Scn2a (sodium voltage-gated channel alpha subunit 2) - Rat Genome Database

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Gene: Scn2a (sodium voltage-gated channel alpha subunit 2) Rattus norvegicus
Analyze
Symbol: Scn2a
Name: sodium voltage-gated channel alpha subunit 2
RGD ID: 3632
Description: Enables leucine zipper domain binding activity; monoatomic ion channel activity; and sodium ion binding activity. Involved in several processes, including nervous system development; neuronal action potential; and sodium ion transmembrane transport. Located in axon initial segment; node of Ranvier; and plasma membrane. Part of voltage-gated sodium channel complex. Human ortholog(s) of this gene implicated in benign familial infantile seizures 3; developmental and epileptic encephalopathy 11; and episodic ataxia. Orthologous to human SCN2A (sodium voltage-gated channel alpha subunit 2); INTERACTS WITH 1-naphthyl isothiocyanate; 2,2',4,4'-Tetrabromodiphenyl ether; 2,2',5,5'-tetrachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: alternative product; NachII; Nav1.2; RII/RIIA; RIIA sodium channel protein; RNSCPIIR; SCN; Scn2a1; Scn2a2; ScpII; sodium channel protein brain II subunit alpha; sodium channel protein type 2 subunit alpha; sodium channel protein type II subunit alpha; sodium channel protein, brain II subunit alpha; Sodium channel voltage-gated type II alpha polypeptide; sodium channel, voltage-gated, type 2, alpha 1 polypeptide; sodium channel, voltage-gated, type 2, alpha 1 subunit; sodium channel, voltage-gated, type II, alpha 1; Sodium channel, voltage-gated, type II, alpha polypeptide; sodium channel, voltage-gated, type II, alpha subunit; voltage-gated sodium channel subunit alpha Nav1.2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Allele / Splice: Scn2aem1Mcwi   Scn2aem2Mcwi  
Genetic Models: LE-Scn2aem1Mcwi
Is Marker For: QTLs:   BpQTLcluster4   Tsu1   Hrtrt17  
Candidate Gene For: Cia11 Hrtrt17
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2350,302,781 - 50,437,504 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl350,302,877 - 50,437,214 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx353,646,466 - 53,788,492 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0362,230,075 - 62,372,108 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0360,013,503 - 60,148,019 (+)NCBIRnor_WKY
Rnor_6.0351,687,910 - 51,822,008 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl351,687,809 - 51,822,250 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0358,322,640 - 58,456,658 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4347,588,413 - 47,722,800 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1347,484,784 - 47,619,172 (+)NCBI
Celera349,896,043 - 50,030,402 (+)NCBICelera
RH 3.4 Map3613.5RGD
Cytogenetic Map3q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
asphyxiating thoracic dystrophy  (ISO)
asphyxiating thoracic dystrophy 1  (ISO)
autism spectrum disorder  (ISO,ISS)
autistic disorder  (ISO)
benign epilepsy with centrotemporal spikes  (ISO)
benign familial infantile epilepsy  (ISO)
benign familial infantile seizures 3  (ISO)
benign familial neonatal epilepsy  (ISO)
benign neonatal seizures  (ISO)
bipolar disorder  (ISO)
developmental and epileptic encephalopathy  (ISO)
developmental and epileptic encephalopathy 11  (ISO)
developmental and epileptic encephalopathy 14  (ISO)
developmental and epileptic encephalopathy 30  (ISO)
Developmental Disabilities  (ISO)
Developmental Disease  (ISO)
Dravet syndrome  (ISO)
dystonia 12  (ISO)
early infantile epileptic encephalopathy  (ISO)
epilepsy  (ISO)
episodic ataxia  (ISO)
Episodic Ataxia Type 9  (ISO)
Febrile Seizures  (ISO)
focal epilepsy  (ISO)
Generalized Epilepsy  (ISO)
generalized epilepsy with febrile seizures plus  (ISO)
generalized epilepsy with febrile seizures plus 7  (ISO)
genetic disease  (ISO)
hemiplegia  (ISO)
hereditary sensory and autonomic neuropathy type 2A  (ISO)
hereditary sensory neuropathy  (ISO)
intellectual disability  (ISO)
Lennox-Gastaut syndrome  (ISO)
Marfanoid Mental Retardation Syndrome, Autosomal  (ISO)
myoclonic-atonic epilepsy  (ISO)
Myoclonus  (ISO)
nephronophthisis  (ISO)
nephronophthisis 1  (ISO)
NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, ARTHROGRYPOSIS, AND STRUCTURAL BRAIN ANOMALIES  (ISO)
Neurodevelopmental Disorders  (ISO)
non-syndromic intellectual disability  (ISO)
Noonan syndrome 1  (ISO)
Osteoporosis, Childhood- or Juvenile-Onset, with Developmental Delay  (ISO)
pyridoxine-dependent epilepsy  (ISO)
spastic ataxia  (ISO)
West syndrome  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Interaction of the Nav1.2a subunit of the voltage-dependent sodium channel with nodal ankyrinG. In vitro mapping of the interacting domains and association in synaptosomes. Bouzidi M, etal., J Biol Chem 2002 Aug 9;277(32):28996-9004.
2. Structural and energetic determinants of apo calmodulin binding to the IQ motif of the Na(V)1.2 voltage-dependent sodium channel. Feldkamp MD, etal., Structure. 2011 May 11;19(5):733-47. doi: 10.1016/j.str.2011.02.009.
3. Dopamine modulation of neuronal Na(+) channels requires binding of A kinase-anchoring protein 15 and PKA by a modified leucine zipper motif. Few WP, etal., Proc Natl Acad Sci U S A. 2007 Mar 20;104(12):5187-92. Epub 2007 Mar 14.
4. 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.
5. Crystallographic insights into sodium-channel modulation by the beta4 subunit. Gilchrist J, etal., Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):E5016-24. doi: 10.1073/pnas.1314557110. Epub 2013 Dec 2.
6. Identification of four new quantitative trait loci regulating arthritis severity and one new quantitative trait locus regulating autoantibody production in rats with collagen-induced arthritis. Griffiths MM, etal., Arthritis Rheum 2000 Jun;43(6):1278-89
7. Coexpression of high-voltage-activated ion channels Kv3.4 and Cav1.2 in pioneer axons during pathfinding in the developing rat forebrain. Huang CY, etal., J Comp Neurol. 2012 Nov 1;520(16):3650-72. doi: 10.1002/cne.23119.
8. Autosomal dominant epilepsy with febrile seizures plus with missense mutations of the (Na+)-channel alpha 1 subunit gene, SCN1A. Ito M, etal., Epilepsy Res 2002 Jan;48(1-2):15-23.
9. The Nav1.2 channel is regulated by GSK3. James TF, etal., Biochim Biophys Acta. 2015 Apr;1850(4):832-44. doi: 10.1016/j.bbagen.2015.01.011. Epub 2015 Jan 20.
10. 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
11. Helix-stabilizing effects of the pentapeptide KIFMK and its related peptides on the sodium channel inactivation gate peptides. Maeda Y, etal., J Pept Res 2001 Nov;58(5):413-23.
12. 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.
13. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
14. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. Structure and function of sodium channel. Noda M and Numa S, J Recept Res 1987;7(1-4):467-97.
16. Structure and function of sodium channel. Noda M and Numa S, J Recept Res 1987;7(1-4):467-97.
17. Existence of distinct sodium channel messenger RNAs in rat brain. Noda M, etal., Nature 1986 Mar 13-19;320(6058):188-92.
18. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
19. SUMOylation of NaV1.2 channels mediates the early response to acute hypoxia in central neurons. Plant LD, etal., Elife. 2016 Dec 28;5. doi: 10.7554/eLife.20054.
20. Sodium currents in medullary neurons isolated from the pre-Botzinger complex region. Ptak K, etal., J Neurosci. 2005 May 25;25(21):5159-70.
21. GOA pipeline RGD automated data pipeline
22. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
23. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
24. Direct interaction between synaptotagmin and the intracellular loop I-II of neuronal voltage-sensitive sodium channels. Sampo B, etal., Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3666-71.
25. Early events in node of Ranvier formation during myelination and remyelination in the PNS. Schafer DP, etal., Neuron Glia Biol. 2006 May;2(2):69-79.
26. A novel SCN2A mutation in family with benign familial infantile seizures. Striano P, etal., Epilepsia. 2006 Jan;47(1):218-20.
27. Gene-based anchoring of the rat genetic linkage and cytogenetic maps: new regional localizations, orientation of the linkage groups, and insights into mammalian chromosome evolution. Szpirer C, etal., Mamm Genome 1998 Sep;9(9):721-34
Additional References at PubMed
PMID:1299025   PMID:10827969   PMID:12829783   PMID:12930796   PMID:12967988   PMID:15548568   PMID:15746173   PMID:16596442   PMID:16723544   PMID:16815341   PMID:17021166   PMID:17537961  
PMID:17928448   PMID:19221510   PMID:19465131   PMID:19692609   PMID:19809503   PMID:20459109   PMID:21795675   PMID:22123950   PMID:22528969   PMID:22871113   PMID:23219908   PMID:23364266  
PMID:24737319   PMID:25724910   PMID:26039939   PMID:26259688   PMID:28256214   PMID:28343066   PMID:28758202   PMID:28916793   PMID:29867081   PMID:29956586   PMID:33051988  


Genomics

Comparative Map Data
Scn2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2350,302,781 - 50,437,504 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl350,302,877 - 50,437,214 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx353,646,466 - 53,788,492 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0362,230,075 - 62,372,108 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0360,013,503 - 60,148,019 (+)NCBIRnor_WKY
Rnor_6.0351,687,910 - 51,822,008 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl351,687,809 - 51,822,250 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0358,322,640 - 58,456,658 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4347,588,413 - 47,722,800 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1347,484,784 - 47,619,172 (+)NCBI
Celera349,896,043 - 50,030,402 (+)NCBICelera
RH 3.4 Map3613.5RGD
Cytogenetic Map3q21NCBI
SCN2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382165,239,414 - 165,392,304 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2165,194,993 - 165,392,310 (+)EnsemblGRCh38hg38GRCh38
GRCh372166,095,924 - 166,248,814 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362165,804,158 - 165,957,066 (+)NCBINCBI36Build 36hg18NCBI36
Build 342165,976,098 - 166,072,046NCBI
Celera2159,706,512 - 159,859,384 (+)NCBICelera
Cytogenetic Map2q24.3NCBI
HuRef2157,978,323 - 158,131,089 (+)NCBIHuRef
CHM1_12166,101,845 - 166,254,789 (+)NCBICHM1_1
T2T-CHM13v2.02165,696,714 - 165,849,575 (+)NCBIT2T-CHM13v2.0
Scn2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39265,451,108 - 65,597,791 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl265,451,115 - 65,597,791 (+)EnsemblGRCm39 Ensembl
GRCm38265,620,764 - 65,767,447 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl265,620,771 - 65,767,447 (+)EnsemblGRCm38mm10GRCm38
MGSCv37265,508,502 - 65,605,504 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36265,471,335 - 65,568,290 (+)NCBIMGSCv36mm8
Celera267,347,826 - 67,445,379 (+)NCBICelera
Cytogenetic Map2C1.3NCBI
cM Map238.61NCBI
Scn2a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554498,721,784 - 8,846,200 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554498,722,043 - 8,846,165 (-)NCBIChiLan1.0ChiLan1.0
SCN2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan12B67,915,794 - 68,067,823 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B52,514,918 - 52,667,225 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B169,873,992 - 170,026,392 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B169,928,323 - 170,027,509 (+)Ensemblpanpan1.1panPan2
SCN2A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13610,472,496 - 10,605,055 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3610,472,361 - 10,602,685 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3610,615,273 - 10,749,736 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03610,604,046 - 10,738,882 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3610,604,041 - 10,738,874 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13610,686,329 - 10,820,763 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03610,658,084 - 10,792,902 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03610,770,872 - 10,905,712 (+)NCBIUU_Cfam_GSD_1.0
Scn2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303127,536,296 - 127,745,013 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493646913,872,701 - 13,971,005 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493646913,872,701 - 14,019,170 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100515171
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1571,864,784 - 71,999,211 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11571,864,753 - 71,999,219 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21580,349,224 - 80,429,339 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SCN2A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11050,717,264 - 50,886,079 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1050,717,271 - 50,888,145 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040148,625,514 - 148,788,747 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Scn2a
857 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:70
Interacting mature miRNAs:88
Transcripts:ENSRNOT00000007069
Prediction methods: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
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat

Markers in Region
D3Mit8  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,302,679 - 50,302,886 (+)MAPPERmRatBN7.2
Rnor_6.0351,687,711 - 51,687,917NCBIRnor6.0
Rnor_5.0358,322,441 - 58,322,647UniSTSRnor5.0
RGSC_v3.4347,588,214 - 47,588,420UniSTSRGSC3.4
RGSC_v3.1347,484,585 - 47,484,792RGD
Celera349,895,844 - 49,896,050UniSTS
RH 3.4 Map3615.3RGD
RH 3.4 Map3615.3UniSTS
SHRSP x BN Map335.0198UniSTS
SHRSP x BN Map335.0198RGD
FHH x ACI Map336.02RGD
Cytogenetic Map3q24UniSTS
D3Wox9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,436,913 - 50,437,042 (+)MAPPERmRatBN7.2
Rnor_6.0351,821,710 - 51,821,836NCBIRnor6.0
Rnor_5.0358,456,360 - 58,456,486UniSTSRnor5.0
RGSC_v3.4347,722,501 - 47,722,628RGDRGSC3.4
RGSC_v3.4347,722,502 - 47,722,628UniSTSRGSC3.4
Celera350,030,104 - 50,030,230UniSTS
Cytogenetic Map3q24UniSTS
D3Wox10  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,436,913 - 50,437,041 (+)MAPPERmRatBN7.2
Rnor_6.0351,821,710 - 51,821,835NCBIRnor6.0
Rnor_5.0358,456,360 - 58,456,485UniSTSRnor5.0
RGSC_v3.4347,722,501 - 47,722,627RGDRGSC3.4
RGSC_v3.4347,722,502 - 47,722,627UniSTSRGSC3.4
Celera350,030,104 - 50,030,229UniSTS
Cytogenetic Map3q24UniSTS
D3Wox14  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,436,785 - 50,437,053 (+)MAPPERmRatBN7.2
Rnor_6.0351,821,582 - 51,821,847NCBIRnor6.0
Rnor_5.0358,456,232 - 58,456,497UniSTSRnor5.0
RGSC_v3.4347,722,374 - 47,722,639UniSTSRGSC3.4
Celera350,029,976 - 50,030,241UniSTS
Cytogenetic Map3q24UniSTS
D3Arb7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,436,912 - 50,437,162 (+)MAPPERmRatBN7.2
Rnor_6.0351,821,709 - 51,821,956NCBIRnor6.0
Rnor_5.0358,456,359 - 58,456,606UniSTSRnor5.0
RGSC_v3.4347,722,501 - 47,722,748UniSTSRGSC3.4
RGSC_v3.4347,722,500 - 47,722,748RGDRGSC3.4
RGSC_v3.1347,618,872 - 47,619,120RGD
Celera350,030,103 - 50,030,350UniSTS
RH 3.4 Map3614.1RGD
RH 3.4 Map3614.1UniSTS
RH 2.0 Map3405.1RGD
SHRSP x BN Map335.0198RGD
FHH x ACI Map334.98RGD
Cytogenetic Map3q24UniSTS
D3Rat240  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,344,842 - 50,345,069 (+)MAPPERmRatBN7.2
Rnor_6.0351,729,860 - 51,730,084NCBIRnor6.0
Rnor_5.0358,364,510 - 58,364,734UniSTSRnor5.0
RGSC_v3.4347,630,436 - 47,630,661RGDRGSC3.4
RGSC_v3.4347,630,437 - 47,630,661UniSTSRGSC3.4
RGSC_v3.1347,526,593 - 47,527,132RGD
Celera349,938,073 - 49,938,297UniSTS
FHH x ACI Map336.02UniSTS
FHH x ACI Map336.02RGD
Cytogenetic Map3q24UniSTS
RH94610  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,435,631 - 50,435,801 (+)MAPPERmRatBN7.2
Rnor_6.0351,820,428 - 51,820,597NCBIRnor6.0
Rnor_5.0358,455,078 - 58,455,247UniSTSRnor5.0
RGSC_v3.4347,721,220 - 47,721,389UniSTSRGSC3.4
Celera350,028,822 - 50,028,991UniSTS
RH 3.4 Map3613.5UniSTS
Cytogenetic Map3q24UniSTS
RH138915  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,413,356 - 50,413,550 (+)MAPPERmRatBN7.2
Rnor_6.0351,798,334 - 51,798,527NCBIRnor6.0
Rnor_5.0358,432,984 - 58,433,177UniSTSRnor5.0
RGSC_v3.4347,698,945 - 47,699,138UniSTSRGSC3.4
Celera350,006,547 - 50,006,740UniSTS
RH 3.4 Map3619.4UniSTS
Cytogenetic Map3q24UniSTS
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


Genetic Models
This gene Scn2a is modified in the following models/strains

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 58
Low 1 1 12 1 3 1 5 5 16 14 38 8 5
Below cutoff 2 42 22 17 16 17 3 5 20 3 3 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007069   ⟹   ENSRNOP00000007069
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,302,877 - 50,434,883 (+)Ensembl
Rnor_6.0 Ensembl351,737,904 - 51,819,679 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087242   ⟹   ENSRNOP00000072059
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,302,877 - 50,437,214 (+)Ensembl
Rnor_6.0 Ensembl351,687,809 - 51,822,250 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098856   ⟹   ENSRNOP00000076431
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,302,877 - 50,437,214 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108259   ⟹   ENSRNOP00000095098
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,302,877 - 50,437,214 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118742   ⟹   ENSRNOP00000087779
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,302,877 - 50,435,212 (+)Ensembl
RefSeq Acc Id: NM_012647   ⟹   NP_036779
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2350,302,879 - 50,437,214 (+)NCBI
Rnor_6.0351,687,910 - 51,822,008 (+)NCBI
Rnor_5.0358,322,640 - 58,456,658 (+)NCBI
RGSC_v3.4347,588,413 - 47,722,800 (+)RGD
Celera349,896,043 - 50,030,402 (+)RGD
Sequence:
RefSeq Acc Id: XM_039104284   ⟹   XP_038960212
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2350,302,781 - 50,437,504 (+)NCBI
RefSeq Acc Id: XM_039104285   ⟹   XP_038960213
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2350,350,983 - 50,437,504 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036779   ⟸   NM_012647
- UniProtKB: A0A8I5YBA6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072059   ⟸   ENSRNOT00000087242
RefSeq Acc Id: ENSRNOP00000007069   ⟸   ENSRNOT00000007069
RefSeq Acc Id: XP_038960212   ⟸   XM_039104284
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K207 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038960213   ⟸   XM_039104285
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K207 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000095098   ⟸   ENSRNOT00000108259
RefSeq Acc Id: ENSRNOP00000087779   ⟸   ENSRNOT00000118742
RefSeq Acc Id: ENSRNOP00000076431   ⟸   ENSRNOT00000098856
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-P04775-F1-model_v2 AlphaFold P04775 1-2005 view protein structure

Transcriptome

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

Promoters
RGD ID:13692106
Promoter ID:EPDNEW_R2629
Type:single initiation site
Name:Scn2a_1
Description:sodium voltage-gated channel alpha subunit 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0351,687,836 - 51,687,896EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3632 AgrOrtholog
BioCyc Gene G2FUF-49554 BioCyc
Ensembl Genes ENSRNOG00000005018 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007069.6 UniProtKB/TrEMBL
  ENSRNOP00000072059 ENTREZGENE
  ENSRNOP00000072059.2 UniProtKB/TrEMBL
  ENSRNOP00000076431 ENTREZGENE
  ENSRNOP00000076431.1 UniProtKB/TrEMBL
  ENSRNOP00000087779.1 UniProtKB/TrEMBL
  ENSRNOP00000095098.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007069.6 UniProtKB/TrEMBL
  ENSRNOT00000087242 ENTREZGENE
  ENSRNOT00000087242.2 UniProtKB/TrEMBL
  ENSRNOT00000098856 ENTREZGENE
  ENSRNOT00000098856.1 UniProtKB/TrEMBL
  ENSRNOT00000108259.1 UniProtKB/TrEMBL
  ENSRNOT00000118742.1 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
  IQ_motif_EF-hand-BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_channel_asu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_chnl_inactivation_gate UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_cytopl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VGCC_Ca_Na UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24766 UniProtKB/Swiss-Prot
NCBI Gene 24766 ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SODIUM CHANNEL PROTEIN TYPE 2 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 SCN2A RGD
PhenoGen Scn2a PhenoGen
PRINTS NACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PS50096 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00015 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Voltage-gated potassium channels UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K207 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5YBA6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GFG6_RAT UniProtKB/TrEMBL
  A0A8I6GL05_RAT UniProtKB/TrEMBL
  A9JQD7_RAT UniProtKB/TrEMBL
  F1M9G9_RAT UniProtKB/TrEMBL
  P04775 ENTREZGENE
  Q9ESV9_RAT UniProtKB/TrEMBL
  SCN2A_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Scn2a  sodium voltage-gated channel alpha subunit 2  Scn2a  sodium channel, voltage-gated, type II, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-13 Scn2a  sodium channel, voltage-gated, type II, alpha subunit  Scn2a1  sodium channel, voltage-gated, type II, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-31 Scn2a1  sodium channel, voltage-gated, type II, alpha 1  Scn2a1  sodium channel, voltage-gated, type 2, alpha 1 subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-20 Scn2a1  sodium channel, voltage-gated, type 2, alpha 1 subunit  Scn2a1  sodium channel, voltage-gated, type 2, alpha 1 polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Scn2a1  sodium channel, voltage-gated, type 2, alpha 1 polypeptide      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_process responsible for generation and propagation of action potentials, chiefly in nerve and muscle 68844