Scn3a (sodium voltage-gated channel alpha subunit 3) - Rat Genome Database

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Gene: Scn3a (sodium voltage-gated channel alpha subunit 3) Rattus norvegicus
Analyze
Symbol: Scn3a
Name: sodium voltage-gated channel alpha subunit 3
RGD ID: 3635
Description: Enables calmodulin binding activity. Involved in cellular response to antibiotic; nervous system development; and response to pyrethroid. Located in axon and neuronal cell body. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 62 and familial focal epilepsy with variable foci 4. Orthologous to human SCN3A (sodium voltage-gated channel alpha subunit 3); INTERACTS WITH 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100360249; Nav1.3; rCG26412-like; SCIII; Scn2a; sodium channel protein brain III subunit alpha; sodium channel protein type 3 subunit alpha; sodium channel protein type 3 subunit alpha-like; sodium channel protein type III subunit alpha; sodium channel protein, brain III subunit alpha; sodium channel, voltage-gated, type 3, alpha subunit; sodium channel, voltage-gated, type III, alpha; sodium channel, voltage-gated, type III, alpha polypeptide; sodium channel, voltage-gated, type III, alpha subunit; voltage-gated sodium channel subtype III; voltage-gated sodium channel subunit alpha Nav1.3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8370,554,496 - 70,666,198 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl370,556,224 - 70,666,198 (-)EnsemblGRCr8
mRatBN7.2350,146,411 - 50,258,119 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl350,148,139 - 50,258,119 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx353,491,661 - 53,601,660 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0362,075,268 - 62,185,269 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0359,858,870 - 59,968,781 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0351,530,897 - 51,643,140 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl351,532,627 - 51,643,140 (-)Ensemblrn6Rnor6.0
Rnor_5.0358,165,763 - 58,277,870 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4347,501,895 - 47,512,863NCBIRGSC_v3.4RGSC_v3.4rn4
Celera349,742,093 - 49,851,946 (-)NCBICelera
RH 3.4 Map3 RGD
Cytogenetic Map3q21NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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. Changes in electrophysiological properties and sodium channel Nav1.3 expression in thalamic neurons after spinal cord injury. Hains BC, etal., Brain. 2005 Oct;128(Pt 10):2359-71. Epub 2005 Aug 18.
4. Upregulation of sodium channel Nav1.3 and functional involvement in neuronal hyperexcitability associated with central neuropathic pain after spinal cord injury. Hains BC, etal., J Neurosci 2003 Oct 1;23(26):8881-92.
5. Primary structure of rat brain sodium channel III deduced from the cDNA sequence. Kayano T, etal., FEBS Lett 1988 Feb 8;228(1):187-94.
6. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
7. Upregulation of persistent and ramp sodium current in dorsal horn neurons after spinal cord injury. Lampert A, etal., Exp Brain Res. 2006 Oct;174(4):660-6. Epub 2006 May 23.
8. Vasa recta voltage-gated Na+ channel Nav1.3 is regulated by calmodulin. Lee-Kwon W, etal., Am J Physiol Renal Physiol. 2007 Jan;292(1):F404-14. Epub 2006 Aug 15.
9. 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.
10. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
11. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
12. GOA pipeline RGD automated data pipeline
13. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
15. Contactin associates with sodium channel Nav1.3 in native tissues and increases channel density at the cell surface. Shah BS, etal., J Neurosci. 2004 Aug 18;24(33):7387-99.
16. Human and rat Nav1.3 voltage-gated sodium channels differ in inactivation properties and sensitivity to the pyrethroid insecticide tefluthrin. Tan J and Soderlund DM, Neurotoxicology. 2009 Jan;30(1):81-9. Epub 2008 Nov 5.
17. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
18. Differential expression of neuronal voltage-gated sodium channel mRNAs during the development of the rat trigeminal ganglion. Thun J, etal., Brain Res. 2009 May 7;1269:11-22. Epub 2009 Mar 6.
19. Deglycosylation altered the gating properties of rNav1.3: glycosylation/deglycosylation homeostasis probably complicates the functional regulation of voltage-gated sodium channel. Xu Q, etal., Neurosci Bull. 2008 Oct;24(5):283-7.
20. Localization of Na+ channel isoforms at the atrioventricular junction and atrioventricular node in the rat. Yoo S, etal., Circulation. 2006 Sep 26;114(13):1360-71. Epub 2006 Sep 11.
Additional References at PubMed
PMID:12967988   PMID:15152043   PMID:15632090   PMID:15746173   PMID:17537961   PMID:18242854   PMID:20420834   PMID:20858468   PMID:22871113   PMID:22928478   PMID:23219908   PMID:23364266  
PMID:23868758   PMID:26101954   PMID:27327156   PMID:28298073   PMID:29388177   PMID:29956586   PMID:30267849   PMID:30889362   PMID:33651884   PMID:34296787   PMID:34726508   PMID:38714229  


Genomics

Comparative Map Data
Scn3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8370,554,496 - 70,666,198 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl370,556,224 - 70,666,198 (-)EnsemblGRCr8
mRatBN7.2350,146,411 - 50,258,119 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl350,148,139 - 50,258,119 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx353,491,661 - 53,601,660 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0362,075,268 - 62,185,269 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0359,858,870 - 59,968,781 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0351,530,897 - 51,643,140 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl351,532,627 - 51,643,140 (-)Ensemblrn6Rnor6.0
Rnor_5.0358,165,763 - 58,277,870 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4347,501,895 - 47,512,863NCBIRGSC_v3.4RGSC_v3.4rn4
Celera349,742,093 - 49,851,946 (-)NCBICelera
RH 3.4 Map3 RGD
Cytogenetic Map3q21NCBI
SCN3A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382165,087,526 - 165,204,050 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2165,087,526 - 165,204,050 (-)Ensemblhg38GRCh38
GRCh372165,944,036 - 166,060,560 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362165,652,276 - 165,768,823 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342165,769,546 - 165,886,060NCBI
Celera2159,554,632 - 159,671,179 (-)NCBICelera
Cytogenetic Map2q24.3NCBI
HuRef2157,826,522 - 157,942,999 (-)NCBIHuRef
CHM1_12165,949,962 - 166,066,539 (-)NCBICHM1_1
T2T-CHM13v2.02165,544,858 - 165,661,382 (-)NCBIT2T-CHM13v2.0
Scn3a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39265,287,462 - 65,397,935 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl265,288,607 - 65,397,971 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38265,457,118 - 65,567,591 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl265,457,118 - 65,567,627 (-)Ensemblmm10GRCm38
MGSCv37265,295,175 - 65,405,549 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36265,260,704 - 65,368,333 (-)NCBIMGSCv36mm8
Celera267,134,509 - 67,244,961 (-)NCBICelera
Cytogenetic Map2C1.3NCBI
cM Map238.55NCBI
Scn3a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554498,896,454 - 9,009,304 (+)Ensembl
ChiLan1.0NW_0049554498,896,454 - 9,009,304 (+)NCBIChiLan1.0ChiLan1.0
SCN3A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21367,748,846 - 67,865,733 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B67,763,601 - 67,880,709 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B52,363,020 - 52,479,818 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B169,722,134 - 169,838,590 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B169,722,134 - 169,838,590 (-)EnsemblpanPan2panpan1.1
SCN3A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13610,300,091 - 10,405,361 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3610,302,191 - 10,377,923 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3610,443,366 - 10,548,111 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03610,431,868 - 10,536,904 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3610,431,875 - 10,536,895 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13610,504,943 - 10,609,699 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03610,485,818 - 10,590,745 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03610,598,953 - 10,703,719 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Scn3a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303127,437,094 - 127,545,534 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493646914,101,868 - 14,179,998 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493646914,072,182 - 14,180,552 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN3A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1571,717,334 - 71,824,160 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11571,717,330 - 71,824,190 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21580,183,966 - 80,256,583 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCN3A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11050,563,560 - 50,679,179 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1050,563,568 - 50,637,179 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666040148,830,543 - 148,945,804 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scn3a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624732251,860 - 328,917 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624732222,657 - 330,959 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Scn3a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1542,951,022 - 43,060,217 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Scn3a
1408 total Variants
miRNA Target Status (No longer updated)

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir214rno-miR-214-3pMirtarbaseexternal_infoMicroarrayFunctional MTI (Weak)18258830

Predicted Target Of
Summary Value
Count of predictions:173
Count of miRNA genes:116
Interacting mature miRNAs:131
Transcripts:ENSRNOT00000006646
Prediction methods:Microtar, Miranda, Rnahybrid, 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
2313079Bss73Bone structure and strength QTL 731.5tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)34790417270710963Rat
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
2313076Bss74Bone structure and strength QTL 7420.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)34790417270710963Rat
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
10450816Scl75Serum cholesterol level QTL 754.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)35860129171157804Rat
10450813Scl74Serum cholesterol level QTL 745.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)35860129171157804Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)33779691982796919Rat
2313093Bmd77Bone mineral density QTL 772.20.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)34790417270710963Rat
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
2313101Bmd76Bone mineral density QTL 763.60.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)34790417270710963Rat
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
2313049Bss72Bone structure and strength QTL 722.60.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)34790417270710963Rat
10450852Stl33Serum triglyceride level QTL 333.40.05blood LDL triglyceride amount (VT:0010699)blood lipoprotein triglyceride level (CMO:0002685)35860129171157804Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
4889975Bmd81Bone mineral density QTL 814.3tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)35911940270710963Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat

Markers in Region
RH94597  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,148,320 - 50,148,457 (+)MAPPERmRatBN7.2
Rnor_6.0351,532,809 - 51,532,945NCBIRnor6.0
Rnor_5.0358,167,675 - 58,167,811UniSTSRnor5.0
RGSC_v3.4347,421,503 - 47,421,639UniSTSRGSC3.4
Celera349,742,275 - 49,742,411UniSTS
RH 3.4 Map3608.11UniSTS
Cytogenetic Map3q21UniSTS
RH139649  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,197,174 - 50,197,375 (+)MAPPERmRatBN7.2
Rnor_6.0351,582,165 - 51,582,365NCBIRnor6.0
Rnor_5.0358,217,031 - 58,217,231UniSTSRnor5.0
Celera349,791,124 - 49,791,324UniSTS
RH 3.4 Map3622.6UniSTS
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


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
16 12 63 149 63 62 31 37 31 6 268 133 11 128 80 92 31 12 12

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001437770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_013119 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761915 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105646 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105648 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AM905325 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y00766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000006646   ⟹   ENSRNOP00000006646
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl370,556,224 - 70,666,198 (-)Ensembl
mRatBN7.2 Ensembl350,148,139 - 50,258,119 (-)Ensembl
Rnor_6.0 Ensembl351,532,627 - 51,643,140 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000081401   ⟹   ENSRNOP00000072091
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl370,556,224 - 70,666,198 (-)Ensembl
mRatBN7.2 Ensembl350,148,139 - 50,258,119 (-)Ensembl
Rnor_6.0 Ensembl351,533,181 - 51,612,397 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000098569   ⟹   ENSRNOP00000078175
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,148,525 - 50,258,119 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000120177   ⟹   ENSRNOP00000092389
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,148,693 - 50,258,119 (-)Ensembl
RefSeq Acc Id: NM_013119   ⟹   NP_037251
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8370,556,224 - 70,666,198 (-)NCBI
mRatBN7.2350,148,139 - 50,258,119 (-)NCBI
Rnor_6.0351,532,627 - 51,643,140 (-)NCBI
Rnor_5.0358,165,763 - 58,277,870 (-)NCBI
Celera349,742,093 - 49,851,946 (-)RGD
Sequence:
RefSeq Acc Id: XM_008761915   ⟹   XP_008760137
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8370,554,496 - 70,664,182 (-)NCBI
mRatBN7.2350,148,693 - 50,256,113 (-)NCBI
Rnor_6.0351,530,897 - 51,641,607 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008761916   ⟹   XP_008760138
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8370,554,496 - 70,666,112 (-)NCBI
mRatBN7.2350,148,693 - 50,258,015 (-)NCBI
Rnor_6.0351,530,897 - 51,613,168 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008761918   ⟹   XP_008760140
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8370,554,496 - 70,666,112 (-)NCBI
mRatBN7.2350,148,693 - 50,258,015 (-)NCBI
Rnor_6.0351,530,897 - 51,613,167 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008761920   ⟹   XP_008760142
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8370,554,496 - 70,666,126 (-)NCBI
mRatBN7.2350,148,693 - 50,227,374 (-)NCBI
Rnor_6.0351,530,897 - 51,613,167 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591972   ⟹   XP_017447461
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8370,554,496 - 70,666,126 (-)NCBI
mRatBN7.2350,148,693 - 50,258,015 (-)NCBI
Rnor_6.0351,530,897 - 51,643,048 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039105646   ⟹   XP_038961574
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8370,554,496 - 70,666,112 (-)NCBI
mRatBN7.2350,148,693 - 50,227,374 (-)NCBI
RefSeq Acc Id: XM_039105647   ⟹   XP_038961575
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8370,554,496 - 70,612,106 (-)NCBI
mRatBN7.2350,148,693 - 50,204,024 (-)NCBI
RefSeq Acc Id: XM_039105648   ⟹   XP_038961576
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8370,584,378 - 70,666,112 (-)NCBI
mRatBN7.2350,176,287 - 50,258,018 (-)NCBI
RefSeq Acc Id: NP_037251   ⟸   NM_013119
- UniProtKB: A6HLX3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760137   ⟸   XM_008761915
- Peptide Label: isoform X1
- UniProtKB: A6HLX3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760138   ⟸   XM_008761916
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K237 (UniProtKB/TrEMBL),   A6HLX3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760140   ⟸   XM_008761918
- Peptide Label: isoform X3
- UniProtKB: A6HLX3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008760142   ⟸   XM_008761920
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017447461   ⟸   XM_017591972
- Peptide Label: isoform X1
- UniProtKB: A6HLX3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000006646   ⟸   ENSRNOT00000006646
Ensembl Acc Id: ENSRNOP00000072091   ⟸   ENSRNOT00000081401
RefSeq Acc Id: XP_038961574   ⟸   XM_039105646
- Peptide Label: isoform X4
- UniProtKB: A6HLX3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038961575   ⟸   XM_039105647
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038961576   ⟸   XM_039105648
- Peptide Label: isoform X7
Ensembl Acc Id: ENSRNOP00000092389   ⟸   ENSRNOT00000120177
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-P08104-F1-model_v2 AlphaFold P08104 1-1951 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:3635 AgrOrtholog
BioCyc Gene G2FUF-49555 BioCyc
Ensembl Genes ENSRNOG00000005007 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000006646 ENTREZGENE
  ENSRNOT00000081401 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_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:497770 UniProtKB/Swiss-Prot
NCBI Gene Scn3a ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot
  SODIUM CHANNEL PROTEIN TYPE 3 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 SCN3A RGD
PhenoGen Scn3a PhenoGen
PRINTS NACHANNEL UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000005007 RatGTEx
Superfamily-SCOP Voltage-gated potassium channels UniProtKB/Swiss-Prot
TIGR TC232529
UniProt A0A0G2K237 ENTREZGENE, UniProtKB/TrEMBL
  A6HLX3 ENTREZGENE, UniProtKB/TrEMBL
  A9JQD9_RAT UniProtKB/TrEMBL
  F1LX08_RAT UniProtKB/TrEMBL
  P08104 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Scn3a  sodium voltage-gated channel alpha subunit 3  Scn3a  sodium channel, voltage-gated, type III, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-29 Scn3a  sodium channel, voltage-gated, type III, alpha subunit  LOC100360249  sodium channel protein type 3 subunit alpha-like  Data merged from RGD:2322502 737654 PROVISIONAL
2014-08-13 Scn3a  sodium channel, voltage-gated, type III, alpha subunit  Scn3a  sodium channel, voltage-gated, type III, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 Scn3a  sodium channel, voltage-gated, type III, alpha  LOC100360303  rCG26412-like  Data merged from RGD:2322349 1643240 APPROVED
2010-05-06 LOC100360249  sodium channel protein type 3 subunit alpha-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-06 LOC100360303  rCG26412-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-31 Scn3a  sodium channel, voltage-gated, type III, alpha  Scn3a  sodium channel, voltage-gated, type 3, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Scn3a  sodium channel, voltage-gated, type 3, alpha subunit  Scn3a  sodium channel, voltage-gated, type III, alpha polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Scn3a  Sodium channel, voltage-gated, type III, alpha polypeptide      Symbol and Name status set to approved 70586 APPROVED