Scn1b (sodium voltage-gated channel beta subunit 1) - Rat Genome Database

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Gene: Scn1b (sodium voltage-gated channel beta subunit 1) Rattus norvegicus
Analyze
Symbol: Scn1b
Name: sodium voltage-gated channel beta subunit 1
RGD ID: 3631
Description: Enables sodium channel regulator activity. Involved in regulation of voltage-gated sodium channel activity and response to pyrethroid. Located in plasma membrane. Part of voltage-gated sodium channel complex. Colocalizes with node of Ranvier. Biomarker of type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in Brugada syndrome 5; developmental and epileptic encephalopathy 52; familial atrial fibrillation; and generalized epilepsy with febrile seizures plus 1. Orthologous to human SCN1B (sodium voltage-gated channel beta subunit 1); PARTICIPATES IN alfentanil pharmacodynamics pathway; bupivacaine pharmacodynamics pathway; buprenorphine pharmacodynamics pathway; INTERACTS WITH (+)-trans-(S)-allethrin; 17beta-estradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: sodium channel regulatory subunit beta-1; sodium channel subunit beta-1; sodium channel voltage-gated type 1 beta polypeptide; sodium channel voltage-gated type I beta polypeptide; sodium channel, voltage-gated, type 1, beta polypeptide; sodium channel, voltage-gated, type I, beta; sodium channel, voltage-gated, type I, beta polypeptide; sodium channel, voltage-gated, type I, beta subunit
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8195,481,298 - 95,491,211 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl195,481,298 - 95,491,197 (-)EnsemblGRCr8
mRatBN7.2186,353,917 - 86,363,820 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl186,353,917 - 86,363,739 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx191,774,394 - 91,784,282 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01100,240,553 - 100,250,441 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0193,532,687 - 93,542,575 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0189,550,738 - 89,560,469 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl189,550,738 - 89,560,719 (-)Ensemblrn6Rnor6.0
Rnor_5.0190,705,285 - 90,715,016 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4186,162,254 - 86,172,128 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera180,722,797 - 80,732,619 (-)NCBICelera
RGSC_v3.1186,240,364 - 86,250,239 (-)NCBI
Cytogenetic Map1q21NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-trans-(S)-allethrin  (EXP)
17beta-estradiol  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
6-propyl-2-thiouracil  (EXP)
acetylsalicylic acid  (ISO)
acrylamide  (EXP,ISO)
alpha-Zearalanol  (EXP)
amiodarone  (ISO)
amitrole  (EXP)
ammonium chloride  (EXP)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
Butylbenzyl phthalate  (ISO)
calcitriol  (ISO)
carmustine  (EXP)
casticin  (ISO)
CGP 52608  (ISO)
chlordecone  (ISO)
cobalt dichloride  (ISO)
corn oil  (EXP)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cyfluthrin  (EXP)
cypermethrin  (EXP)
decabromodiphenyl ether  (EXP)
dibenz[a,h]anthracene  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
fenpropathrin  (EXP)
fenvalerate  (EXP)
flutamide  (EXP)
furan  (EXP)
hydroquinone O-beta-D-glucopyranoside  (ISO)
lipopolysaccharide  (ISO)
methotrexate  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
okadaic acid  (ISO)
paracetamol  (EXP,ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenytoin  (ISO)
pirinixic acid  (EXP)
progesterone  (EXP)
prostaglandin F2alpha  (EXP)
rotenone  (EXP)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium atom  (EXP,ISO)
sodium fluoride  (ISO)
testosterone  (ISO)
tetrodotoxin  (EXP)
tioguanine  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
tris(2-butoxyethyl) phosphate  (ISO)
urethane  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
axon  (IEA)
cell projection  (IEA)
intercalated disc  (IEA,ISO)
node of Ranvier  (IDA,IEA,ISO)
perikaryon  (IEA)
plasma membrane  (IDA,IEA,ISO,TAS)
sodium channel complex  (IEA,ISO)
T-tubule  (IEA,ISO)
voltage-gated sodium channel complex  (IBA,IDA,IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
alfentanil pharmacodynamics pathway  (ISO)
bupivacaine pharmacodynamics pathway  (ISO)
buprenorphine pharmacodynamics pathway  (ISO)
chloroprocaine pharmacodynamics pathway  (ISO)
citalopram pharmacodynamics pathway  (ISO)
cocaine pharmacodynamics pathway  (ISO)
codeine and morphine pharmacodynamics pathway  (ISO)
desipramine pharmacodynamics pathway  (ISO)
diphenoxylate pharmacodynamics pathway  (ISO)
escitalopram pharmacodynamics pathway  (ISO)
ethylmorphine pharmacodynamics pathway  (ISO)
fentanyl pharmacodynamics pathway  (ISO)
fluoxetine pharmacodynamics pathway  (ISO)
heroin pharmacodynamics pathway  (ISO)
hydrocodone pharmacodynamics pathway  (ISO)
hydromorphone pharmacodynamics pathway  (ISO)
imipramine pharmacodynamics pathway  (ISO)
levacetylmethadol pharmacodynamics pathway  (ISO)
levobupivacaine phgarmacodynamics pathway  (ISO)
levorphanol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
lidocaine pharmacokinetics pathway  (ISO)
mepivacaine pharmacodynamics pathway  (ISO)
methadone pharmacodynamics pathway  (ISO)
nalbuphine pharmacodynamics pathway  (ISO)
naloxone pharmacodynamics pathway  (ISO)
naltrexone pharmacodynamics pathway  (ISO)
nicotine pharmacodynamics pathway  (ISO)
oxybuprocaine pharmacodynamics pathway  (ISO)
oxycodone pharmacodynamics pathway  (ISO)
oxymorphone pharmacodynamics pathway  (ISO)
pentazocine pharmacodynamics pathway  (ISO)
prilocaine pharmacodynamics pathway  (ISO)
procaine pharmacodynamics pathway  (ISO)
remifentanil pharmacodynamics pathway  (ISO)
ropivacaine pharmacodynamics pathway  (ISO)
tramadol pharmacodynamics pathway  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Post-transcriptional gene silencing of KChIP2 and Navbeta1 in neonatal rat cardiac myocytes reveals a functional association between Na and Ito currents. Deschenes I, etal., J Mol Cell Cardiol. 2008 Sep;45(3):336-46. Epub 2008 May 12.
2. Characterization of sodium channel alpha- and beta-subunits in rat and mouse cardiac myocytes. Dhar Malhotra J, etal., Circulation. 2001 Mar 6;103(9):1303-10.
3. Genes encoding the beta 1 subunit of voltage-dependent Na+ channel in rat, mouse and human contain conserved introns. Dib-Hajj SD and Waxman SG, FEBS Lett 1995 Dec 27;377(3):485-8.
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. Primary structure and functional expression of the beta 1 subunit of the rat brain sodium channel. Isom LL, etal., Science 1992 May 8;256(5058):839-42.
6. Cloning, localization, and functional expression of sodium channel beta1A subunits. Kazen-Gillespie KA, etal., J Biol Chem 2000 Jan 14;275(2):1079-88.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. The beta 1 subunit mRNA of the rat brain Na+ channel is expressed in glial cells. Oh Y and Waxman SG, Proc Natl Acad Sci U S A 1994 Oct 11;91(21):9985-9.
10. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
11. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
12. Sodium channel beta1 and beta3 subunits associate with neurofascin through their extracellular immunoglobulin-like domain. Ratcliffe CF, etal., J Cell Biol. 2001 Jul 23;154(2):427-34.
13. GOA pipeline RGD automated data pipeline
14. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
16. Shortening and intracellular Ca2+ in ventricular myocytes and expression of genes encoding cardiac muscle proteins in early onset type 2 diabetic Goto-Kakizaki rats. Salem KA, etal., Exp Physiol. 2012 May 11.
17. 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.
18. Characterization of specific allosteric effects of the Na+ channel β1 subunit on the Nav1.4 isoform. Sánchez-Solano A, etal., Eur Biophys J. 2017 Jul;46(5):485-494. doi: 10.1007/s00249-016-1193-3. Epub 2016 Dec 23.
19. 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.
20. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
21. Modulatory effect of auxiliary beta1 subunit on Nav1.3 voltage-gated sodium channel expressed in Xenopus oocyte. Wang YW, etal., Chin Med J (Engl). 2007 Apr 20;120(8):721-3.
Additional References at PubMed
PMID:8125980   PMID:10769382   PMID:12477932   PMID:14622265   PMID:14667580   PMID:15102918   PMID:15178439   PMID:15272007   PMID:15452131   PMID:17884088   PMID:18158113   PMID:18178574  
PMID:18354028   PMID:18464934   PMID:19710327   PMID:19808477   PMID:21051419   PMID:22247482   PMID:22292491   PMID:22425777   PMID:24138709   PMID:26528804   PMID:28758202   PMID:30190309  
PMID:36541246  


Genomics

Comparative Map Data
Scn1b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8195,481,298 - 95,491,211 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl195,481,298 - 95,491,197 (-)EnsemblGRCr8
mRatBN7.2186,353,917 - 86,363,820 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl186,353,917 - 86,363,739 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx191,774,394 - 91,784,282 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01100,240,553 - 100,250,441 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0193,532,687 - 93,542,575 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0189,550,738 - 89,560,469 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl189,550,738 - 89,560,719 (-)Ensemblrn6Rnor6.0
Rnor_5.0190,705,285 - 90,715,016 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4186,162,254 - 86,172,128 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera180,722,797 - 80,732,619 (-)NCBICelera
RGSC_v3.1186,240,364 - 86,250,239 (-)NCBI
Cytogenetic Map1q21NCBI
SCN1B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381935,030,470 - 35,040,449 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1935,030,447 - 35,040,455 (+)Ensemblhg38GRCh38
GRCh371935,521,374 - 35,531,353 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361940,213,374 - 40,223,193 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341940,213,373 - 40,217,014NCBI
Celera1932,237,030 - 32,244,951 (+)NCBICelera
Cytogenetic Map19q13.11NCBI
HuRef1932,031,550 - 32,039,386 (+)NCBIHuRef
CHM1_11935,523,533 - 35,533,294 (+)NCBICHM1_1
T2T-CHM13v2.01937,575,088 - 37,585,067 (+)NCBIT2T-CHM13v2.0
Scn1b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39730,815,949 - 30,826,436 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl730,815,949 - 30,826,428 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38731,116,524 - 31,127,023 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl731,116,524 - 31,127,003 (-)Ensemblmm10GRCm38
MGSCv37731,901,543 - 31,911,964 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36730,825,284 - 30,835,705 (-)NCBIMGSCv36mm8
Celera725,685,753 - 25,696,176 (-)NCBICelera
Cytogenetic Map7B1NCBI
cM Map719.3NCBI
Scn1b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554684,375,157 - 4,383,502 (+)Ensembl
ChiLan1.0NW_0049554684,375,517 - 4,383,383 (+)NCBIChiLan1.0ChiLan1.0
SCN1B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22041,041,639 - 41,051,647 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11943,024,053 - 43,034,048 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01931,974,499 - 31,984,488 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11940,714,949 - 40,724,052 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1940,711,281 - 40,724,052 (+)EnsemblpanPan2panpan1.1
SCN1B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11117,504,428 - 117,510,666 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1117,503,828 - 117,511,727 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1116,904,982 - 116,912,817 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01118,101,274 - 118,110,870 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1118,101,277 - 118,109,849 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11117,664,454 - 117,672,298 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01117,289,863 - 117,297,724 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01118,346,453 - 118,354,295 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Scn1b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934910,450,449 - 10,457,966 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365701,186,711 - 1,195,388 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365701,187,916 - 1,195,423 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl644,597,482 - 44,607,481 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1644,597,461 - 44,607,488 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2640,022,785 - 40,032,360 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SCN1B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1629,962,993 - 29,972,845 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl629,962,843 - 29,973,325 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660737,732,359 - 7,742,427 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scn1b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247948,439,600 - 8,450,179 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247948,439,609 - 8,449,731 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Scn1b
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12164,901,091 - 164,910,943 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Scn1b
20 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:102
Count of miRNA genes:74
Interacting mature miRNAs:87
Transcripts:ENSRNOT00000028653
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)151940904101229020Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)187889942132889942Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)139728272132889942Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)151940904168768703Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)192963855109494029Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)187785026142582336Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183019780128019780Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)166404680111404680Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)18126986099645535Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)166009857160501508Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)193903998191260518Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)166400974132889942Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)184107164115183752Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)191302413136302413Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)151511344153680016Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16540563796805205Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)186622262131622262Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)158769992103769992Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)166077886111077886Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of, or within a discrete space in an open field apparatus (CMO:0001514)192683681137683681Rat
152025249Scl82Serum cholesterol level QTL 824.77blood cholesterol amount (VT:0000180)152891222109116986Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)186993904131993904Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)187558587132558587Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)192683681137683681Rat

Markers in Region
U85786  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2186,353,982 - 86,354,124 (+)MAPPERmRatBN7.2
Rnor_6.0189,550,804 - 89,550,945NCBIRnor6.0
Rnor_5.0190,705,351 - 90,705,492UniSTSRnor5.0
RGSC_v3.4186,162,320 - 86,162,461UniSTSRGSC3.4
Celera180,722,863 - 80,723,004UniSTS
Cytogenetic Map1q21UniSTS
PMC15797P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2186,354,090 - 86,354,306 (+)MAPPERmRatBN7.2
Rnor_6.0189,550,912 - 89,551,127NCBIRnor6.0
Rnor_5.0190,705,459 - 90,705,674UniSTSRnor5.0
RGSC_v3.4186,162,428 - 86,162,643UniSTSRGSC3.4
Celera180,722,971 - 80,723,186UniSTS
Cytogenetic Map1q21UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 65 149 91 90 59 85 59 6 347 183 11 128 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000028653   ⟹   ENSRNOP00000028653
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl195,481,298 - 95,491,197 (-)Ensembl
mRatBN7.2 Ensembl186,353,917 - 86,363,739 (-)Ensembl
Rnor_6.0 Ensembl189,550,739 - 89,560,719 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000079091   ⟹   ENSRNOP00000074323
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl189,550,739 - 89,560,469 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000092133   ⟹   ENSRNOP00000070450
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl195,481,298 - 95,489,636 (-)Ensembl
mRatBN7.2 Ensembl186,353,917 - 86,362,259 (-)Ensembl
Rnor_6.0 Ensembl189,550,738 - 89,559,960 (-)Ensembl
RefSeq Acc Id: NM_001271045   ⟹   NP_001257974
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8195,481,298 - 95,491,197 (-)NCBI
mRatBN7.2186,353,917 - 86,363,820 (-)NCBI
Rnor_6.0189,550,738 - 89,560,469 (-)NCBI
Rnor_5.0190,705,285 - 90,715,016 (-)NCBI
Celera180,722,797 - 80,732,533 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001271046   ⟹   NP_001257975
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8195,481,298 - 95,490,520 (-)NCBI
mRatBN7.2186,353,917 - 86,363,143 (-)NCBI
Rnor_6.0189,550,738 - 89,559,960 (-)NCBI
Rnor_5.0190,705,285 - 90,715,016 (-)NCBI
Celera180,722,797 - 80,732,022 (-)NCBI
Sequence:
RefSeq Acc Id: NM_017288   ⟹   NP_058984
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8195,481,298 - 95,491,197 (-)NCBI
mRatBN7.2186,353,917 - 86,363,820 (-)NCBI
Rnor_6.0189,550,738 - 89,560,459 (-)NCBI
Rnor_5.0190,705,285 - 90,715,016 (-)NCBI
RGSC_v3.4186,162,254 - 86,172,128 (-)RGD
Celera180,722,797 - 80,732,619 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063287840   ⟹   XP_063143910
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8195,487,222 - 95,491,211 (-)NCBI
RefSeq Acc Id: NP_058984   ⟸   NM_017288
- Peptide Label: isoform 1 precursor
- UniProtKB: Q505J0 (UniProtKB/Swiss-Prot),   Q00954 (UniProtKB/Swiss-Prot),   A6JA73 (UniProtKB/TrEMBL),   A0A0G2JXY6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257974   ⟸   NM_001271045
- Peptide Label: isoform 1 precursor
- UniProtKB: Q505J0 (UniProtKB/Swiss-Prot),   Q00954 (UniProtKB/Swiss-Prot),   A6JA73 (UniProtKB/TrEMBL),   A0A0G2JXY6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257975   ⟸   NM_001271046
- Peptide Label: isoform 2
- UniProtKB: A0A0G2JXY6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000074323   ⟸   ENSRNOT00000079091
Ensembl Acc Id: ENSRNOP00000070450   ⟸   ENSRNOT00000092133
Ensembl Acc Id: ENSRNOP00000028653   ⟸   ENSRNOT00000028653
RefSeq Acc Id: XP_063143910   ⟸   XM_063287840
- Peptide Label: isoform X1
- UniProtKB: Q9QXU3 (UniProtKB/TrEMBL)
Protein Domains
Ig-like   Ig-like C2-type   Immunoglobulin V-set

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q00954-F1-model_v2 AlphaFold Q00954 1-218 view protein structure

Transcriptome

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

Promoters
RGD ID:13689945
Promoter ID:EPDNEW_R470
Type:single initiation site
Name:Scn1b_2
Description:sodium voltage-gated channel beta subunit 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R471  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0189,560,392 - 89,560,452EPDNEW
RGD ID:13689950
Promoter ID:EPDNEW_R471
Type:initiation region
Name:Scn1b_1
Description:sodium voltage-gated channel beta subunit 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R470  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0189,560,799 - 89,560,859EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3631 AgrOrtholog
BioCyc Gene G2FUF-60045 BioCyc
Ensembl Genes ENSRNOG00000021102 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000028653 ENTREZGENE
  ENSRNOT00000028653.6 UniProtKB/Swiss-Prot
  ENSRNOT00000092133 ENTREZGENE
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7316686 IMAGE-MGC_LOAD
InterPro Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig_V-set UniProtKB/Swiss-Prot
  Na_channel_b1/b3 UniProtKB/Swiss-Prot
KEGG Report rno:29686 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105455 IMAGE-MGC_LOAD
NCBI Gene 29686 ENTREZGENE
PANTHER PTHR10546 UniProtKB/Swiss-Prot
  PTHR10546:SF2 UniProtKB/Swiss-Prot
Pfam V-set UniProtKB/Swiss-Prot
PharmGKB SCN1B RGD
PhenoGen Scn1b PhenoGen
RatGTEx ENSRNOG00000021102 RatGTEx
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot
TIGR TC217838
UniProt A0A0G2JXY6 ENTREZGENE, UniProtKB/TrEMBL
  A6JA73 ENTREZGENE, UniProtKB/TrEMBL
  Q00954 ENTREZGENE
  Q505J0 ENTREZGENE
  Q9QXU3 ENTREZGENE, UniProtKB/TrEMBL
  SCN1B_RAT UniProtKB/Swiss-Prot
UniProt Secondary Q505J0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Scn1b  sodium voltage-gated channel beta subunit 1  Scn1b  sodium channel, voltage-gated, type I, beta subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-11-11 Scn1b  sodium channel, voltage-gated, type I, beta subunit  Scn1b  sodium channel, voltage-gated, type I, beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Scn1b  sodium channel, voltage-gated, type I, beta    sodium channel, voltage-gated, type I, beta polypeptide  Name updated 1299863 APPROVED
2003-04-09 Scn1b  sodium channel, voltage-gated, type I, beta polypeptide    sodium channel, voltage-gated, type 1, beta polypeptide   Symbol and Name status set to approved 629479 APPROVED
2002-06-10 Scn1b  sodium channel, voltage-gated, type 1, beta polypeptide       Name updated 70585 PROVISIONAL