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Gene: Scn9a (sodium voltage-gated channel alpha subunit 9) Rattus norvegicus

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Symbol:

Scn9a

Name:

sodium voltage-gated channel alpha subunit 9

RGD ID:

69368

Description:

Predicted to enable voltage-gated sodium channel activity. Involved in behavioral response to formalin induced pain and negative regulation of action potential. Located in axon. 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

Alliance Orthologs

More Info

more info ...

Allele / Splice:

Scn9a*^tm1Amgn

Genetic Models:

SD-Scn9a*^tm1Amgn/Crl

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	71,553,185 - 71,701,377 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	3	71,553,189 - 71,701,377 (-)	Ensembl				GRCr8
mRatBN7.2	3	51,145,148 - 51,293,342 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	51,145,146 - 51,293,516 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	3	54,489,348 - 54,634,230 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	63,072,952 - 63,217,828 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	60,852,549 - 60,997,783 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	52,583,953 - 52,664,209 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	52,583,951 - 52,664,209 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	3	59,207,264 - 59,286,961 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	3	48,438,725 - 48,518,893	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	3	50,729,098 - 50,808,151 (-)	NCBI		Celera
Cytogenetic Map	3	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Charcot-Marie-Tooth disease dominant intermediate B (ISO)

Chronic Pain (ISO)

Congenital Indifference to Pain, Autosomal Recessive (ISO)

Congenital Pain Insensitivity (ISO)

Dravet syndrome (ISO)

early myoclonic encephalopathy (ISO)

epilepsy (ISO)

erythromelalgia (ISO)

Familial Febrile Seizures 3B (ISO)

generalized epilepsy with febrile seizures plus 7 (ISO)

genetic disease (ISO)

hereditary sensory and autonomic neuropathy type 2A (ISO)

hereditary sensory neuropathy (ISO)

Herpesviridae Infections (ISO)

Neuralgia (ISO)

paroxysmal extreme pain disorder (ISO)

Postherpetic Neuralgia (ISO)

Pruritus (ISO)

Small Fiber Neuropathy (ISO)

syringomyelia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,3,7,8-Tetrachlorodibenzofuran (EXP)

6-propyl-2-thiouracil (EXP,ISO)

aflatoxin B1 (ISO)

ammonium chloride (EXP)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (EXP,ISO)

bisphenol A (EXP,ISO)

butanal (ISO)

butyric acid (ISO)

caffeine (ISO)

cannabidiol (ISO)

carbamazepine (ISO)

chlorpyrifos (ISO)

cisplatin (ISO)

copper(II) sulfate (ISO)

Cuprizon (EXP)

cyclosporin A (ISO)

diiodine (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

ethanol (EXP,ISO)

fonofos (ISO)

malathion (ISO)

manganese atom (ISO)

manganese(0) (ISO)

manganese(II) chloride (ISO)

mexiletine (ISO)

mono(2-ethylhexyl) phthalate (ISO)

monosodium L-glutamate (ISO)

nickel atom (ISO)

paracetamol (ISO)

parathion (ISO)

permethrin (ISO)

quercetin (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sodium atom (ISO)

terbufos (ISO)

tetrodotoxin (ISO)

tributylstannane (EXP)

trichostatin A (ISO)

triptonide (ISO)

urethane (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

action potential propagation (IEA,ISO,ISS)

behavioral response to formalin induced pain (IMP)

behavioral response to pain (ISO)

circadian rhythm (IEA,ISO)

detection of mechanical stimulus involved in sensory perception (IEA,ISO)

detection of temperature stimulus involved in sensory perception of pain (IEA,ISO)

inflammatory response (ISO)

membrane depolarization during action potential (IBA,IEA,ISO)

monoatomic cation transmembrane transport (IEA)

monoatomic ion transmembrane transport (IEA)

monoatomic ion transport (IEA)

negative regulation of action potential (IMP)

neuronal action potential (IBA,IEA,ISO)

post-embryonic development (ISO)

response to toxic substance (ISO)

rhythmic excitation (NAS)

sensory perception of pain (IBA,IEA,ISO,ISS)

sodium ion transmembrane transport (IBA,IEA)

sodium ion transport (IEA)

transmembrane transport (IEA)

Cellular Component

axon (IBA,IDA,IEA)

axon terminus (IEA,ISO,ISS)

membrane (IEA)

monoatomic ion channel complex (IEA)

neuron projection (IEA)

node of Ranvier (IEA,ISO)

plasma membrane (IEA,ISO)

voltage-gated sodium channel complex (IBA,IEA)

Molecular Function

monoatomic cation channel activity (IEA)

monoatomic ion channel activity (IEA)

protein binding (ISO)

sodium channel activity (IEA)

voltage-gated sodium channel activity (IBA,IEA,ISO,ISS)

Phenotype Annotations Click to see Annotation Detail View

Mammalian Phenotype

abnormal afterhyperpolarization (IMP)

abnormal pain threshold (IMP)

decreased susceptibility to induced hypothermia (IMP)

impaired ability to fire action potentials (IMP)

increased chemical nociceptive threshold (IMP)

increased thermal nociceptive threshold (IMP)

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	PMID:38167752

Genomics

Comparative Map Data

Scn9a
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	71,553,185 - 71,701,377 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	3	71,553,189 - 71,701,377 (-)	Ensembl				GRCr8
mRatBN7.2	3	51,145,148 - 51,293,342 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	51,145,146 - 51,293,516 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	3	54,489,348 - 54,634,230 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	63,072,952 - 63,217,828 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	60,852,549 - 60,997,783 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	52,583,953 - 52,664,209 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	52,583,951 - 52,664,209 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	3	59,207,264 - 59,286,961 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	3	48,438,725 - 48,518,893	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	3	50,729,098 - 50,808,151 (-)	NCBI		Celera
Cytogenetic Map	3	q21	NCBI

SCN9A
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	166,195,185 - 166,375,987 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	166,195,185 - 166,376,001 (-)	Ensembl			hg38	GRCh38
GRCh37	2	167,051,695 - 167,232,454 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	166,759,941 - 166,876,560 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	2	166,880,315 - 166,993,821	NCBI
Celera	2	160,661,621 - 160,841,488 (-)	NCBI		Celera
Cytogenetic Map	2	q24.3	NCBI
HuRef	2	158,932,999 - 159,113,694 (-)	NCBI		HuRef
CHM1_1	2	167,057,860 - 167,238,542 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	2	166,652,733 - 166,833,467 (-)	NCBI		T2T-CHM13v2.0

Scn9a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	66,310,424 - 66,465,456 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	66,310,424 - 66,465,306 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	2	66,480,080 - 66,635,114 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	66,480,080 - 66,634,962 (-)	Ensembl			mm10	GRCm38
MGSCv37	2	66,318,137 - 66,473,009 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	2	66,280,919 - 66,435,791 (-)	NCBI		MGSCv36	mm8
Celera	2	68,159,792 - 68,315,357 (-)	NCBI		Celera
Cytogenetic Map	2	C1.3	NCBI
cM Map	2	39.13	NCBI

Scn9a
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955449	7,923,801 - 8,017,569 (+)	Ensembl
ChiLan1.0	NW_004955449	7,858,156 - 8,017,569 (+)	NCBI	ChiLan1.0	ChiLan1.0

SCN9A
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	13	68,850,849 - 69,028,376 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2B	68,865,826 - 69,043,323 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2B	53,468,290 - 53,643,747 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2B	170,944,974 - 171,119,275 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2B	170,944,974 - 171,054,013 (-)	Ensembl			panPan2	panpan1.1

SCN9A
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	36	11,287,358 - 11,382,897 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	36	11,290,625 - 11,383,255 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	36	11,431,905 - 11,590,849 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	36	11,421,333 - 11,580,725 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	36	11,422,611 - 11,517,286 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	36	11,503,582 - 11,662,869 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	36	11,475,664 - 11,634,434 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	36	11,588,422 - 11,748,250 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Scn9a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405303	128,464,705 - 128,638,949 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936469	13,064,043 - 13,152,974 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936469	13,063,971 - 13,153,030 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SCN9A
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	15	72,748,705 - 72,912,382 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	15	72,745,706 - 72,912,352 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	15	81,262,169 - 81,433,272 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SCN9A
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	10	51,711,446 - 51,898,856 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	10	51,714,931 - 51,829,621 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666040	147,611,948 - 147,803,960 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Scn9a
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624787	3,997,887 - 4,085,449 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624787	3,995,319 - 4,148,230 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Scn9a
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	5	43,909,197 - 43,989,917 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Scn9a
1724 total Variants

miRNA Target Status (No longer updated)

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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1300178	Hrtrt4	Heart rate QTL 4	3.74		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	51490129	111359995	Rat
634317	Bw117	Body weight QTL 117	3.58		abdominal fat pad mass (VT:1000711)	abdominal fat pad weight to body weight ratio (CMO:0000095)	3	59863663	73704481	Rat
1331795	Rf30	Renal function QTL 30	3.708		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	3	59863663	87321459	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	51581665	184004958	Rat
1354589	Bw31	Body weight QTL 31	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	53651826	98651826	Rat
2303593	Gluco46	Glucose level QTL 46	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	48876619	93876619	Rat
1354590	Despr11	Despair related QTL 11		0.000031	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	3	48876619	93876619	Rat
2298542	Neuinf11	Neuroinflammation QTL 11	3.9		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	3	35403199	97383526	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	67641776	167835660	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	58601291	153936591	Rat
631832	Sach1	Saccharin preference QTL 1	2.7	0.02	consumption behavior trait (VT:0002069)	calculated saccharin drink intake volume (CMO:0001600)	3	47904172	92904172	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	49872657	138829559	Rat
1331777	Bw24	Body weight QTL 24	3.503		body mass (VT:0001259)	body weight (CMO:0000012)	3	59863663	87321459	Rat
631647	Bp122	Blood pressure QTL 122	6.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	51092561	96092561	Rat
1300169	Bp177	Blood pressure QTL 177	2.96		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	3	36425116	81425116	Rat
9590286	Uminl1	Urine mineral level QTL 1	3.5	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	3	48657744	93657744	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	70845569	136091483	Rat
4889966	Bss95	Bone structure and strength QTL 95	4.4		tibia area (VT:1000281)	tibia-fibula cross-sectional area (CMO:0001718)	3	37796919	82796919	Rat
2302276	Bw82	Body weight QTL 82	4.32		body mass (VT:0001259)	body weight (CMO:0000012)	3	59863663	83358329	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	67641995	130815812	Rat
738019	Anxrr10	Anxiety related response QTL 10	3.9		exploratory behavior trait (VT:0010471)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	3	58925062	103925062	Rat
631841	Niddm39	Non-insulin dependent diabetes mellitus QTL 39	3.36		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	70311536	115311536	Rat
9590136	Scort3	Serum corticosterone level QTL 3	23.37	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	48657744	93657744	Rat
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	50766145	95766145	Rat
61356	Bp37	Blood pressure QTL 37	3		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	51092561	96092561	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	36721849	110333156	Rat
1558650	Cm48	Cardiac mass QTL 48	4	0.0001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	3	50766145	95766145	Rat
8694196	Abfw2	Abdominal fat weight QTL 2	16.58	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	3	48657744	93657744	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	1	141509147	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	42158111	124558371	Rat
2325840	Bp345	Blood pressure QTL 345		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	38708931	83708931	Rat
8552950	Pigfal12	Plasma insulin-like growth factor 1 level QTL 12	7.3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	3	48657744	93657744	Rat
631676	Cm8	Cardiac mass QTL 8	7.03	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	3	37363734	82363734	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	36101403	81101403	Rat
8694386	Bw159	Body weight QTL 159	4.52	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	3	48657744	93657744	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	42158111	124558371	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	5675975	141509147	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	67641995	130815812	Rat

Markers in Region

RH138415

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	51,145,235 - 51,145,412 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	52,584,041 - 52,584,217	NCBI	Rnor6.0
Rnor_5.0	3	59,207,352 - 59,207,528	UniSTS	Rnor5.0
RGSC_v3.4	3	48,438,813 - 48,438,989	UniSTS	RGSC3.4
Celera	3	50,729,186 - 50,729,362	UniSTS
RH 3.4 Map	3	605.31	UniSTS
Cytogenetic Map	3	q21	UniSTS

Scn3a

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	50,432,608 - 50,433,887 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	51,817,586 - 51,818,864	NCBI	Rnor6.0
Rnor_5.0	3	58,452,236 - 58,453,514	UniSTS	Rnor5.0
RGSC_v3.4	3	47,718,197 - 47,719,475	UniSTS	RGSC3.4
Celera	3	50,025,799 - 50,027,077	UniSTS
Cytogenetic Map	7	q36	UniSTS
Cytogenetic Map	3	q21	UniSTS
Cytogenetic Map	8	q32	UniSTS
Cytogenetic Map	3	q24	UniSTS

Genetic Models

This gene Scn9a is modified in the following models/strains:

SD-Scn9a*^tm1Amgn/Crl

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

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
9	6	21	149	47	44	15	17	15	6	149	60	4	141	59	75	29	24	24

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_133289	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063284599	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063284600	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC117350	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC122968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF000368	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AM905326	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GM841633	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U79568	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000065126 ⟹ ENSRNOP00000059170

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	3	71,553,189 - 71,701,377 (-)	Ensembl
mRatBN7.2 Ensembl	3	51,145,146 - 51,293,516 (-)	Ensembl
Rnor_6.0 Ensembl	3	52,583,951 - 52,664,209 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000079020 ⟹ ENSRNOP00000068852

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	52,587,297 - 52,664,209 (-)	Ensembl

RefSeq Acc Id:

NM_133289 ⟹ NP_579823

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	71,553,189 - 71,701,377 (-)	NCBI
mRatBN7.2	3	51,145,148 - 51,293,342 (-)	NCBI
Rnor_6.0	3	52,583,953 - 52,664,209 (-)	NCBI
Rnor_5.0	3	59,207,264 - 59,286,961 (-)	NCBI
RGSC_v3.4	3	48,438,725 - 48,518,893 (-)	RGD
Celera	3	50,729,098 - 50,808,151 (-)	RGD

Sequence:

show sequence

ATGGCGATGCTGCCTCCTCCAGGACCTCAGAGTTTCGTTCACTTCACAAAACAGTCCCTTGCCC
TCATTGAACAGCGTATTTCTGAAGAAAAAGCCAAGGAACACAAAGACGAAAAGAAAGATGATGA
GGAAGAAGGCCCCAAGCCCAGCAGTGACTTGGAAGCTGGGAAACAGCTCCCCTTCATCTATGGA
GACATTCCCCCTGGAATGGTGTCAGAGCCCCTGGAGGACCTGGACCCATACTATGCTGACAAAA
AAACTTTTATAGTATTGAACAAAGGGAAAGCAATCTTCCGTTTCAACGCCACCCCTGCTTTGTA
CATGCTGTCTCCCTTCAGTCCTCTAAGAAGAATATCTATTAAGATCTTAGTGCACTCCTTATTC
AGCATGCTAATCATGTGCACAATTCTGACGAACTGCATATTCATGACCTTGAGCAACCCTCCAG
AATGGACCAAAAATGTAGAGTACACTTTTACTGGGATATATACTTTTGAATCACTCATAAAAAT
CCTTGCAAGAGGCTTTTGCGTGGGAGAATTCACCTTCCTCCGTGACCCTTGGAACTGGCTGGAC
TTTGTTGTCATTGTTTTTGCGTATTTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTC
GAACTTTCAGAGTCTTGAGAGCTTTGAAAACTATTTCTGTAATCCCAGGACTAAAGACCATCGT
GGGGGCCCTGATCCAGTCAGTGAAGAAGCTCTCTGACGTCATGATCCTCACTGTGTTCTGTCTC
AGTGTGTTTGCACTAATTGGACTACAGCTGTTTATGGGCAACTTGAAGCATAAATGTTTCAGGA
AGGAACTCGAAGAGAATGAAACATTAGAAAGTATCATGAATACTGCTGAGAGTGAAGAAGAATT
GAAAAAATATTTTTATTACTTGGAGGGATCCAAAGATGCTCTACTCTGCGGCTTCAGCACAGAT
TCAGGGCAGTGTCCAGAAGGCTACATCTGTGTGAAGGCTGGCAGAAACCCGGATTATGGCTACA
CGAGCTTTGACACATTCAGCTGGGCCTTCTTGGCCTTGTTTCGGCTAATGACTCAGGACTACTG
GGAGAACCTTTACCAACAGACTCTGCGTGCTGCTGGCAAAACCTACATGATTTTCTTTGTCGTG
GTTATTTTTCTGGGCTCCTTTTACCTGATAAACTTGATCCTGGCTGTGGTAGCCATGGCGTATG
AGGAACAGAACCAGGCCAACATCGAAGAAGCTAAACAGAAAGAGTTAGAATTTCAGCAGATGTT
AGACCGACTCAAAAAGGAGCAGGAAGAAGCTGAGGCGATCGCTGCAGCTGCTGCTGAGTTCACG
AGTATAGGGCGGAGCAGGATCATGGGACTCTCTGAGAGCTCTTCAGAAACCTCCAGGCTGAGCT
CAAAGAGTGCCAAGGAGAGAAGAAACCGAAGAAAGAAAAAGAAACAGAAGATGTCCAGTGGCGA
GGAAAAGGGTGACGATGAGAAGCTGTCCAAGTCAGGATCAGAGGAAAGCATCCGAAAGAAAAGT
TTCCATCTCGGTGTGGAAGGGCACCACCGGACCCGGGAAAAGAGGCTGTCCACCCCCAACCAGT
CGCCACTCAGCATTCGCGGGTCCCTGTTTTCTGCCAGGCGCAGCAGCAGGACGAGTCTCTTCAG
TTTTAAGGGGCGAGGAAGAGATCTGGGATCTGAGACAGAATTCGCTGATGATGAGCATAGCATT
TTTGGAGACAACGAGAGCAGAAGGGGTTCACTATTCGTACCCCATAGACCCCGGGAGCGGCGCA
GCAGTAACATCAGTCAGGCCAGTAGGTCCCCGCCAGTGCTACCGGTGAACGGGAAGATGCACAG
TGCAGTGGACTGCAATGGCGTCGTGTCGCTTGTTGATGGACCCTCAGCCCTCATGCTCCCCAAT
GGACAGCTTCTTCCAGAGGTGATAATAGATAAGGCAACTTCCGACGACAGCGGCACGACTAATC
AGATGCGCAAAAAAAGGCTCTCTAGTTCTTACTTCTTGTCTGAGGACATGCTGAATGACCCGCA
TCTCAGGCAAAGGGCCATGAGCAGGGCGAGCATACTGACCAACACTGTGGAAGAACTTGAAGAA
TCTAGACAAAAATGTCCACCATGGTGGTACAGATTTGCTCACACATTTTTAATCTGGAATTGCT
CTCCATATTGGATAAAATTCAAAAAGCTCATCTATTTTATTGTGATGGATCCTTTTGTAGATCT
TGCAATTACCATTTGCATAGTTTTAAACACCTTATTTATGGCTATGGAGCACCACCCAATGACT
GAAGAATTCAAAAATGTCCTTGCAGTGGGGAACTTGATCTTTACAGGGATCTTCGCAGCTGAAA
TGGTACTGAAGTTAATAGCCATGGACCCCTATGAGTATTTCCAAGTAGGGTGGAATATTTTTGA
CAGCCTAATTGTGACGCTGAGTTTGATAGAGCTTTTCCTAGCAGATGTGGAAGGATTATCAGTT
CTGCGGTCATTCAGATTGCTCCGAGTCTTCAAGTTGGCAAAGTCCTGGCCCACACTGAACATGC
TCATTAAGATCATCGGCAACTCGGTGGGCGCACTGGGCAACCTGACCCTGGTGCTGGCCATCAT
CGTCTTCATTTTTGCCGTGGTCGGCATGCAGCTGTTTGGAAAGAGCTACAAGGAGTGTGTCTGC
AAGATCAATGTGGACTGCAAGCTGCCGCGCTGGCACATGAACGACTTCTTCCACTCCTTCCTCA
TCGTGTTCCGAGTGCTGTGTGGGGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTCGCGGG
CCAGACCATGTGCCTTATTGTTTACATGATGGTCATGGTGATTGGGAACCTTGTGGTCCTGAAC
CTGTTTCTGGCTCTTTTGCTGAGTTCCTTTAGTTCTGACAATCTTACAGCAATTGAGGAAGACA
CCGATGCAAACAACCTCCAGATCGCAGTGGCCAGAATTAAGAGGGGAATCAATTACGTGAAACA
GACCCTGCGTGAATTCATTCTAAAATCATTTTCCAAAAAGCCAAAGGGCTCCAAGGACACAAAA
CGAACAGCAGATCCCAACAACAAGAAAGAAAACTATATTTCAAACCGTACCCTTGCGGAGATGA
GCAAGGATCACAATTTCCTCAAAGAAAAGGATAGGATCAGTGGTTATGGCAGCAGTCTAGACAA
AAGCTTTATGGATGAAAATGATTACCAGTCCTTTATCCATAACCCCAGCCTCACAGTGACAGTG
CCAATTGCACCTGGGGAGTCTGATTTGGAGATTATGAACACAGAAGAGCTTAGCAGTGACTCAG
ACAGTGACTACAGCAAAGAGAAACGGAACCGATCAAGCTCTTCTGAGTGCAGCACTGTTGACAA
CCCTCTGCCAGGAGAAGAGGAGGCTGAAGCAGAGCCCGTAAACGCAGATGAGCCTGAAGCCTGC
TTTACAGATGGTTGTGTGAGGAGATTTCCATGCTGCCAAGTTAATGTAGACTCTGGGAAAGGGA
AAGTTTGGTGGACCATCAGGAAGACGTGCTACAGGATAGTTGAACACAGCTGGTTTGAAAGCTT
CATCGTTCTCATGATCCTGCTCAGCAGTGGAGCTCTGGCTTTTGAAGATATCTATATTGAAAAG
AAAAAGACCATTAAGATTATCCTGGAGTATGCTGACAAGATATTCACCTACATCTTCATTCTGG
AAATGCTTCTAAAATGGGTCGCATATGGGTATAAAACATATTTCACTAATGCCTGGTGTTGGCT
GGACTTCTTAATTGTTGATGTGTCTCTAGTTACTTTAGTAGCCAACACTCTTGGCTACTCAGAC
CTTGGCCCCATTAAATCTCTACGGACACTGAGGGCCCTAAGACCCCTAAGAGCCTTGTCTAGAT
TTGAAGGAATGAGGGTAGTGGTCAACGCACTCATAGGAGCAATCCCTTCCATCATGAACGTGCT
TCTCGTGTGCCTTATATTCTGGCTAATATTTAGCATCATGGGAGTCAATCTGTTTGCTGGCAAG
TTCTATGAGTGTGTCAACACCACCGATGGGTCACGATTTCCTACATCTCAAGTTGCAAACCGTT
CTGAGTGTTTTGCCCTGATGAACGTTAGTGGAAATGTGCGATGGAAAAACCTGAAAGTAAACTT
CGACAACGTTGGGCTTGGTTACCTGTCGCTGCTTCAAGTTGCAACATTCAAGGGCTGGATGGAT
ATTATGTATGCAGCAGTTGACTCTGTTAATGTAAATGAACAGCCGAAATACGAATACAGTCTCT
ACATGTACATTTACTTTGTCATCTTCATCATCTTCGGCTCATTCTTCACGTTGAACCTGTTCAT
TGGTGTCATCATAGATAATTTCAACCAACAGAAAAAAAAGCTTGGAGGTCAAGATATCTTTATG
ACAGAAGAACAGAAGAAATACTATAATGCAATGAAGAAGCTTGGGTCCAAAAAACCACAAAAAC
CAATTCCAAGGCCAGGGAACAAATTCCAAGGATGTATATTTGACTTAGTGACAAACCAAGCTTT
TGATATCACCATCATGGTTCTTATATGCCTCAACATGGTAACCATGATGGTAGAAAAAGAGGGG
CAAACTGAGTACATGGATTATGTTTTACACTGGATCAACATGGTCTTCATTATCCTGTTCACTG
GGGAGTGTGTGCTGAAGCTAATCTCCCTCAGACATTACTACTTCACTGTGGGTTGGAACATTTT
TGATTTTGTGGTAGTGATCCTCTCCATTGTAGGAATGTTTCTCGCTGAGATGATAGAGAAGTAT
TTCGTGTCCCCTACCCTGTTCCGAGTCATCCGCCTGGCCAGGATTGGACGAATCCTACGCCTGA
TCAAAGGCGCCAAGGGGATCCGCACTCTGCTCTTTGCTTTGATGATGTCCCTTCCTGCGCTGTT
CAACATCGGCCTCCTGCTTTTCCTGGTCATGTTCATCTACGCCATCTTTGGGATGTCCAACTTT
GCCTACGTTAAAAAGGAGGCTGGAATTAATGACATGTTCAACTTTGAGACTTTTGGCAACAGCA
TGATCTGCTTGTTCCAAATCACCACCTCTGCCGGCTGGGACGGACTGCTGGCCCCCATCCTCAA
CAGCGCACCTCCCGACTGTGACCCTAAAAAAGTTCACCCAGGAAGTTCAGTGGAAGGGGACTGT
GGGAACCCATCCGTGGGGATTTTTTACTTTGTCAGCTACATCATCATATCCTTCCTGGTGGTGG
TGAACATGTACATCGCTGTCATCCTGGAGAACTTCAGCGTCGCCACCGAAGAGAGCACTGAGCC
TCTGAGTGAGGACGACTTTGAGATGTTCTACGAGGTCTGGGAGAAGTTCGACCCTGACGCCACT
CAGTTCATAGAGTTCTGCAAGCTCTCTGACTTTGCAGCTGCCCTGGATCCTCCCCTCCTCATCG
CAAAGCCAAACAAAGTCCAGCTCATTGCCATGGACCTGCCCATGGTGAGTGGAGACCGCATCCA
CTGCCTGGACATCTTGTTTGCTTTTACAAAGCGGGTCCTGGGTGAGGGTGGAGAGATGGATTCT
CTTCGTTCACAGATGGAAGAAAGGTTCATGTCAGCCAATCCTTCTAAAGTGTCCTATGAACCCA
TCACGACCACACTGAAGAGAAAACAAGAGGAGGTGTCCGCGACTATCATTCAGCGTGCTTACAG
ACGGTATCGCCTCAGACAACACGTCAAGAATATATCGAGTATATACATAAAAGATGGAGACAGG
GATGATGATTTGCCCAATAAAGAAGATACAGTTTTTGATAACGTGAACGAGAACTCAAGTCCGG
AAAAGACAGATGTAACTGCCTCAACCATCTCGCCACCTTCCTATGACAGTGTCACAAAGCCAGA
TCAAGAGAAATATGAAACAGACAAAACAGAGAAGGAAGACAAAGAGAAAGATGAAAGCAGGAAA
TAGAGCTTTGGTTTTGATACACTGTTGACAGCCTGTGAAGGTTGACTCACTCGTGTTAGTAAGA
CTCTTTTACGGAGGTCTATGCCAAACTCTTTTTATCAAAAAATTCTCAAAGGCAGCACAGCCAT
TAGCTCTGATCCAACGAGGCAGAGGGCAGCATTTACACATGGCTATGTTTTGCTTTGGTAAATG
ATTCTTTTAAGATTTGAGAGTGTAACTCTGAAGGGAAGAGCCATCACTGCATTCAAGGGTGACT
TAGACATTCTAAAAATCAGAAAACCAAGTCAAACATTTTCTCATTTGCCTCCATGTCTTTTCTC
TAGGTTCTAAATAAATGTGCACCCATGTGAATCTAGAAATCCAGGCATACATGCACACATGCAC
ACAGTCACAAATACAAACAGGATTGGCTACGATTTCAAATTCTATGTAAATGTTTCACTTTGGT
TTGCAATGAAATTTCCTTGTAAAGGAAATGGGATTAGTGACGAAGGTTTTGTCAAAACATCTTA
TTATTAGGGAATCAGAATCTTTAATCTAAAAAGAATTCAGTTTATATTTTTGAGGTGCTGAAAC
TTATCCTACATTGCGTCAAAAGCAACTTATAGGAATCTATAAGATGTCATGGAATTGAAAAACG
TATGTGGGCTATTTATTTAAGAAATCACTTTCATTTGTATATTAGCATCATTCACCTTGATTTA
TGGACATCTTGGACATTGTGTGGTCACATGATGCTCCCACAAAATTGTTTAGCTGAAACTTCAG
GCACACATCACAGAGAACAGCTACCCAGTCTTACGCTCCACCCTGTTCATACAATAACCACAGA
CCTTTAAACATTATTTGGAATATAAATATTAGGTTTCTCAATATAAACATGTGAATATTAACAG
AAAAGTTAATTTACAGCGTTTTACTTACTAATGTCTATCCAATCTAGTTTGCACAATGAGACAG
CTCTCACCTCTTACAGCCAGTTGCCACATTTCTCTTCTTACGAAGCTTCGGTTTGTCAGACTTT
ATCTCTAAGCAAATTCTATGTTTCCTTTTTAATGAAACGTATCCTGAAAAGCGATTAGCTACTT
GATACTTTAGTGCTTGTTTGAGCAGATGACTGGAGCATGGTATGTACCCCATCTTTTAAAATAC
AATCCTTAATGTGTTTGGCAGCTTCCCAAGTTACAGGGAACGCCGGGCTTTTAATATCTCTCCG
TTCACCAGGTGTTTTGTATGAATGAAATGACATTCAAAGAGTGAGTCTCATTGGCTTGCTTTAT
TACCAACGACTTTCCTAAATGAGGAACTAATCCTCTGAAGCACTATTATATCCCCTTGTAAATA
ACATAGATGTCACTTCGTTCTTAATATTCTAATCCATGGTGTGACATATATTTTGCATTGATCA
GTAAAGTAGTCTGGGATAACCATTTTAAGAGCATATACATTTTGAGGTAGGTGAAGTTAATCTA
CCAAGGATTAGAAACCTACTCCAAGTTTTTAAAGTACTTGATAAAAATGAATGACCCTGACAAA
TTCTCTCATAATTTTATTCCAGCAATGTGAAATCTTTCCTCCAACACTTTATCCTTGCAGAGAA
GAAAGAAAAAACAAAGATAAGCCCATGGGCCATGTAAACAAAGGGGCTTTATCTAGAAGATTCT
GAGAGAACCTTTGAAGTAAATATGTAAAACATACTTCCTCAGTTTGCCTTTGAAATTAAAAAGT
AACACAAAAATATGGATTTAATAAGTCATCAAAACACATTCTTTATTTCTGGCCCAGTTTAAAG
GAAAGGATTAAAAATCCCTATAGAGGGGGGGGGACAGAGAGAGAAAGAGGGAGAGAAGAAACAA
AGTACTAGGGACAAAAAGATTAGACAGAATACGTCCAGGTTTTCACACTATGGGCTTTGTCCGG
GATGCTGTATAAAAGTCTCTTTCCAAATGTTTGTCATAAGGGGATCGAAGAAATTAAGTGCAAG
ACTAAAGGTTGTTTACAGATATCATTAATCATTAACAGTTTGGGAAGCTGCTTTTACATTTCTA
TGGAAGATGCCAAGGAATGCTAAGCCAGACAATACAGATGCATTGTGCATCTGTCAAGCGGCTA
AAATATGTTTGGGCAACTTAATTAGGGAAACCACCCCAACCCTTACATTTCTGACAATTTTAAA
TACAATTTAATTAAAGAAATCAGTACTTTTATTATTTCACATTCCTAAAATATAACTATATCGT
CCATTTTTATTGATATTATATGTGTGGATGTTTGTTGTAGATTATCTGTAATTTACTATTAATG
TTTTTACACTGATTTTTGTGAAAATTTAAAATATGTTGGCAACTGGTTCCTCAACACAATTTTT
TTAGCATTACAAAAAATAAACAGGTATAAAATTTCTCTTTTTTCTACATCATGTTGAACATATT
TCATTCTGATTTACACAATTTTAAATGTAATATTATTTTATATGCATATGTTTATCTCCAAAAT
CACTACTTATGACATCATATCAATTAAAAATGGTATTTGACACTAGGACTGTATTTAGTAAAAG
TTAAAAGCTTTCACCCTTTTTCATGTTGATTAGGGTTTGCACTAACTATAAAATGTCACCCACG
GAAGCTACTAGTCACTGAAATTATTTTACCTATTGGTGGAGAATGGTGACTGGCCAGAAAATAT
GAGTTAGCATTAAGTAGAAGACAGCGTACGTGACCACAAATCCATGCAGGTAGTTTGCGTGAAA
ACGGGAGAATCTCATTTTTCTGTTTTGTCTCTTCTCACTGTGCAAAAAGGACAAGAAATCTTTG
GGCTATTTCTAAATTCGAATTGTCACAATTTGCAATCATAAATGTTTAGCACGACTTTGTAGAA
TTTTGATAGTTTTATAAAAGAGTGAAAAACAAATGCATATGTAAATAAAGCAGCCCATACTAAC
GGATTCATCAAATGTTAATATGTAAATAAAGCAGCCCATACTAGCAGATTCATCAATGTTAATA
TGTAAATACAGCAGCCCACATGAGCAGATTCGTCATATGCTAAGGGAATTAATTAAAAGGAAGC
AACTAAATAAGGATGGTCAGTGATTGATCTGGGTTTAGAACTTGTGTTTGGACCCACCAATTTT
TAAGTATGTATTCTCACTTTATTAGTTTTCTAAAGAAAGCAATCAAGAATTGCTCCCAGAAAAT
GAGTAAGTAGCCATGAATATATGGATGCTGTTTACCAAACCCATAGACCCATGAATGCTCCAAA
CGTCTGAGTTTGTAAAAAAAAATACATTGTAGTTATACTTGACAATTTAAAATGTTAATAGAAT
CTAAAATAAAAGTCGCTTAAAAGTCGACGCGGCCGC

hide sequence

RefSeq Acc Id:

XM_063284599 ⟹ XP_063140669

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	71,553,185 - 71,632,172 (-)	NCBI

RefSeq Acc Id:

XM_063284600 ⟹ XP_063140670

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	71,553,185 - 71,632,172 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_579823	(Get FASTA)	NCBI Sequence Viewer
	XP_063140669	(Get FASTA)	NCBI Sequence Viewer
	XP_063140670	(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
Ensembl Protein	ENSRNOP00000059170
GenBank Protein	O08562	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_579823 ⟸ NM_133289

- UniProtKB:

O08562 (UniProtKB/Swiss-Prot), A0A8L2QSN0 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAMLPPPGPQSFVHFTKQSLALIEQRISEEKAKEHKDEKKDDEEEGPKPSSDLEAGKQLPFIYG
DIPPGMVSEPLEDLDPYYADKKTFIVLNKGKAIFRFNATPALYMLSPFSPLRRISIKILVHSLF
SMLIMCTILTNCIFMTLSNPPEWTKNVEYTFTGIYTFESLIKILARGFCVGEFTFLRDPWNWLD
FVVIVFAYLTEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCL
SVFALIGLQLFMGNLKHKCFRKELEENETLESIMNTAESEEELKKYFYYLEGSKDALLCGFSTD
SGQCPEGYICVKAGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTLRAAGKTYMIFFVV
VIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQKELEFQQMLDRLKKEQEEAEAIAAAAAEFT
SIGRSRIMGLSESSSETSRLSSKSAKERRNRRKKKKQKMSSGEEKGDDEKLSKSGSEESIRKKS
FHLGVEGHHRTREKRLSTPNQSPLSIRGSLFSARRSSRTSLFSFKGRGRDLGSETEFADDEHSI
FGDNESRRGSLFVPHRPRERRSSNISQASRSPPVLPVNGKMHSAVDCNGVVSLVDGPSALMLPN
GQLLPEVIIDKATSDDSGTTNQMRKKRLSSSYFLSEDMLNDPHLRQRAMSRASILTNTVEELEE
SRQKCPPWWYRFAHTFLIWNCSPYWIKFKKLIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMT
EEFKNVLAVGNLIFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLIELFLADVEGLSV
LRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVC
KINVDCKLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCMEVAGQTMCLIVYMMVMVIGNLVVLN
LFLALLLSSFSSDNLTAIEEDTDANNLQIAVARIKRGINYVKQTLREFILKSFSKKPKGSKDTK
RTADPNNKKENYISNRTLAEMSKDHNFLKEKDRISGYGSSLDKSFMDENDYQSFIHNPSLTVTV
PIAPGESDLEIMNTEELSSDSDSDYSKEKRNRSSSSECSTVDNPLPGEEEAEAEPVNADEPEAC
FTDGCVRRFPCCQVNVDSGKGKVWWTIRKTCYRIVEHSWFESFIVLMILLSSGALAFEDIYIEK
KKTIKIILEYADKIFTYIFILEMLLKWVAYGYKTYFTNAWCWLDFLIVDVSLVTLVANTLGYSD
LGPIKSLRTLRALRPLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGK
FYECVNTTDGSRFPTSQVANRSECFALMNVSGNVRWKNLKVNFDNVGLGYLSLLQVATFKGWMD
IMYAAVDSVNVNEQPKYEYSLYMYIYFVIFIIFGSFFTLNLFIGVIIDNFNQQKKKLGGQDIFM
TEEQKKYYNAMKKLGSKKPQKPIPRPGNKFQGCIFDLVTNQAFDITIMVLICLNMVTMMVEKEG
QTEYMDYVLHWINMVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVILSIVGMFLAEMIEKY
FVSPTLFRVIRLARIGRILRLIKGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNF
AYVKKEAGINDMFNFETFGNSMICLFQITTSAGWDGLLAPILNSAPPDCDPKKVHPGSSVEGDC
GNPSVGIFYFVSYIIISFLVVVNMYIAVILENFSVATEESTEPLSEDDFEMFYEVWEKFDPDAT
QFIEFCKLSDFAAALDPPLLIAKPNKVQLIAMDLPMVSGDRIHCLDILFAFTKRVLGEGGEMDS
LRSQMEERFMSANPSKVSYEPITTTLKRKQEEVSATIIQRAYRRYRLRQHVKNISSIYIKDGDR
DDDLPNKEDTVFDNVNENSSPEKTDVTASTISPPSYDSVTKPDQEKYETDKTEKEDKEKDESRK

hide sequence

Ensembl Acc Id:

ENSRNOP00000068852 ⟸ ENSRNOT00000079020

Ensembl Acc Id:

ENSRNOP00000059170 ⟸ ENSRNOT00000065126

RefSeq Acc Id:	XP_063140670 ⟸ XM_063284600
- Peptide Label:	isoform X2
- UniProtKB:	A0A8L2QSN0 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_063140669 ⟸ XM_063284599
- Peptide Label:	isoform X1
- UniProtKB:	A0A8L2QSN0 (UniProtKB/TrEMBL)

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

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:69368	AgrOrtholog
BioCyc Gene	G2FUF-49539	BioCyc
Ensembl Genes	ENSRNOG00000006639	Ensembl, ENTREZGENE
Ensembl Transcript	ENSRNOT00000065126	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
	IQ_motif_EF-hand-BS	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:78956	UniProtKB/Swiss-Prot
NCBI Gene	78956	ENTREZGENE
PANTHER	PTHR10037	UniProtKB/Swiss-Prot
	PTHR10037:SF221	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
PhenoGen	Scn9a	PhenoGen
PRINTS	NACHANNEL	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000006639	RatGTEx
SMART	SM00015	UniProtKB/Swiss-Prot
Superfamily-SCOP	Voltage-gated potassium channels	UniProtKB/Swiss-Prot
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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Mammalian Phenotype

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Mammalian Phenotype