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 sodium ion transport and response to pyrethroid. Located in node of Ranvier and plasma membrane. Part of voltage-gated sodium channel complex. 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 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
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8195,481,298 - 95,491,211 (-)NCBIGRCr8
mRatBN7.2186,353,917 - 86,363,820 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl186,353,917 - 86,363,739 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx191,774,394 - 91,784,282 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01100,240,553 - 100,250,441 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0193,532,687 - 93,542,575 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0189,550,738 - 89,560,469 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl189,550,738 - 89,560,719 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0190,705,285 - 90,715,016 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4186,162,254 - 86,172,128 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1186,240,364 - 86,250,239 (-)NCBI
Celera180,722,797 - 80,732,619 (-)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-trans-(S)-allethrin  (EXP)
17beta-estradiol  (EXP)
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)
6-propyl-2-thiouracil  (EXP)
acetylsalicylic acid  (ISO)
acrylamide  (EXP,ISO)
alpha-Zearalanol  (EXP)
amiodarone  (ISO)
ammonium chloride  (EXP)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
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)
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)
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
intercalated disc  (IEA,ISO)
node of Ranvier  (IDA,IEA,ISO)
perikaryon  (IEA)
plasma membrane  (IDA,ISO,TAS)
sodium channel complex  (ISO)
T-tubule  (IEA,ISO)
voltage-gated sodium channel complex  (IBA,IDA,IEA,ISO)

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 (-)NCBIGRCr8
mRatBN7.2186,353,917 - 86,363,820 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl186,353,917 - 86,363,739 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx191,774,394 - 91,784,282 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01100,240,553 - 100,250,441 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0193,532,687 - 93,542,575 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0189,550,738 - 89,560,469 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl189,550,738 - 89,560,719 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0190,705,285 - 90,715,016 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4186,162,254 - 86,172,128 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1186,240,364 - 86,250,239 (-)NCBI
Celera180,722,797 - 80,732,619 (-)NCBICelera
Cytogenetic Map1q21NCBI
SCN1B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381935,030,470 - 35,040,449 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1935,030,470 - 35,040,449 (+)EnsemblGRCh38hg38GRCh38
GRCh371935,521,374 - 35,531,353 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361940,213,374 - 40,223,193 (+)NCBINCBI36Build 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 Ensembl
GRCm38731,116,524 - 31,127,023 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl731,116,524 - 31,127,003 (-)EnsemblGRCm38mm10GRCm38
MGSCv37731,901,543 - 31,911,964 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1116,904,982 - 116,912,817 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01118,101,274 - 118,110,870 (-)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247948,439,609 - 8,449,731 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Scn1b
54 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)165789093115540829Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)166023617118608521Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)17219768090508767Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)177494165122494165Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)177857876122857876Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)177876254106047988Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)178350581123350581Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)178430536123430536Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)17843075491209302Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)178479925123479925Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)180592172125592172Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)182174743118944897Rat
738022Anxrr13Anxiety related response QTL 134.60.00039locomotor behavior trait (VT:0001392)number of 20 x 20 cm floor squares crossed into, out of or within a discrete space in an experimental apparatus (CMO:0001514)183547917128547917Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)185424647100358001Rat

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
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 1
Medium 21 3 1 1 1 8 10 33 13 6 6 8
Low 3 12 42 28 18 28 21 14 30 5
Below cutoff 8 12 12 12 8 8 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000028653   ⟹   ENSRNOP00000028653
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl186,353,917 - 86,363,739 (-)Ensembl
Rnor_6.0 Ensembl189,550,739 - 89,560,719 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079091   ⟹   ENSRNOP00000074323
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl189,550,739 - 89,560,469 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092133   ⟹   ENSRNOP00000070450
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
Reference Protein Sequences
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:
RefSeq Acc Id: ENSRNOP00000074323   ⟸   ENSRNOT00000079091
RefSeq Acc Id: ENSRNOP00000070450   ⟸   ENSRNOT00000092133
RefSeq 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, UniProtKB/TrEMBL
  ENSRNOG00055032690 UniProtKB/Swiss-Prot
  ENSRNOG00060032696 UniProtKB/Swiss-Prot
  ENSRNOG00065033819 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000028653 ENTREZGENE
  ENSRNOT00000028653.6 UniProtKB/Swiss-Prot
  ENSRNOT00000092133 ENTREZGENE
  ENSRNOT00000092133.2 UniProtKB/TrEMBL
  ENSRNOT00055056501 UniProtKB/Swiss-Prot
  ENSRNOT00060056693 UniProtKB/Swiss-Prot
  ENSRNOT00065058089 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7316686 IMAGE-MGC_LOAD
InterPro Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_channel_b1/b3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29686 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:105455 IMAGE-MGC_LOAD
NCBI Gene 29686 ENTREZGENE
PANTHER PTHR10546 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10546:SF2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB SCN1B RGD
PhenoGen Scn1b PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
  PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000021102 RatGTEx
  ENSRNOG00055032690 RatGTEx
  ENSRNOG00060032696 RatGTEx
  ENSRNOG00065033819 RatGTEx
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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