Scn4a (sodium voltage-gated channel alpha subunit 4) - Rat Genome Database

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Gene: Scn4a (sodium voltage-gated channel alpha subunit 4) Rattus norvegicus
Analyze
Symbol: Scn4a
Name: sodium voltage-gated channel alpha subunit 4
RGD ID: 3636
Description: Predicted to enable voltage-gated sodium channel activity. Involved in choline transport; potassium ion transport; and sodium ion transmembrane transport. Located in plasma membrane. Human ortholog(s) of this gene implicated in congenital myasthenic syndrome 16; congenital myopathy 22A; congenital myopathy 22B; hyperkalemic periodic paralysis; and paramyotonia congenita of Von Eulenburg. Orthologous to human SCN4A (sodium voltage-gated channel alpha subunit 4); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: microI; mu-1; Nav1.4; NCHVS; skM1; sodium channel protein skeletal muscle subunit alpha; sodium channel protein type 4 subunit alpha; sodium channel protein type IV subunit alpha; sodium channel voltage-gated type 4 alpha polypeptide; Sodium channel voltage-gated type IV alpha polypeptide; sodium channel, voltage-gated, type 4, alpha polypeptide; sodium channel, voltage-gated, type 4, alpha subunit; sodium channel, voltage-gated, type IV, alpha; Sodium channel, voltage-gated, type IV, alpha polypeptide; sodium channel, voltage-gated, type IV, alpha subunit; voltage-gated sodium channel subunit alpha Nav1.4
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
GRCr81091,745,459 - 91,796,452 (-)NCBIGRCr8
mRatBN7.21091,246,936 - 91,296,670 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1091,246,936 - 91,296,545 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1096,301,564 - 96,351,302 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01095,764,729 - 95,814,463 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01091,175,309 - 91,225,142 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01094,505,026 - 94,557,803 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1094,505,026 - 94,557,764 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01094,256,140 - 94,305,964 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41095,710,710 - 95,760,323 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11095,725,079 - 95,774,693 (-)NCBI
Celera1089,922,418 - 89,970,101 (-)NCBICelera
RH 3.4 Map10988.7RGD
Cytogenetic Map10q32.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
axon  (IBA,IEA)
plasma membrane  (IDA,ISO,ISS)
voltage-gated sodium channel complex  (IBA,IEA,ISO,ISS)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Late onset painful cold-aggravated myotonia: three families with SCN4A L1436P mutation. Bissay V, etal., Neuromuscul Disord. 2011 Aug;21(8):590-3. doi: 10.1016/j.nmd.2011.05.006. Epub 2011 Jun 12.
2. Severe infantile hyperkalaemic periodic paralysis and paramyotonia congenita: broadening the clinical spectrum associated with the T704M mutation in SCN4A. Brancati F, etal., J Neurol Neurosurg Psychiatry. 2003 Sep;74(9):1339-41.
3. Expression of skeletal muscle-type voltage-gated Na+ channel in rat and human prostate cancer cell lines. Diss JK, etal., FEBS Lett 1998 May 1;427(1):5-10.
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
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. Thyrotoxic periodic paralysis associated with a mutation in the sodium channel gene SCN4A. Lane AH, etal., J Pediatr Endocrinol Metab. 2004 Dec;17(12):1679-82.
8. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
9. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
15. Primary structure and functional expression of a mammalian skeletal muscle sodium channel. Trimmer JS, etal., Neuron 1989 Jul;3(1):33-49.
16. Genetic basis of tetrodotoxin resistance in pufferfishes. Venkatesh B, etal., Curr Biol. 2005 Nov 22;15(22):2069-72. doi: 10.1016/j.cub.2005.10.068.
17. A sodium channel knockin mutant (NaV1.4-R669H) mouse model of hypokalemic periodic paralysis. Wu F, etal., J Clin Invest. 2011 Oct;121(10):4082-94. doi: 10.1172/JCI57398. Epub 2011 Sep 1.
18. A molecular switch between the outer and the inner vestibules of the voltage-gated Na+ channel. Zarrabi T, etal., J Biol Chem. 2010 Dec 10;285(50):39458-70. doi: 10.1074/jbc.M110.132886. Epub 2010 Oct 6.
Additional References at PubMed
PMID:9525869   PMID:11834499   PMID:12397382   PMID:12766226   PMID:12967988   PMID:15746172   PMID:15992775   PMID:16239540   PMID:16432696   PMID:16873405   PMID:17237232   PMID:17591984  
PMID:17698594   PMID:18698149   PMID:18824591   PMID:18977767   PMID:19052238   PMID:19097141   PMID:20459109   PMID:20660662   PMID:21099342   PMID:22374989   PMID:22722661   PMID:23322038  
PMID:25133704   PMID:26636939   PMID:28012039   PMID:28202723   PMID:30190309  


Genomics

Comparative Map Data
Scn4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81091,745,459 - 91,796,452 (-)NCBIGRCr8
mRatBN7.21091,246,936 - 91,296,670 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1091,246,936 - 91,296,545 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1096,301,564 - 96,351,302 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01095,764,729 - 95,814,463 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01091,175,309 - 91,225,142 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01094,505,026 - 94,557,803 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1094,505,026 - 94,557,764 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01094,256,140 - 94,305,964 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41095,710,710 - 95,760,323 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11095,725,079 - 95,774,693 (-)NCBI
Celera1089,922,418 - 89,970,101 (-)NCBICelera
RH 3.4 Map10988.7RGD
Cytogenetic Map10q32.1NCBI
SCN4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381763,938,554 - 63,972,918 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1763,938,554 - 63,972,918 (-)EnsemblGRCh38hg38GRCh38
GRCh371762,015,914 - 62,050,278 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361759,369,646 - 59,404,010 (-)NCBINCBI36Build 36hg18NCBI36
Build 341759,369,645 - 59,404,010NCBI
Celera1756,403,975 - 56,438,354 (-)NCBICelera
Cytogenetic Map17q23.3NCBI
HuRef1757,383,629 - 57,417,946 (-)NCBIHuRef
CHM1_11762,079,833 - 62,114,196 (-)NCBICHM1_1
T2T-CHM13v2.01764,809,317 - 64,843,693 (-)NCBIT2T-CHM13v2.0
Scn4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911106,208,374 - 106,256,385 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11106,209,418 - 106,244,114 (-)EnsemblGRCm39 Ensembl
GRCm3811106,317,545 - 106,365,559 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11106,318,592 - 106,353,288 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711106,179,907 - 106,210,704 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611106,135,394 - 106,165,480 (-)NCBIMGSCv36mm8
Celera11118,049,260 - 118,080,125 (-)NCBICelera
Cytogenetic Map11E1NCBI
cM Map1168.91NCBI
Scn4a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554787,861,585 - 7,906,192 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554787,861,585 - 7,906,192 (+)NCBIChiLan1.0ChiLan1.0
SCN4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21980,119,592 - 80,155,917 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11784,939,899 - 84,975,867 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01758,034,146 - 58,066,644 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11763,128,550 - 63,161,043 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1763,128,550 - 63,161,043 (-)Ensemblpanpan1.1panPan2
SCN4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1911,849,066 - 11,893,689 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl911,851,347 - 11,877,767 (-)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0913,510,606 - 13,554,819 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl913,510,606 - 13,539,011 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1912,457,351 - 12,500,840 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0915,030,745 - 15,074,957 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0915,032,962 - 15,077,426 (+)NCBIUU_Cfam_GSD_1.0
Scn4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560214,610,329 - 14,653,543 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365414,543,102 - 4,569,862 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365414,541,061 - 4,570,212 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN4A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1215,002,175 - 15,047,582 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11215,001,356 - 15,048,092 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21214,992,881 - 15,039,475 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SCN4A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11657,273,143 - 57,331,677 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1657,282,252 - 57,331,035 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607727,910,000 - 27,944,696 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scn4a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248491,436,047 - 1,483,531 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248491,436,372 - 1,483,531 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Scn4a
445 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:134
Count of miRNA genes:97
Interacting mature miRNAs:113
Transcripts:ENSRNOT00000016841
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
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108256485692369470Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1080515287101325465Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1088539139107211142Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)107877551698279596Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1090627439107057807Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107437208494965338Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090404397107211142Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087307617107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091228102104060283Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)108402232193995963Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107255241693995749Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090627439107211142Rat
2313856Bp342Blood pressure QTL 3424.40.0001life span trait (VT:0005372)age at time of death (CMO:0001193)108730761796121100Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)90404397107211142Rat
2301398Kidm38Kidney mass QTL 380.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)108400727295933025Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1090404397107211142Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1090404397107211142Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107624608594965338Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
12880055Am11Aortic mass QTL 110.004aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)108400727295933025Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)90404397107211142Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1090404397107211142Rat

Markers in Region
D10Wox43  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21091,246,495 - 91,246,643 (+)MAPPERmRatBN7.2
Rnor_6.01094,504,586 - 94,504,733NCBIRnor6.0
Rnor_5.01094,255,796 - 94,255,943UniSTSRnor5.0
RGSC_v3.41095,710,270 - 95,710,417UniSTSRGSC3.4
Celera1089,921,978 - 89,922,125UniSTS
Cytogenetic Map10q32.1UniSTS
BE099716  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21091,277,612 - 91,277,767 (+)MAPPERmRatBN7.2
Rnor_6.01094,538,828 - 94,538,982NCBIRnor6.0
Rnor_5.01094,286,913 - 94,287,067UniSTSRnor5.0
RGSC_v3.41095,741,387 - 95,741,541UniSTSRGSC3.4
Celera1089,951,614 - 89,951,768UniSTS
RH 3.4 Map10981.4UniSTS
Cytogenetic Map10q32.1UniSTS
RH94568  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21091,246,961 - 91,247,113 (+)MAPPERmRatBN7.2
Rnor_6.01094,505,052 - 94,505,203NCBIRnor6.0
Rnor_5.01094,256,262 - 94,256,413UniSTSRnor5.0
RGSC_v3.41095,710,736 - 95,710,887UniSTSRGSC3.4
Celera1089,922,444 - 89,922,595UniSTS
RH 3.4 Map10988.7UniSTS
Cytogenetic Map10q32.1UniSTS
UniSTS:224857  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21091,247,409 - 91,247,480 (+)MAPPERmRatBN7.2
Rnor_6.01094,505,500 - 94,505,570NCBIRnor6.0
Rnor_5.01094,256,710 - 94,256,780UniSTSRnor5.0
RGSC_v3.41095,711,184 - 95,711,254UniSTSRGSC3.4
Celera1089,922,892 - 89,922,962UniSTS
Cytogenetic Map10q32.1UniSTS


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 8 11 8
Low 2 37 11 20 12 10 11
Below cutoff 6 38 22 8 22 54 23 31

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016841   ⟹   ENSRNOP00000016841
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1091,246,936 - 91,296,545 (-)Ensembl
Rnor_6.0 Ensembl1094,505,026 - 94,557,764 (-)Ensembl
RefSeq Acc Id: NM_013178   ⟹   NP_037310
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81091,746,715 - 91,796,324 (-)NCBI
mRatBN7.21091,246,936 - 91,296,545 (-)NCBI
Rnor_6.01094,505,026 - 94,557,764 (-)NCBI
Rnor_5.01094,256,140 - 94,305,964 (-)NCBI
RGSC_v3.41095,710,710 - 95,760,323 (-)RGD
Celera1089,922,418 - 89,970,101 (-)RGD
Sequence:
RefSeq Acc Id: XM_006247559   ⟹   XP_006247621
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81091,745,459 - 91,796,452 (-)NCBI
mRatBN7.21091,247,923 - 91,296,670 (-)NCBI
Rnor_6.01094,506,013 - 94,557,803 (-)NCBI
Rnor_5.01094,256,140 - 94,305,964 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_037310 (Get FASTA)   NCBI Sequence Viewer  
  XP_006247621 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41682 (Get FASTA)   NCBI Sequence Viewer  
  CAA76659 (Get FASTA)   NCBI Sequence Viewer  
  EDM06395 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000016841
  ENSRNOP00000016841.4
GenBank Protein P15390 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_037310   ⟸   NM_013178
- UniProtKB: P15390 (UniProtKB/Swiss-Prot),   O70611 (UniProtKB/Swiss-Prot),   D3ZW75 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006247621   ⟸   XM_006247559
- Peptide Label: isoform X1
- UniProtKB: P15390 (UniProtKB/Swiss-Prot),   O70611 (UniProtKB/Swiss-Prot),   D3ZW75 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016841   ⟸   ENSRNOT00000016841
Protein Domains
Ion transport   IQ   Sodium ion transport-associated

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P15390-F1-model_v2 AlphaFold P15390 1-1840 view protein structure

Transcriptome

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

Promoters
RGD ID:13697844
Promoter ID:EPDNEW_R8369
Type:single initiation site
Name:Scn4a_1
Description:sodium voltage-gated channel alpha subunit 4
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_6.01094,557,792 - 94,557,852EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3636 AgrOrtholog
BioCyc Gene G2FUF-22951 BioCyc
Ensembl Genes ENSRNOG00000012134 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016841 ENTREZGENE
  ENSRNOT00000016841.5 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_a4su_mammal 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
  VGCC_Ca_Na UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25722 UniProtKB/Swiss-Prot
NCBI Gene 25722 ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SODIUM CHANNEL PROTEIN TYPE 4 SUBUNIT ALPHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Scn4a PhenoGen
PRINTS NACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NACHANNEL4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PS50096 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012134 RatGTEx
Superfamily-SCOP Voltage-gated potassium channels UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC220002
UniProt A6HK40_RAT UniProtKB/TrEMBL
  D3ZW75 ENTREZGENE, UniProtKB/TrEMBL
  O70611 ENTREZGENE
  P15390 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O70611 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Scn4a  sodium voltage-gated channel alpha subunit 4  Scn4a  sodium channel, voltage-gated, type IV, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-09-16 Scn4a  sodium channel, voltage-gated, type IV, alpha subunit  Scn4a  sodium channel, voltage-gated, type IV, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-12-15 Scn4a  sodium channel, voltage-gated, type IV, alpha  Scn4a  sodium channel, voltage-gated, type IV, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-10-22 Scn4a  sodium channel, voltage-gated, type IV, alpha subunit  Scn4a  sodium channel, voltage-gated, type 4, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Scn4a  sodium channel, voltage-gated, type 4, alpha subunit  Scn4a  sodium channel, voltage-gated, type IV, alpha polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Scn4a  sodium channel, voltage-gated, type IV, alpha polypeptide      Symbol and Name status set to approved 625702 APPROVED
2002-06-10 Scn4a  sodium channel, voltage-gated, type 4, alpha polypeptide       Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression preferentially expressed in skeletal muscle 69983