Scn10a (sodium voltage-gated channel alpha subunit 10) - Rat Genome Database

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Gene: Scn10a (sodium voltage-gated channel alpha subunit 10) Rattus norvegicus
Analyze
Symbol: Scn10a
Name: sodium voltage-gated channel alpha subunit 10
RGD ID: 3629
Description: Exhibits voltage-gated sodium channel activity. Involved in odontogenesis of dentin-containing tooth; sensory perception of pain; and sodium ion transport. Localizes to several cellular components, including clathrin complex; glutamatergic synapse; and integral component of presynaptic membrane. Used to study sciatic neuropathy. Human ortholog(s) of this gene implicated in familial episodic pain syndrome 2. Orthologous to human SCN10A (sodium voltage-gated channel alpha subunit 10); PARTICIPATES IN alfentanil pharmacodynamics pathway; bupivacaine pharmacodynamics pathway; buprenorphine pharmacodynamics pathway; INTERACTS WITH (+)-trans-(S)-allethrin; allethrin; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Na(V)1.8; Nav1.8; peripheral nerve sodium channel 3; PN3; sensory neuron sodium channel; sodium channel protein type 10 subunit alpha; sodium channel protein type X subunit alpha; sodium channel type X alpha polypeptide; sodium channel voltage-gated type X alpha polypeptide; sodium channel, voltage-gated, type 10, alpha polypeptide; sodium channel, voltage-gated, type X, alpha; sodium channel, voltage-gated, type X, alpha polypeptide; sodium channel, voltage-gated, type X, alpha subunit; voltage-gated sodium channel subunit alpha Nav1.8
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
mRatBN7.28119,350,723 - 119,462,882 (-)NCBI
Rnor_6.0 Ensembl8128,298,594 - 128,416,650 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08128,298,593 - 128,416,896 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08127,503,061 - 127,620,197 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48124,578,222 - 124,690,458 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18124,597,959 - 124,710,195 (-)NCBI
Celera8118,500,856 - 118,611,564 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Additional References at PubMed
PMID:9450690   PMID:9839820   PMID:11487631   PMID:14759526   PMID:14960304   PMID:15047701   PMID:15178439   PMID:16029194   PMID:16545521   PMID:17108087   PMID:17568746   PMID:17950013  
PMID:18552876   PMID:18782866   PMID:19056867   PMID:19164297   PMID:19269275   PMID:19320998   PMID:19575990   PMID:19607921   PMID:19953341   PMID:20028484   PMID:20062061   PMID:20482896  
PMID:20720009   PMID:21041692   PMID:21276017   PMID:21562192   PMID:21572961   PMID:22127815   PMID:22225591   PMID:22342308   PMID:23064159   PMID:23139220   PMID:23449670   PMID:24606981  
PMID:24724624   PMID:24763188   PMID:24990156   PMID:24998131   PMID:25503076   PMID:26005195   PMID:26597700   PMID:26764239   PMID:27327156   PMID:27631681   PMID:27905525   PMID:30860870  


Genomics

Comparative Map Data
Scn10a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28119,350,723 - 119,462,882 (-)NCBI
Rnor_6.0 Ensembl8128,298,594 - 128,416,650 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.08128,298,593 - 128,416,896 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.08127,503,061 - 127,620,197 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48124,578,222 - 124,690,458 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18124,597,959 - 124,710,195 (-)NCBI
Celera8118,500,856 - 118,611,564 (-)NCBICelera
Cytogenetic Map8q32NCBI
SCN10A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl338,696,802 - 38,816,286 (-)EnsemblGRCh38hg38GRCh38
GRCh38338,696,807 - 38,816,217 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37338,738,298 - 38,857,708 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36338,713,841 - 38,810,505 (-)NCBINCBI36hg18NCBI36
Build 34338,713,840 - 38,810,505NCBI
Celera338,677,898 - 38,774,543 (-)NCBI
Cytogenetic Map3p22.2NCBI
HuRef338,781,159 - 38,877,645 (-)NCBIHuRef
CHM1_1338,690,433 - 38,787,099 (-)NCBICHM1_1
Scn10a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399119,437,522 - 119,548,388 (-)NCBIGRCm39mm39
GRCm39 Ensembl9119,437,522 - 119,548,388 (-)Ensembl
GRCm389119,608,456 - 119,719,322 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9119,608,456 - 119,719,322 (-)EnsemblGRCm38mm10GRCm38
MGSCv379119,517,584 - 119,603,478 (-)NCBIGRCm37mm9NCBIm37
MGSCv369119,457,165 - 119,543,058 (-)NCBImm8
Celera9120,082,167 - 120,168,344 (-)NCBICelera
Cytogenetic Map9F3NCBI
cM Map971.33NCBI
Scn10a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542725,157,179 - 25,243,473 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542725,157,179 - 25,244,020 (+)NCBIChiLan1.0ChiLan1.0
SCN10A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1338,876,068 - 38,972,247 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl338,876,068 - 38,972,247 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0338,593,765 - 38,691,172 (-)NCBIMhudiblu_PPA_v0panPan3
SCN10A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1238,420,468 - 8,527,414 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl238,420,472 - 8,527,383 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha238,460,551 - 8,567,500 (-)NCBI
ROS_Cfam_1.0238,708,298 - 8,817,466 (-)NCBI
UMICH_Zoey_3.1238,523,267 - 8,630,160 (-)NCBI
UNSW_CanFamBas_1.0238,664,475 - 8,771,500 (-)NCBI
UU_Cfam_GSD_1.0238,658,580 - 8,765,552 (-)NCBI
Scn10a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118194,871,017 - 194,982,033 (-)NCBI
SpeTri2.0NW_00493647328,010,123 - 28,102,124 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN10A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1323,481,999 - 23,570,452 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11323,481,537 - 23,570,454 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21325,726,454 - 25,805,806 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCN10A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.115624,962 - 724,018 (+)NCBI
ChlSab1.1 Ensembl15625,742 - 721,963 (+)Ensembl
Scn10a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247312,254,445 - 2,356,174 (+)NCBI

Position Markers
D8Rat4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28119,434,019 - 119,434,168 (+)MAPPER
Rnor_6.08128,388,056 - 128,388,204NCBIRnor6.0
Rnor_5.08127,591,320 - 127,591,468UniSTSRnor5.0
RGSC_v3.48124,661,862 - 124,662,011RGDRGSC3.4
RGSC_v3.48124,661,863 - 124,662,011UniSTSRGSC3.4
RGSC_v3.18124,681,600 - 124,681,748RGD
Celera8118,582,992 - 118,583,140UniSTS
RH 3.4 Map81286.3RGD
RH 3.4 Map81286.3UniSTS
RH 2.0 Map81002.9RGD
SHRSP x BN Map880.7899RGD
Cytogenetic Map8q32UniSTS
D8Got185  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28119,429,949 - 119,430,216 (+)MAPPER
Rnor_6.08128,383,986 - 128,384,252NCBIRnor6.0
Rnor_5.08127,587,250 - 127,587,516UniSTSRnor5.0
RGSC_v3.48124,657,792 - 124,658,059RGDRGSC3.4
RGSC_v3.48124,657,793 - 124,658,059UniSTSRGSC3.4
RGSC_v3.18124,677,530 - 124,677,796RGD
Celera8118,578,924 - 118,579,186UniSTS
RH 3.4 Map81285.0UniSTS
RH 3.4 Map81285.0RGD
RH 2.0 Map81023.5RGD
Cytogenetic Map8q32UniSTS
BE096280  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28119,350,741 - 119,350,905 (+)MAPPER
Rnor_6.08128,298,612 - 128,298,775NCBIRnor6.0
Rnor_5.08127,503,080 - 127,503,243UniSTSRnor5.0
RGSC_v3.48124,578,241 - 124,578,404UniSTSRGSC3.4
Celera8118,500,875 - 118,501,038UniSTS
RH 3.4 Map81285.3UniSTS
Cytogenetic Map8q32UniSTS


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:72
Count of miRNA genes:62
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000046864
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 hemolymphoid system nervous system reproductive system respiratory system
High
Medium
Low 1 1 8 14 1
Below cutoff 1 39 10 13 40 9 10

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000046864   ⟹   ENSRNOP00000047944
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8128,298,594 - 128,416,650 (-)Ensembl
RefSeq Acc Id: NM_017247   ⟹   NP_058943
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,350,723 - 119,462,614 (-)NCBI
Rnor_6.08128,298,593 - 128,416,650 (-)NCBI
Rnor_5.08127,503,061 - 127,620,197 (-)NCBI
RGSC_v3.48124,578,222 - 124,690,458 (-)RGD
Celera8118,500,856 - 118,611,564 (-)RGD
Sequence:
RefSeq Acc Id: XM_017595503   ⟹   XP_017450992
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,298,593 - 128,416,896 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595504   ⟹   XP_017450993
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,298,593 - 128,416,669 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595505   ⟹   XP_017450994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,298,593 - 128,416,683 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039080963   ⟹   XP_038936891
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,359,931 - 119,413,213 (-)NCBI
RefSeq Acc Id: XM_039080964   ⟹   XP_038936892
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,350,723 - 119,462,882 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_058943   ⟸   NM_017247
- Sequence:
RefSeq Acc Id: XP_017450992   ⟸   XM_017595503
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017450994   ⟸   XM_017595505
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017450993   ⟸   XM_017595504
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000047944   ⟸   ENSRNOT00000046864
RefSeq Acc Id: XP_038936892   ⟸   XM_039080964
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038936891   ⟸   XM_039080963
- Peptide Label: isoform X1
Protein Domains
IQ

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)
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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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 128325713 128325714 C T snv WKY/Gcrc (RGD), BBDP/Wor (RGD), WKY/N (MCW), WKY/NHsd (RGD)
8 128341436 128341437 A G snv MR/N (MCW), Buf/N (MCW), WN/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3629 AgrOrtholog
Ensembl Genes ENSRNOG00000032473 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000047944 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000046864 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot
InterPro Ion_trans_dom UniProtKB/Swiss-Prot
  Na_channel_a10su UniProtKB/Swiss-Prot
  Na_channel_asu UniProtKB/Swiss-Prot
  Na_chnl_inactivation_gate UniProtKB/Swiss-Prot
  Na_trans_assoc UniProtKB/Swiss-Prot
  VGCC_Ca_Na UniProtKB/Swiss-Prot
  Volt_channel_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:29571 UniProtKB/Swiss-Prot
NCBI Gene 29571 ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot
  PTHR10037:SF208 UniProtKB/Swiss-Prot
Pfam Ion_trans UniProtKB/Swiss-Prot
  Na_trans_assoc UniProtKB/Swiss-Prot
PhenoGen Scn10a PhenoGen
PRINTS NACHANNEL UniProtKB/Swiss-Prot
TIGR TC208312
UniProt Q0Q789_RAT UniProtKB/TrEMBL
  Q62968 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q63554 UniProtKB/Swiss-Prot
  Q6EWG6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Scn10a  sodium voltage-gated channel alpha subunit 10  Scn10a  sodium channel, voltage-gated, type X, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-09-16 Scn10a  sodium channel, voltage-gated, type X, alpha subunit  Scn10a  sodium channel, voltage-gated, type X, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-12-15 Scn10a  sodium channel, voltage-gated, type X, alpha  Scn10a  sodium channel, voltage-gated, type X, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-18 Scn10a  sodium channel, voltage-gated, type X, alpha subunit  Scn10a  sodium channel, voltage-gated, type X, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-13 Scn10a  sodium channel, voltage-gated, type X, alpha  Scn10a  sodium channel, voltage-gated, type 10, alpha polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Scn10a  sodium channel, voltage-gated, type 10, alpha polypeptide      Symbol and Name status set to approved 1299863 APPROVED
2002-06-10 Scn10a  sodium channel, voltage-gated, type 10, alpha polypeptide      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed primarily in small sensory neurons of the peripheral nervous system 69978