Scn11a (sodium voltage-gated channel alpha subunit 11) - Rat Genome Database

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Gene: Scn11a (sodium voltage-gated channel alpha subunit 11) Rattus norvegicus
Analyze
Symbol: Scn11a
Name: sodium voltage-gated channel alpha subunit 11
RGD ID: 3630
Description: Predicted to have voltage-gated sodium channel activity. Predicted to be involved in several processes, including neuronal action potential; regulation of sensory perception of pain; and sodium ion transmembrane transport. Localizes to axon; glutamatergic synapse; and integral component of presynaptic membrane. Human ortholog(s) of this gene implicated in familial episodic pain syndrome 3 and hereditary sensory and autonomic neuropathy type 7. Orthologous to human SCN11A (sodium voltage-gated channel alpha subunit 11); INTERACTS WITH 6-propyl-2-thiouracil; amitriptyline; atrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: NaN; sensory neuron sodium channel 2; sodium channel protein type 11 subunit alpha; sodium channel protein type XI subunit alpha; sodium channel voltage-gated type 11 alpha polypeptide; sodium channel voltage-gated type XI alpha polypeptide; sodium channel, voltage-gated, type 11, alpha polypeptide; sodium channel, voltage-gated, type XI, alpha; sodium channel, voltage-gated, type XI, alpha polypeptide; sodium channel, voltage-gated, type XI, alpha subunit; sodium channel, voltage-gated, type11, alpha polypeptide; voltage-gated sodium channel NAV1.9b; voltage-gated sodium channel subunit alpha Nav1.9
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
mRatBN7.28119,495,550 - 119,567,044 (-)NCBI
Rnor_6.0 Ensembl8128,450,801 - 128,521,109 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08128,450,793 - 128,527,510 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08127,654,010 - 127,724,293 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48124,724,493 - 124,794,654 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18124,744,232 - 124,814,391 (-)NCBI
Celera8118,645,022 - 118,713,950 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:11487631   PMID:12428758   PMID:12536125   PMID:16029194   PMID:16822986   PMID:17363266   PMID:17950013   PMID:18552876   PMID:19056867   PMID:19269275   PMID:19575990   PMID:22342308  
PMID:23264124   PMID:24036948   PMID:24424281   PMID:24507022   PMID:24732443   PMID:25959819   PMID:28913981   PMID:29388177  


Genomics

Comparative Map Data
Scn11a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28119,495,550 - 119,567,044 (-)NCBI
Rnor_6.0 Ensembl8128,450,801 - 128,521,109 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08128,450,793 - 128,527,510 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08127,654,010 - 127,724,293 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48124,724,493 - 124,794,654 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18124,744,232 - 124,814,391 (-)NCBI
Celera8118,645,022 - 118,713,950 (-)NCBICelera
Cytogenetic Map8q32NCBI
SCN11A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl338,845,764 - 39,052,157 (-)EnsemblGRCh38hg38GRCh38
GRCh38338,845,764 - 39,051,944 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37338,887,255 - 39,093,435 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36338,862,264 - 38,967,056 (-)NCBINCBI36hg18NCBI36
Build 34338,862,263 - 38,967,056NCBI
Celera338,826,267 - 38,932,035 (-)NCBI
Cytogenetic Map3p22.2NCBI
HuRef338,929,417 - 39,033,960 (-)NCBIHuRef
CHM1_1338,838,871 - 38,946,272 (-)NCBICHM1_1
Scn11a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399119,582,829 - 119,654,522 (-)NCBIGRCm39mm39
GRCm39 Ensembl9119,582,825 - 119,654,522 (-)Ensembl
GRCm389119,753,763 - 119,825,456 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9119,753,759 - 119,825,456 (-)EnsemblGRCm38mm10GRCm38
MGSCv379119,662,881 - 119,734,574 (-)NCBIGRCm37mm9NCBIm37
MGSCv369119,602,461 - 119,672,558 (-)NCBImm8
Celera9120,223,700 - 120,294,696 (-)NCBICelera
Cytogenetic Map9F3NCBI
cM Map971.33NCBI
Scn11a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542724,989,615 - 25,109,550 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542724,917,709 - 25,109,499 (+)NCBIChiLan1.0ChiLan1.0
SCN11A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1339,024,090 - 39,131,293 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl339,024,921 - 39,128,015 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0338,741,485 - 38,948,400 (-)NCBIMhudiblu_PPA_v0panPan3
SCN11A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1238,559,804 - 8,651,448 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl238,559,952 - 8,651,500 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha238,599,916 - 8,691,489 (-)NCBI
ROS_Cfam_1.0238,852,382 - 8,933,244 (-)NCBI
UMICH_Zoey_3.1238,662,540 - 8,754,003 (-)NCBI
UNSW_CanFamBas_1.0238,803,937 - 8,896,178 (-)NCBI
UU_Cfam_GSD_1.0238,797,979 - 8,889,539 (-)NCBI
Scn11a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118195,023,309 - 195,117,394 (-)NCBI
SpeTri2.0NW_00493647328,162,528 - 28,248,474 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN11A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1323,602,977 - 23,692,220 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11323,602,378 - 23,692,281 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21325,889,505 - 25,951,832 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCN11A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.115466,295 - 575,460 (+)NCBI
ChlSab1.1 Ensembl15467,210 - 575,110 (+)Ensembl
Vero_WHO_p1.0NW_0236660639,093,710 - 9,305,205 (+)NCBI
Scn11a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247312,065,228 - 2,203,215 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)883894304128894304Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)889058229132243842Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8104682575133307652Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8107769005129956433Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:248
Count of miRNA genes:162
Interacting mature miRNAs:182
Transcripts:ENSRNOT00000034025
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 endocrine system hemolymphoid system nervous system renal system reproductive system respiratory system
High
Medium 2
Low 2 8 19 15 4
Below cutoff 1 49 2 21 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034025   ⟹   ENSRNOP00000033224
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8128,450,801 - 128,521,109 (-)Ensembl
RefSeq Acc Id: NM_019265   ⟹   NP_062138
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,496,761 - 119,567,044 (-)NCBI
Rnor_6.08128,450,793 - 128,521,109 (-)NCBI
Rnor_5.08127,654,010 - 127,724,293 (-)NCBI
RGSC_v3.48124,724,493 - 124,794,654 (-)RGD
Celera8118,645,022 - 118,713,950 (-)RGD
Sequence:
RefSeq Acc Id: XM_017595515   ⟹   XP_017451004
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,450,793 - 128,527,510 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595516   ⟹   XP_017451005
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,450,793 - 128,521,037 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595517   ⟹   XP_017451006
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,450,793 - 128,520,877 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595518   ⟹   XP_017451007
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,450,793 - 128,521,245 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595519   ⟹   XP_017451008
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,450,793 - 128,519,257 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039080974   ⟹   XP_038936902
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,495,550 - 119,561,299 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_062138   ⟸   NM_019265
- UniProtKB: O88457 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017451004   ⟸   XM_017595515
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451007   ⟸   XM_017595518
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017451005   ⟸   XM_017595516
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017451006   ⟸   XM_017595517
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017451008   ⟸   XM_017595519
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000033224   ⟸   ENSRNOT00000034025
RefSeq Acc Id: XP_038936902   ⟸   XM_039080974
- Peptide Label: isoform X1
Protein Domains
Ion_trans   Na_trans_assoc

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 (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)
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/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 (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)
Visual CSV TAB Printer
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)
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)
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
FHH/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)
FHH/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
FHL/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)
FHL/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
GH/OmrMcwi (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)
GK/Ox (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
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 (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)
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
LH/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
LL/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/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
M520/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
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)
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
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
SBH/Ygl (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: 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)
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: 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)
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
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 (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 (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:3630 AgrOrtholog
Ensembl Genes ENSRNOG00000032884 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000033224 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034025 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ion_trans_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_channel_a11su UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_channel_asu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_chnl_inactivation_gate UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VGCC_Ca_Na UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29701 UniProtKB/Swiss-Prot
NCBI Gene 29701 ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10037:SF210 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Scn11a PhenoGen
PRINTS NACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC224161
UniProt F1M9X1_RAT UniProtKB/TrEMBL
  O88457 ENTREZGENE
  Q810E2_RAT UniProtKB/TrEMBL
  SCNBA_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Scn11a  sodium voltage-gated channel alpha subunit 11  Scn11a  sodium channel, voltage-gated, type XI, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-02-27 Scn11a  sodium channel, voltage-gated, type XI, alpha subunit  Scn11a  sodium channel, voltage-gated, type XI, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Scn11a  sodium channel, voltage-gated, type XI, alpha    sodium channel, voltage-gated, type11, alpha polypeptide  Name updated 1299863 APPROVED
2004-12-14 Scn11a  sodium channel, voltage-gated, type11, alpha polypeptide      Symbol and Name status set to approved 1299863 APPROVED
2002-06-10 Scn11a  sodium channel, voltage-gated, type11, alpha polypeptide      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_drugs channel may be tetrodotoxin resistant 69981