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; sodium ion binding activity; and voltage-gated sodium channel activity. Involved in several processes, including cellular response to antibiotic; neuronal action potential; and response to pyrethroid. Located in axon and neuronal cell body. Part of voltage-gated sodium channel complex. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 62 and focal epilepsy. 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: PROVISIONAL
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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8370,554,496 - 70,666,198 (-)NCBIGRCr8
mRatBN7.2350,146,411 - 50,258,119 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl350,148,139 - 50,258,119 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx353,491,661 - 53,601,660 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0362,075,268 - 62,185,269 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0359,858,870 - 59,968,781 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0351,530,897 - 51,643,140 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl351,532,627 - 51,643,140 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0358,165,763 - 58,277,870 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4347,501,895 - 47,512,863NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera349,742,093 - 49,851,946 (-)NCBICelera
RH 3.4 Map3 RGD
Cytogenetic Map3q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
axon  (IBA,IDA,IEA)
membrane  (ISO)
neuronal cell body  (IDA)
sarcoplasm  (IEA,ISO)
voltage-gated sodium channel complex  (IBA,IDA,IEA,TAS)

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  


Genomics

Comparative Map Data
Scn3a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8370,554,496 - 70,666,198 (-)NCBIGRCr8
mRatBN7.2350,146,411 - 50,258,119 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl350,148,139 - 50,258,119 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx353,491,661 - 53,601,660 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0362,075,268 - 62,185,269 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0359,858,870 - 59,968,781 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0351,530,897 - 51,643,140 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl351,532,627 - 51,643,140 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0358,165,763 - 58,277,870 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4347,501,895 - 47,512,863NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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 (-)EnsemblGRCh38hg38GRCh38
GRCh372165,944,036 - 166,060,560 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362165,652,276 - 165,768,823 (-)NCBINCBI36Build 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 Ensembl
GRCm38265,457,118 - 65,567,591 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl265,457,118 - 65,567,627 (-)EnsemblGRCm38mm10GRCm38
MGSCv37265,295,175 - 65,405,549 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3610,443,366 - 10,548,111 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03610,431,868 - 10,536,904 (-)NCBIROS_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_1.0
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624732222,657 - 330,959 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Scn3a
447 total Variants
miRNA Target Status

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 (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
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
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
2313049Bss72Bone structure and strength QTL 722.60.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)32749462150302886Rat
2313076Bss74Bone structure and strength QTL 7420.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)32749462150302886Rat
2313079Bss73Bone structure and strength QTL 731.5tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)32749462150302886Rat
2313093Bmd77Bone mineral density QTL 772.20.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)32749462150302886Rat
2313101Bmd76Bone mineral density QTL 763.60.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)32749462150302886Rat
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
10450852Stl33Serum triglyceride level QTL 333.40.05blood LDL triglyceride amount (VT:0010699)blood lipoprotein triglyceride level (CMO:0002685)33819223350749747Rat
10450816Scl75Serum cholesterol level QTL 754.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)33819223350749747Rat
10450813Scl74Serum cholesterol level QTL 745.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)33819223350749747Rat
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
4889975Bmd81Bone mineral density QTL 814.3tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)33871036550302886Rat
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

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
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 64
Low 2 27 14 7 8 10 10 31 36 9 8
Below cutoff 1 16 17 15 12 15 1 4 5 2

Sequence


RefSeq Acc Id: ENSRNOT00000006646   ⟹   ENSRNOP00000006646
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,148,139 - 50,258,119 (-)Ensembl
Rnor_6.0 Ensembl351,532,627 - 51,643,140 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081401   ⟹   ENSRNOP00000072091
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,148,139 - 50,258,119 (-)Ensembl
Rnor_6.0 Ensembl351,533,181 - 51,612,397 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098569   ⟹   ENSRNOP00000078175
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,148,525 - 50,258,119 (-)Ensembl
RefSeq 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: PROVISIONAL
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
- UniProtKB: A6HLX3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447461   ⟸   XM_017591972
- Peptide Label: isoform X1
- UniProtKB: A6HLX3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006646   ⟸   ENSRNOT00000006646
RefSeq 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
RefSeq Acc Id: ENSRNOP00000092389   ⟸   ENSRNOT00000120177
RefSeq Acc Id: ENSRNOP00000078175   ⟸   ENSRNOT00000098569
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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006646 ENTREZGENE
  ENSRNOT00000006646.8 UniProtKB/TrEMBL
  ENSRNOT00000081401.2 UniProtKB/TrEMBL
  ENSRNOT00000098569.1 UniProtKB/TrEMBL
  ENSRNOT00000120177.1 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
  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:497770 UniProtKB/Swiss-Prot
NCBI Gene Scn3a ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SODIUM CHANNEL PROTEIN TYPE 3 SUBUNIT ALPHA 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
PharmGKB SCN3A RGD
PhenoGen Scn3a PhenoGen
PRINTS NACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000005007 RatGTEx
Superfamily-SCOP Voltage-gated potassium channels UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC232529
UniProt A0A0G2K237 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZKG7_RAT UniProtKB/TrEMBL
  A0A8I6AHR7_RAT 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