-of-function genetic model: Deficient nociceptive and neuropathic pain behavior with retained olfactory function and intra-epidermal nerve fibers. Grubinska B, etal., Mol Pain. 2019 Jan-Dec;15:1744806919881846. doi: 10.1177/1744806919881846.
4. Genetic mapping of the peripheral sodium channel genes, Scn9a and Scn10a, in the mouse. Kozak CA and Sangameswaran L, Mamm Genome 1996 Oct;7(10):787-8.
5. 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.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Autosomal dominant erythermalgia associated with a novel mutation in the voltage-gated sodium channel alpha subunit Nav1.7. Michiels JJ, etal., Arch Neurol. 2005 Oct;62(10):1587-90.
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. Sodium-calcium exchanger and multiple sodium channel isoforms in intra-epidermal nerve terminals. Persson AK, etal., Mol Pain. 2010 Nov 30;6:84. doi: 10.1186/1744-8069-6-84.
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Identification of PN1, a predominant voltage-dependent sodium channel expressed principally in peripheral neurons. Toledo-Aral JJ, etal., Proc Natl Acad Sci U S A 1997 Feb 18;94(4):1527-32.
15. Mutations in SCN9A, encoding a sodium channel alpha subunit, in patients with primary erythermalgia. Yang Y, etal., J Med Genet. 2004 Mar;41(3):171-4.
Additional References at PubMed
PMID:9169448   PMID:15314237   PMID:16029194   PMID:17145499   PMID:17149708   PMID:17722032   PMID:17950013   PMID:18579738   PMID:19690272   PMID:21569247   PMID:21601570   PMID:22484465  
PMID:23134641   PMID:23242737   PMID:23449670   PMID:23924059   PMID:24253930   PMID:24445633   PMID:24480965   PMID:25453779   PMID:26310938   PMID:27327156   PMID:27514860   PMID:27765894  
PMID:27905525   PMID:27940916   PMID:28123009   PMID:28349234   PMID:28582470   PMID:29115943   PMID:29138838   PMID:29166836   PMID:29388177   PMID:29790813   PMID:29956586   PMID:30425258  
PMID:31032358   PMID:31087766   PMID:31681845   PMID:31888677   PMID:32407275   PMID:33063281   PMID:35418262   PMID:36773735  


Genomics

Comparative Map Data
Scn9a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2351,145,148 - 51,293,342 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl351,145,146 - 51,293,516 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx354,489,348 - 54,634,230 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0363,072,952 - 63,217,828 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0360,852,549 - 60,997,783 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0352,583,953 - 52,664,209 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl352,583,951 - 52,664,209 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0359,207,264 - 59,286,961 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4348,438,725 - 48,518,893NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera350,729,098 - 50,808,151 (-)NCBICelera
Cytogenetic Map3q21NCBI
SCN9A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382166,195,185 - 166,375,987 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2166,195,185 - 166,376,001 (-)EnsemblGRCh38hg38GRCh38
GRCh372167,051,695 - 167,232,497 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362166,759,941 - 166,876,560 (-)NCBINCBI36Build 36hg18NCBI36
Build 342166,880,315 - 166,993,821NCBI
Celera2160,661,621 - 160,841,488 (-)NCBICelera
Cytogenetic Map2q24.3NCBI
HuRef2158,932,999 - 159,113,694 (-)NCBIHuRef
CHM1_12167,057,860 - 167,238,542 (-)NCBICHM1_1
T2T-CHM13v2.02166,652,733 - 166,833,467 (-)NCBIT2T-CHM13v2.0
Scn9a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39266,310,424 - 66,465,456 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl266,310,424 - 66,465,306 (-)EnsemblGRCm39 Ensembl
GRCm38266,480,080 - 66,635,114 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl266,480,080 - 66,634,962 (-)EnsemblGRCm38mm10GRCm38
MGSCv37266,318,137 - 66,473,009 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36266,280,919 - 66,435,791 (-)NCBIMGSCv36mm8
Celera268,159,792 - 68,315,357 (-)NCBICelera
Cytogenetic Map2C1.3NCBI
cM Map239.13NCBI
Scn9a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554497,923,801 - 8,017,569 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554497,858,156 - 8,017,569 (+)NCBIChiLan1.0ChiLan1.0
SCN9A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan12B68,865,826 - 69,043,323 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B53,468,290 - 53,643,747 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B170,944,974 - 171,119,275 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B170,944,974 - 171,054,013 (-)Ensemblpanpan1.1panPan2
SCN9A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13611,287,358 - 11,382,897 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3611,290,625 - 11,383,255 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3611,431,905 - 11,590,849 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03611,421,333 - 11,580,725 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3611,422,611 - 11,517,286 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13611,503,582 - 11,662,869 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03611,475,664 - 11,634,434 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03611,588,422 - 11,748,250 (-)NCBIUU_Cfam_GSD_1.0
Scn9a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303128,464,705 - 128,638,949 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493646913,064,043 - 13,152,974 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493646913,063,971 - 13,153,030 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN9A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1572,748,705 - 72,912,382 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11572,745,706 - 72,912,352 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21581,262,169 - 81,433,272 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCN9A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11051,711,446 - 51,898,856 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1051,714,931 - 51,829,621 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040147,611,948 - 147,803,960 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scn9a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247873,997,887 - 4,085,449 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247873,995,319 - 4,148,230 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Scn9a
1769 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:296
Count of miRNA genes:177
Interacting mature miRNAs:208
Transcripts:ENSRNOT00000065126
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)31695470861954708Rat
10450804Scl70Serum cholesterol level QTL 704.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
10450794Scl69Serum cholesterol level QTL 696.30.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
2302055Pia30Pristane induced arthritis QTL 303.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)32793691972936919Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)32824968773249687Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)32824968773249687Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)32824968773249687Rat
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)32824968773249687Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32824968773249687Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)32846857173468571Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)32846857173468571Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)33068464275684642Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)33068464275684642Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
11565451Bw177Body weight QTL 1770.002body mass (VT:0001259)body weight (CMO:0000012)33142640370668733Rat
11565452Kidm57Kidney mass QTL 570.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33142640370668733Rat
12879866Cm94Cardiac mass QTL 940.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33142640370668733Rat
12879867Cm95Cardiac mass QTL 950.047heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33142640370668733Rat
12879868Am6Aortic mass QTL 60.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33142640370668733Rat
2301400Cm68Cardiac mass QTL 680.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33142640370668733Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33370334761017857Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)33851780383517803Rat
634317Bw117Body weight QTL 1173.58abdominal fat pad mass (VT:1000711)abdominal fat pad weight to body weight ratio (CMO:0000095)33945463753296578Rat
2302276Bw82Body weight QTL 824.32body mass (VT:0001259)body weight (CMO:0000012)33945463762951183Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)33945463789115240Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)33945463789115240Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34382736490905114Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat

Markers in Region
RH138415  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2351,145,235 - 51,145,412 (+)MAPPERmRatBN7.2
Rnor_6.0352,584,041 - 52,584,217NCBIRnor6.0
Rnor_5.0359,207,352 - 59,207,528UniSTSRnor5.0
RGSC_v3.4348,438,813 - 48,438,989UniSTSRGSC3.4
Celera350,729,186 - 50,729,362UniSTS
RH 3.4 Map3605.31UniSTS
Cytogenetic Map3q21UniSTS
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


Genetic Models
This gene Scn9a is modified in the following models/strains

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 circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 27
Low 1 14 6 39 12 18
Below cutoff 2 12 8 6 4 6 6 6 8 7 20 9 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065126   ⟹   ENSRNOP00000059170
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl351,145,146 - 51,293,516 (-)Ensembl
Rnor_6.0 Ensembl352,583,951 - 52,664,209 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079020   ⟹   ENSRNOP00000068852
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl352,587,297 - 52,664,209 (-)Ensembl
RefSeq Acc Id: NM_133289   ⟹   NP_579823
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2351,145,148 - 51,293,342 (-)NCBI
Rnor_6.0352,583,953 - 52,664,209 (-)NCBI
Rnor_5.0359,207,264 - 59,286,961 (-)NCBI
RGSC_v3.4348,438,725 - 48,518,893 (-)RGD
Celera350,729,098 - 50,808,151 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_579823 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB50403 (Get FASTA)   NCBI Sequence Viewer  
  AAB80701 (Get FASTA)   NCBI Sequence Viewer  
  CAP18983 (Get FASTA)   NCBI Sequence Viewer  
  CAT16528 (Get FASTA)   NCBI Sequence Viewer  
  O08562 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_579823   ⟸   NM_133289
- UniProtKB: O08562 (UniProtKB/Swiss-Prot),   A0A8L2QSN0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068852   ⟸   ENSRNOT00000079020
RefSeq Acc Id: ENSRNOP00000059170   ⟸   ENSRNOT00000065126
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-O08562-F1-model_v2 AlphaFold O08562 1-1984 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:69368 AgrOrtholog
BioCyc Gene G2FUF-49539 BioCyc
Ensembl Genes ENSRNOG00000006639 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059170 ENTREZGENE
  ENSRNOP00000059170.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065126 ENTREZGENE
  ENSRNOT00000065126.4 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.70 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.20.120.350 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  iswi atpase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ion_trans_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IQ_motif_EF-hand-BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_channel_asu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_chnl_inactivation_gate UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_cytopl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VGCC_Ca_Na UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:78956 UniProtKB/Swiss-Prot
NCBI Gene 78956 ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10037:SF221 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_cytopl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Scn9a PhenoGen
PRINTS NACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00015 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Voltage-gated potassium channels UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2QSN0 ENTREZGENE, UniProtKB/TrEMBL
  A9JQE0_RAT UniProtKB/TrEMBL
  O08562 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Scn9a  sodium voltage-gated channel alpha subunit 9  Scn9a  sodium channel, voltage-gated, type IX, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-03-13 Scn9a  sodium channel, voltage-gated, type IX, alpha subunit  Scn9a  sodium channel, voltage-gated, type IX, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Scn9a  sodium channel, voltage-gated, type IX, alpha    sodium channel, voltage-gated, type 9, alpha polypeptide  Name updated 1299863 APPROVED
2002-06-10 Scn9a  sodium channel, voltage-gated, type 9, alpha polypeptide      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_regulation mRNA expression is induced by NGF in PC12 cells 634047