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: Exhibits sodium channel regulator activity. Involved in regulation of voltage-gated sodium channel activity and response to pyrethroid. Localizes to 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; 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also 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 Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2186,353,917 - 86,363,836 (-)NCBI
Rnor_6.0 Ensembl189,550,738 - 89,560,719 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0189,550,738 - 89,560,469 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0190,705,285 - 90,715,016 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4186,162,254 - 86,172,128 (-)NCBIRGSC3.4rn4RGSC3.4
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 Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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
1. Deschenes I, etal., J Mol Cell Cardiol. 2008 Sep;45(3):336-46. Epub 2008 May 12.
2. Dhar Malhotra J, etal., Circulation. 2001 Mar 6;103(9):1303-10.
3. Dib-Hajj SD and Waxman SG, FEBS Lett 1995 Dec 27;377(3):485-8.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Isom LL, etal., Science 1992 May 8;256(5058):839-42.
6. Kazen-Gillespie KA, etal., J Biol Chem 2000 Jan 14;275(2):1079-88.
7. MGD data from the GO Consortium
8. NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. Oh Y and Waxman SG, Proc Natl Acad Sci U S A 1994 Oct 11;91(21):9985-9.
10. OMIM Disease Annotation Pipeline
11. Pipeline to import SMPDB annotations from SMPDB into RGD
12. Ratcliffe CF, etal., J Cell Biol. 2001 Jul 23;154(2):427-34.
13. RGD automated data pipeline
14. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. RGD automated import pipeline for gene-chemical interactions
16. Salem KA, etal., Exp Physiol. 2012 May 11.
17. Sampo B, etal., Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3666-71.
18. 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. Tan J and Soderlund DM, Neurotoxicology. 2009 Jan;30(1):81-9. Epub 2008 Nov 5.
20. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
21. 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  


Genomics

Comparative Map Data
Scn1b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2186,353,917 - 86,363,836 (-)NCBI
Rnor_6.0 Ensembl189,550,738 - 89,560,719 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0189,550,738 - 89,560,469 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0190,705,285 - 90,715,016 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4186,162,254 - 86,172,128 (-)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl1935,030,470 - 35,040,449 (+)EnsemblGRCh38hg38GRCh38
GRCh381935,030,470 - 35,040,449 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371935,521,374 - 35,531,353 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361940,213,374 - 40,223,193 (+)NCBINCBI36hg18NCBI36
Build 341940,213,373 - 40,217,014NCBI
Celera1932,237,030 - 32,244,951 (+)NCBI
Cytogenetic Map19q13.11NCBI
HuRef1932,031,550 - 32,039,386 (+)NCBIHuRef
CHM1_11935,523,533 - 35,533,294 (+)NCBICHM1_1
Scn1b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39730,815,949 - 30,826,448 (-)NCBIGRCm39mm39
GRCm39 Ensembl730,815,949 - 30,826,428 (-)Ensembl
GRCm38731,116,524 - 31,127,023 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl731,116,524 - 31,127,003 (-)EnsemblGRCm38mm10GRCm38
MGSCv37731,901,543 - 31,911,964 (-)NCBIGRCm37mm9NCBIm37
MGSCv36730,825,284 - 30,835,705 (-)NCBImm8
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
PanPan1.11940,714,949 - 40,724,052 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01931,974,499 - 31,984,488 (+)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.01118,101,274 - 118,110,870 (-)NCBI
UMICH_Zoey_3.11117,664,454 - 117,672,298 (-)NCBI
UNSW_CanFamBas_1.01117,289,863 - 117,297,724 (-)NCBI
UU_Cfam_GSD_1.01118,346,453 - 118,354,295 (-)NCBI
Scn1b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934910,450,449 - 10,457,966 (+)NCBI
SpeTri2.0NW_0049365701,187,916 - 1,195,423 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl644,597,713 - 44,607,490 (+)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1629,962,993 - 29,972,845 (+)NCBI
ChlSab1.1 Ensembl629,962,843 - 29,973,325 (+)Ensembl
Scn1b
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247948,439,609 - 8,449,731 (-)NCBI

Position Markers
U85786  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2186,353,982 - 86,354,124 (+)MAPPER
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 (+)MAPPER
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


QTLs in Region (Rnor_6.0)
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)15655769122614963Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13537750894364229Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14957857794578577Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15052271494225616Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157761301104391981Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)158209327103209327Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)164588516125875986Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)166113339122614963Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)16722768394201552Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)179134941113593716Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)179689548124689548Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)17968976594909507Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)183502376128502376Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)183656882126240667Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185779320130779320Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185917265130917265Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)186776571131776571Rat
2300324Fetw1Fetal weight QTL 112.10.005fetal growth trait (VT:0004201)fetal body weight (CMO:0002080)188634585106002500Rat

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.


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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl189,550,739 - 89,560,719 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079091   ⟹   ENSRNOP00000074323
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl189,550,739 - 89,560,469 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092133   ⟹   ENSRNOP00000070450
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
mRatBN7.2186,353,917 - 86,363,653 (-)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
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
mRatBN7.2186,353,917 - 86,363,739 (-)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_039109814   ⟹   XP_038965742
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2186,359,843 - 86,363,836 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_058984   ⟸   NM_017288
- Peptide Label: isoform 1 precursor
- UniProtKB: Q00954 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257974   ⟸   NM_001271045
- Peptide Label: isoform 1 precursor
- UniProtKB: Q00954 (UniProtKB/Swiss-Prot)
- 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_038965742   ⟸   XM_039109814
- Peptide Label: isoform X1
Protein Domains
Ig-like C2-type   IGv

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3631 AgrOrtholog
Ensembl Genes ENSRNOG00000021102 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000028653 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000070450 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074323 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000028653 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000079091 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000092133 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7316686 IMAGE-MGC_LOAD
InterPro 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
MGC_CLONE MGC:105455 IMAGE-MGC_LOAD
NCBI Gene 29686 ENTREZGENE
PANTHER PTHR10546 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam V-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB SCN1B RGD
PhenoGen Scn1b PhenoGen
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC217838
UniProt A0A0G2JXY6 ENTREZGENE, UniProtKB/TrEMBL
  Q00954 ENTREZGENE
  Q9QXU3_RAT 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