Scn8a (sodium voltage-gated channel alpha subunit 8) - Rat Genome Database

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Gene: Scn8a (sodium voltage-gated channel alpha subunit 8) Rattus norvegicus
Analyze
Symbol: Scn8a
Name: sodium voltage-gated channel alpha subunit 8
RGD ID: 3638
Description: Enables sodium ion binding activity and voltage-gated sodium channel activity. Involved in nervous system development; neuronal action potential; and sodium ion transport. Located in several cellular components, including glutamatergic synapse; main axon; and parallel fiber to Purkinje cell synapse. Is integral component of postsynaptic density membrane. Part of voltage-gated sodium channel complex. Is integral component of presynaptic active zone membrane. Biomarker of congestive heart failure. Human ortholog(s) of this gene implicated in benign familial neonatal epilepsy and developmental and epileptic encephalopathy 13. Orthologous to human SCN8A (sodium voltage-gated channel alpha subunit 8); INTERACTS WITH (+)-pilocarpine; (+)-trans-(S)-allethrin; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Na+ channel; naCh6; peripheral nerve protein type 4; PN4; sodium channel 6; sodium channel protein type 8 subunit alpha; sodium channel protein type VIII subunit alpha; sodium channel voltage-gated type VIII alpha polypeptide; sodium channel, voltage gated, type VIII, alpha subunit; sodium channel, voltage-gated, type 8, alpha polypeptide; sodium channel, voltage-gated, type 8, alpha subunit; sodium channel, voltage-gated, type VIII, alpha; sodium channel, voltage-gated, type VIII, alpha polypeptide; voltage-gated sodium channel subunit alpha Nav1.6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27131,982,152 - 132,156,075 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7131,982,480 - 132,151,292 (+)Ensembl
Rnor_6.07142,575,629 - 142,683,659 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7142,575,672 - 142,684,114 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07140,377,038 - 140,485,139 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47139,686,180 - 139,794,282 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17139,762,616 - 139,870,727 (+)NCBI
Celera7128,450,559 - 128,618,862 (+)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

Additional References at PubMed
PMID:2544627   PMID:3674018   PMID:7670495   PMID:7751906   PMID:11807096   PMID:12204355   PMID:12920299   PMID:15170223   PMID:15272007   PMID:16014723   PMID:16029194   PMID:17537961  
PMID:17662136   PMID:17884088   PMID:17928448   PMID:19306853   PMID:19465131   PMID:20466935   PMID:21078353   PMID:21439942   PMID:22465659   PMID:22871113   PMID:23622763   PMID:23640885  
PMID:25239001   PMID:25686526   PMID:25725044   PMID:25874799   PMID:27653482   PMID:27905510   PMID:28655185   PMID:29956586   PMID:30699332  


Genomics

Comparative Map Data
Scn8a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27131,982,152 - 132,156,075 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7131,982,480 - 132,151,292 (+)Ensembl
Rnor_6.07142,575,629 - 142,683,659 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7142,575,672 - 142,684,114 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07140,377,038 - 140,485,139 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47139,686,180 - 139,794,282 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17139,762,616 - 139,870,727 (+)NCBI
Celera7128,450,559 - 128,618,862 (+)NCBICelera
Cytogenetic Map7q36NCBI
SCN8A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1251,590,266 - 51,812,864 (+)EnsemblGRCh38hg38GRCh38
GRCh381251,591,233 - 51,812,864 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371251,985,017 - 52,206,648 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361250,271,287 - 50,488,574 (+)NCBINCBI36hg18NCBI36
Build 341250,271,286 - 50,488,365NCBI
Celera1250,787,152 - 51,004,408 (+)NCBI
Cytogenetic Map12q13.13NCBI
HuRef1249,089,349 - 49,239,456 (+)NCBIHuRef
CHM1_11251,951,468 - 52,173,106 (+)NCBICHM1_1
Scn8a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915100,766,600 - 100,943,819 (+)NCBIGRCm39mm39
GRCm39 Ensembl15100,767,739 - 100,943,819 (+)Ensembl
GRCm3815100,869,863 - 101,045,938 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15100,869,858 - 101,045,938 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715100,701,114 - 100,876,360 (+)NCBIGRCm37mm9NCBIm37
MGSCv3615100,764,359 - 100,868,722 (+)NCBImm8
Celera15103,017,992 - 103,192,774 (+)NCBICelera
Cytogenetic Map15F1NCBI
cM Map1556.39NCBI
Scn8a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555472,086,178 - 2,195,971 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555472,086,215 - 2,201,300 (+)NCBIChiLan1.0ChiLan1.0
SCN8A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11237,725,471 - 38,057,190 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1237,730,900 - 37,876,357 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01236,950,057 - 37,172,235 (-)NCBIMhudiblu_PPA_v0panPan3
SCN8A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1273,174,257 - 3,348,349 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl273,176,013 - 3,296,482 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2742,959,130 - 43,080,423 (+)NCBI
ROS_Cfam_1.0273,170,259 - 3,346,792 (-)NCBI
UMICH_Zoey_3.1273,189,615 - 3,363,479 (-)NCBI
UNSW_CanFamBas_1.0273,173,058 - 3,350,013 (-)NCBI
UU_Cfam_GSD_1.02743,304,862 - 43,478,762 (+)NCBI
Scn8a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494563,880,790 - 64,000,520 (-)NCBI
SpeTri2.0NW_0049365129,164,310 - 9,281,795 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN8A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl516,977,700 - 17,169,564 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1516,977,468 - 17,173,831 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2517,560,130 - 17,767,953 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SCN8A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11147,770,513 - 47,983,843 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1147,838,358 - 47,978,399 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037198,106,707 - 198,322,669 (-)NCBIVero_WHO_p1.0
Scn8a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624816498,737 - 631,850 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
BE103200  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27132,073,788 - 132,073,944 (+)MAPPERmRatBN7.2
Rnor_6.07142,606,192 - 142,606,347NCBIRnor6.0
Rnor_5.07140,407,601 - 140,407,756UniSTSRnor5.0
RGSC_v3.47139,716,743 - 139,716,898UniSTSRGSC3.4
Celera7128,541,585 - 128,541,740UniSTS
RH 3.4 Map71073.2UniSTS
Cytogenetic Map7q36UniSTS
AU049240  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27132,064,031 - 132,064,255 (+)MAPPERmRatBN7.2
Rnor_6.07142,596,435 - 142,596,658NCBIRnor6.0
Rnor_5.07140,397,844 - 140,398,067UniSTSRnor5.0
RGSC_v3.47139,706,986 - 139,707,209UniSTSRGSC3.4
Celera7128,531,844 - 128,532,051UniSTS
Cytogenetic Map7q36UniSTS
AU049825  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27132,008,213 - 132,008,426 (+)MAPPERmRatBN7.2
Rnor_6.07142,540,553 - 142,540,765NCBIRnor6.0
Rnor_5.07140,343,152 - 140,343,364UniSTSRnor5.0
RGSC_v3.47139,651,335 - 139,651,547UniSTSRGSC3.4
Celera7128,476,324 - 128,476,536UniSTS
Cytogenetic Map7q36UniSTS
G64248  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27132,150,549 - 132,150,811 (+)MAPPERmRatBN7.2
Rnor_6.07142,682,919 - 142,683,180NCBIRnor6.0
Rnor_5.07140,484,399 - 140,484,660UniSTSRnor5.0
RGSC_v3.47139,793,542 - 139,793,803UniSTSRGSC3.4
Celera7128,618,122 - 128,618,383UniSTS
Cytogenetic Map7q36UniSTS
Scn3a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,432,608 - 50,433,887 (+)MAPPERmRatBN7.2
Rnor_6.0351,817,586 - 51,818,864NCBIRnor6.0
Rnor_5.0358,452,236 - 58,453,514UniSTSRnor5.0
RGSC_v3.4347,718,197 - 47,719,475UniSTSRGSC3.4
Celera350,025,799 - 50,027,077UniSTS
Cytogenetic Map7q36UniSTS
Cytogenetic Map3q21UniSTS
Cytogenetic Map8q32UniSTS
Cytogenetic Map3q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:261
Count of miRNA genes:169
Interacting mature miRNAs:192
Transcripts:ENSRNOT00000008160
Prediction methods:Microtar, 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
Medium 66 2 2
Low 20 24 10 8 10 8 33 39 8
Below cutoff 3 20 33 31 11 31 8 8 3 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008160   ⟹   ENSRNOP00000008160
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7131,982,480 - 132,151,292 (+)Ensembl
Rnor_6.0 Ensembl7142,575,677 - 142,683,213 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080923   ⟹   ENSRNOP00000075703
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7131,982,480 - 132,151,292 (+)Ensembl
Rnor_6.0 Ensembl7142,575,672 - 142,684,114 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114577   ⟹   ENSRNOP00000082508
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7131,982,480 - 132,151,292 (+)Ensembl
RefSeq Acc Id: NM_019266   ⟹   NP_062139
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,982,480 - 132,151,290 (+)NCBI
Rnor_6.07142,575,629 - 142,683,659 (+)NCBI
Rnor_5.07140,377,038 - 140,485,139 (+)NCBI
RGSC_v3.47139,686,180 - 139,794,282 (+)RGD
Celera7128,450,559 - 128,618,862 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078605   ⟹   XP_038934533
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,982,153 - 132,156,075 (+)NCBI
RefSeq Acc Id: XM_039078606   ⟹   XP_038934534
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,982,153 - 132,156,075 (+)NCBI
RefSeq Acc Id: XM_039078607   ⟹   XP_038934535
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,982,153 - 132,156,075 (+)NCBI
RefSeq Acc Id: XM_039078608   ⟹   XP_038934536
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,982,153 - 132,156,075 (+)NCBI
RefSeq Acc Id: XM_039078609   ⟹   XP_038934537
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27132,043,414 - 132,156,075 (+)NCBI
RefSeq Acc Id: XM_039078610   ⟹   XP_038934538
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,982,152 - 132,140,170 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_062139   ⟸   NM_019266
- UniProtKB: O88420 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008160   ⟸   ENSRNOT00000008160
RefSeq Acc Id: ENSRNOP00000075703   ⟸   ENSRNOT00000080923
RefSeq Acc Id: XP_038934538   ⟸   XM_039078610
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038934534   ⟸   XM_039078606
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038934536   ⟸   XM_039078608
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038934533   ⟸   XM_039078605
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038934535   ⟸   XM_039078607
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934537   ⟸   XM_039078609
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000082508   ⟸   ENSRNOT00000114577
Protein Domains
Ion_trans   IQ   Na_trans_assoc   Na_trans_cytopl

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (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
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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (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
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (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
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
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)
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
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (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
WKY/NHsd (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
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 140425694 140425695 A T snv F344/Jcl (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3638 AgrOrtholog
Ensembl Genes ENSRNOG00000005309 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008160 UniProtKB/TrEMBL
  ENSRNOP00000075703 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008160 UniProtKB/TrEMBL
  ENSRNOT00000080923 UniProtKB/TrEMBL
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ion_trans_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IQ_motif_EF-hand-BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_channel_a8su UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_channel_asu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_chnl_inactivation_gate UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_cytopl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VGCC_Ca_Na UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29710 UniProtKB/Swiss-Prot
NCBI Gene 29710 ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_cytopl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00612 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Scn8a PhenoGen
PRINTS NACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NACHANNEL8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PS50096 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00015 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC209146
UniProt A0A0G2KB93_RAT UniProtKB/TrEMBL
  F1LMH2_RAT UniProtKB/TrEMBL
  O88420 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O88421 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Scn8a  sodium voltage-gated channel alpha subunit 8  Scn8a  sodium channel, voltage gated, type VIII, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-09-16 Scn8a  sodium channel, voltage gated, type VIII, alpha subunit  Scn8a  sodium channel, voltage-gated, type VIII, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-12-15 Scn8a  sodium channel, voltage-gated, type VIII, alpha  Scn8a  sodium channel, voltage gated, type VIII, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-03-25 Scn8a  sodium channel, voltage gated, type VIII, alpha subunit  Scn8a  sodium channel, voltage-gated, type 8, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Scn8a  sodium channel, voltage-gated, type 8, alpha subunit  Scn8a  sodium channel, voltage-gated, type VIII, alpha polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Scn8a  sodium channel, voltage-gated, type VIII, alpha polypeptide    sodium channel, voltage-gated, type 8, alpha polypeptide  Name updated 1299863 APPROVED
2002-06-10 Scn8a  sodium channel, voltage-gated, type 8, alpha polypeptide      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_transcript a splice variant rPN4a exists 69984