Kcnc2 (potassium voltage-gated channel subfamily C member 2) - Rat Genome Database

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Gene: Kcnc2 (potassium voltage-gated channel subfamily C member 2) Rattus norvegicus
Analyze
Symbol: Kcnc2
Name: potassium voltage-gated channel subfamily C member 2
RGD ID: 628829
Description: Enables delayed rectifier potassium channel activity; transmembrane transporter binding activity; and voltage-gated ion channel activity involved in regulation of presynaptic membrane potential. Involved in several processes, including cellular response to nitric oxide; globus pallidus development; and protein complex oligomerization. Located in several cellular components, including axon; basolateral plasma membrane; and neuronal cell body membrane. Is integral component of plasma membrane. Part of voltage-gated potassium channel complex. Orthologous to human KCNC2 (potassium voltage-gated channel subfamily C member 2); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-Tetrachlorodibenzofuran; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: KShIIIA; Kv3.2; potassium channel voltage-gated Shaw-related subfamily C member 2; potassium channel, voltage gated Shaw-related subfamily C, member 2; potassium voltage gated channel, Shaw-related subfamily, member 2; shaw-like potassium channel; voltage-gated potassium channel subunit Kv3.2
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
mRatBN7.2747,700,035 - 47,883,979 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl747,700,288 - 47,883,968 (+)Ensembl
Rnor_6.0754,978,453 - 55,159,362 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl754,980,120 - 55,159,351 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0754,998,077 - 55,177,456 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4751,326,602 - 51,487,958 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1751,347,043 - 51,508,400 (+)NCBI
Celera744,495,328 - 44,675,986 (+)NCBICelera
Cytogenetic Map7q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
epilepsy  (ISO)
glioblastoma  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Bobik M, etal., Brain Res. 2004 Nov 12;1026(2):168-78.
2. Cheung HC, etal., BMC Genomics. 2008 May 12;9:216. doi: 10.1186/1471-2164-9-216.
3. Devaux J, etal., J Neurosci. 2003 Jun 1;23(11):4509-18.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Grabert J and Wahle P, Neuroscience. 2008 Oct 15;156(3):618-29. doi: 10.1016/j.neuroscience.2008.08.008. Epub 2008 Aug 12.
6. Grabert J and Wahle P, Neuroscience. 2009 Jan 23;158(2):654-64. doi: 10.1016/j.neuroscience.2008.07.035. Epub 2008 Jul 25.
7. Hernandez-Pineda R, etal., J Neurophysiol. 1999 Sep;82(3):1512-28.
8. Kanda VA, etal., Biophys J. 2011 Sep 21;101(6):1364-75. doi: 10.1016/j.bpj.2011.08.014. Epub 2011 Sep 20.
9. Lau D, etal., J Neurosci. 2000 Dec 15;20(24):9071-85.
10. Luneau C, etal., FEBS Lett 1991 Aug 19;288(1-2):163-7.
11. McCormack T, etal., Proc Natl Acad Sci U S A 1990 Jul;87(13):5227-31.
12. McCormack T, etal., Proc Natl Acad Sci U S A 1991 May 1;88(9):4060.
13. McDonald AJ and Mascagni F, Neuroscience. 2006;138(2):537-47. Epub 2006 Jan 18.
14. MGD data from the GO Consortium
15. Moreno H, etal., J Neurosci. 1995 Aug;15(8):5486-501.
16. Moreno H, etal., J Physiol. 2001 Feb 1;530(Pt 3):345-58.
17. Ponce A, etal., J Membr Biol. 1997 Sep 15;159(2):149-59.
18. Rettig J, etal., EMBO J 1992 Jul;11(7):2473-86.
19. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. RGD automated import pipeline for gene-chemical interactions
21. Rudy B, etal., Proc Natl Acad Sci U S A 1992 May 15;89(10):4603-7.
22. Tavian D, etal., Neurol Sci. 2011 Aug;32(4):571-7. doi: 10.1007/s10072-010-0446-7. Epub 2011 Jan 14.
23. Wang Z, etal., J Physiol. 2007 Nov 1;584(Pt 3):755-67. Epub 2007 Sep 13.
24. Yeung SY, etal., J Neurosci. 2005 Sep 21;25(38):8735-45.
Additional References at PubMed
PMID:10531438   PMID:12000114   PMID:15240761   PMID:17761775   PMID:19332619   PMID:22871113  


Genomics

Comparative Map Data
Kcnc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2747,700,035 - 47,883,979 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl747,700,288 - 47,883,968 (+)Ensembl
Rnor_6.0754,978,453 - 55,159,362 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl754,980,120 - 55,159,351 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0754,998,077 - 55,177,456 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4751,326,602 - 51,487,958 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1751,347,043 - 51,508,400 (+)NCBI
Celera744,495,328 - 44,675,986 (+)NCBICelera
Cytogenetic Map7q22NCBI
KCNC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1275,040,077 - 75,209,839 (-)EnsemblGRCh38hg38GRCh38
GRCh381275,040,078 - 75,209,839 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371275,433,858 - 75,603,619 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361273,720,163 - 73,889,778 (-)NCBINCBI36hg18NCBI36
Build 341273,720,162 - 73,889,778NCBI
Celera1275,101,336 - 75,270,876 (-)NCBI
Cytogenetic Map12q21.1NCBI
HuRef1272,483,472 - 72,653,079 (-)NCBIHuRef
CHM1_11275,399,235 - 75,568,820 (-)NCBICHM1_1
Kcnc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910112,105,803 - 112,302,209 (+)NCBIGRCm39mm39
GRCm39 Ensembl10112,107,026 - 112,302,929 (+)Ensembl
GRCm3810112,269,898 - 112,466,304 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10112,271,121 - 112,467,024 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710111,708,179 - 111,903,360 (+)NCBIGRCm37mm9NCBIm37
MGSCv3610111,675,233 - 111,870,414 (+)NCBImm8
Celera10114,210,354 - 114,400,944 (+)NCBICelera
Cytogenetic Map10D2NCBI
cM Map1060.3NCBI
Kcnc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540514,422,396 - 14,600,341 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540514,420,447 - 14,599,780 (-)NCBIChiLan1.0ChiLan1.0
KCNC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11275,419,465 - 75,588,535 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01272,566,924 - 72,736,270 (-)NCBIMhudiblu_PPA_v0panPan3
KCNC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11015,599,428 - 15,822,579 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1015,643,962 - 15,818,097 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1015,541,357 - 15,767,201 (-)NCBI
ROS_Cfam_1.01015,785,996 - 16,011,988 (-)NCBI
ROS_Cfam_1.0 Ensembl1015,789,212 - 16,007,557 (-)Ensembl
UMICH_Zoey_3.11015,595,746 - 15,821,564 (-)NCBI
UNSW_CanFamBas_1.01015,848,484 - 16,075,795 (-)NCBI
UU_Cfam_GSD_1.01015,974,622 - 16,200,463 (-)NCBI
Kcnc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494542,033,763 - 42,220,108 (+)NCBI
SpeTri2.0NW_0049365683,508,212 - 3,694,459 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KCNC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl538,326,408 - 38,533,110 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1538,326,408 - 38,535,826 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2541,759,389 - 41,781,754 (-)NCBISscrofa10.2Sscrofa10.2susScr3
KCNC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11170,603,034 - 70,770,625 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1170,603,003 - 70,768,859 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037174,772,549 - 174,940,514 (+)NCBIVero_WHO_p1.0
Kcnc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475022,807,234 - 22,996,614 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D7Rat26  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0755,072,862 - 55,073,022NCBIRnor6.0
Celera744,590,656 - 44,590,819UniSTS
RH 3.4 Map7412.9RGD
RH 3.4 Map7412.9UniSTS
RH 2.0 Map7380.4RGD
SHRSP x BN Map731.05RGD
Cytogenetic Map7q12-q22UniSTS
D7Rat169  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2747,719,466 - 47,719,673 (+)MAPPERmRatBN7.2
Rnor_6.0754,998,209 - 54,998,415NCBIRnor6.0
Rnor_5.0755,017,742 - 55,017,948UniSTSRnor5.0
RGSC_v3.4751,344,691 - 51,344,898RGDRGSC3.4
RGSC_v3.4751,344,692 - 51,344,898UniSTSRGSC3.4
RGSC_v3.1751,365,111 - 51,365,507RGD
Celera744,513,417 - 44,513,623UniSTS
FHH x ACI Map726.78UniSTS
FHH x ACI Map726.78RGD
Cytogenetic Map7q12-q22UniSTS
D7Got205  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0755,072,801 - 55,073,014NCBIRnor6.0
Celera744,590,664 - 44,590,881UniSTS
Cytogenetic Map7q12-q22UniSTS
BF404636  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2747,881,223 - 47,881,330 (+)MAPPERmRatBN7.2
Rnor_6.0755,156,607 - 55,156,713NCBIRnor6.0
Rnor_5.0755,174,701 - 55,174,807UniSTSRnor5.0
RGSC_v3.4751,485,214 - 51,485,320UniSTSRGSC3.4
Celera744,673,242 - 44,673,348UniSTS
RH 3.4 Map7417.8UniSTS
Cytogenetic Map7q12-q22UniSTS
AU046555  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2747,721,167 - 47,721,291 (+)MAPPERmRatBN7.2
mRatBN7.2747,721,167 - 47,721,315 (+)MAPPERmRatBN7.2
Rnor_6.0754,999,910 - 55,000,057NCBIRnor6.0
Rnor_6.0754,999,910 - 55,000,033NCBIRnor6.0
Rnor_5.0755,019,621 - 55,019,744UniSTSRnor5.0
Rnor_5.0755,019,621 - 55,019,768UniSTSRnor5.0
RGSC_v3.4751,346,393 - 51,346,540UniSTSRGSC3.4
RGSC_v3.4751,346,393 - 51,346,516UniSTSRGSC3.4
Celera744,515,109 - 44,515,256UniSTS
Celera744,515,109 - 44,515,232UniSTS
Cytogenetic Map7q12-q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)72940968353612950Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73429328279293282Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat
2303629Vencon3Ventilatory control QTL 37.25respiration trait (VT:0001943)respiration rate (CMO:0000289)74110969256793354Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)74278731487787314Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74322875088228750Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)743747099102228765Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74486753389867533Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74659007091590070Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)74725178365728867Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)74765143992651439Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)74765143992651439Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)74765143992651439Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)74765143992651439Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)74765143992651439Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)74765143992651439Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)74765143992651439Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:649
Count of miRNA genes:275
Interacting mature miRNAs:337
Transcripts:ENSRNOT00000005690, ENSRNOT00000005700, ENSRNOT00000005773, ENSRNOT00000049943
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 8 31
Low 1 4 35 7
Below cutoff 3 20 11 5 13 5 7 7 6 12 30 9 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_139216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_139217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241327 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078411 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078412 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039078416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005486545 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC109965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC127978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AX839889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M34052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M59211 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M59313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M84202 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M84203 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000005690   ⟹   ENSRNOP00000005690
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl747,701,378 - 47,883,968 (+)Ensembl
Rnor_6.0 Ensembl754,980,120 - 55,159,351 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000005773   ⟹   ENSRNOP00000005773
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl747,701,421 - 47,881,436 (+)Ensembl
Rnor_6.0 Ensembl754,980,163 - 55,156,819 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099049   ⟹   ENSRNOP00000084708
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl747,700,288 - 47,880,696 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105247   ⟹   ENSRNOP00000088724
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl747,700,288 - 47,883,968 (+)Ensembl
RefSeq Acc Id: NM_139216   ⟹   NP_631962
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2747,701,378 - 47,883,968 (+)NCBI
Rnor_6.0754,980,120 - 55,159,351 (+)NCBI
Rnor_5.0754,998,077 - 55,177,456 (+)NCBI
RGSC_v3.4751,326,602 - 51,487,958 (+)RGD
Celera744,495,328 - 44,675,986 (+)RGD
Sequence:
RefSeq Acc Id: NM_139217   ⟹   NP_631963
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2747,701,421 - 47,881,436 (+)NCBI
Rnor_6.0754,980,163 - 55,156,819 (+)NCBI
Rnor_5.0754,998,077 - 55,177,456 (+)NCBI
RGSC_v3.4751,326,602 - 51,487,958 (+)RGD
Celera744,495,371 - 44,673,454 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006241327   ⟹   XP_006241389
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2747,700,035 - 47,883,979 (+)NCBI
Rnor_6.0754,978,783 - 55,159,362 (+)NCBI
Rnor_5.0754,998,077 - 55,177,456 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594660   ⟹   XP_017450149
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2747,700,511 - 47,883,979 (+)NCBI
Rnor_6.0754,979,277 - 55,159,362 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594661   ⟹   XP_017450150
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2747,700,035 - 47,880,956 (+)NCBI
Rnor_6.0754,978,783 - 55,156,287 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594662   ⟹   XP_017450151
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2747,700,035 - 47,883,979 (+)NCBI
Rnor_6.0754,978,453 - 55,159,362 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078411   ⟹   XP_038934339
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2747,700,035 - 47,883,979 (+)NCBI
RefSeq Acc Id: XM_039078412   ⟹   XP_038934340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2747,700,035 - 47,883,979 (+)NCBI
RefSeq Acc Id: XM_039078413   ⟹   XP_038934341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2747,700,035 - 47,883,979 (+)NCBI
RefSeq Acc Id: XM_039078414   ⟹   XP_038934342
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2747,700,035 - 47,879,837 (+)NCBI
RefSeq Acc Id: XM_039078416   ⟹   XP_038934344
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2747,700,035 - 47,883,979 (+)NCBI
RefSeq Acc Id: XR_005486545
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2747,700,035 - 47,882,895 (+)NCBI
Protein Sequences
Protein RefSeqs NP_631962 (Get FASTA)   NCBI Sequence Viewer  
  NP_631963 (Get FASTA)   NCBI Sequence Viewer  
  XP_006241389 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450149 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450150 (Get FASTA)   NCBI Sequence Viewer  
  XP_017450151 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934339 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934340 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934341 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934342 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934344 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41819 (Get FASTA)   NCBI Sequence Viewer  
  AAA41820 (Get FASTA)   NCBI Sequence Viewer  
  AAA42142 (Get FASTA)   NCBI Sequence Viewer  
  AAA42143 (Get FASTA)   NCBI Sequence Viewer  
  CAE85434 (Get FASTA)   NCBI Sequence Viewer  
  EDM16703 (Get FASTA)   NCBI Sequence Viewer  
  EDM16704 (Get FASTA)   NCBI Sequence Viewer  
  EDM16705 (Get FASTA)   NCBI Sequence Viewer  
  EDM16706 (Get FASTA)   NCBI Sequence Viewer  
  EDM16707 (Get FASTA)   NCBI Sequence Viewer  
  EDM16708 (Get FASTA)   NCBI Sequence Viewer  
  EDM16709 (Get FASTA)   NCBI Sequence Viewer  
  EDM16710 (Get FASTA)   NCBI Sequence Viewer  
  EDM16711 (Get FASTA)   NCBI Sequence Viewer  
  EDM16712 (Get FASTA)   NCBI Sequence Viewer  
  P22462 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_631962   ⟸   NM_139216
- Peptide Label: isoform a
- UniProtKB: P22462 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_631963   ⟸   NM_139217
- Peptide Label: isoform b
- UniProtKB: P22462 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006241389   ⟸   XM_006241327
- Peptide Label: isoform X1
- UniProtKB: P22462 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017450151   ⟸   XM_017594662
- Peptide Label: isoform X3
- UniProtKB: P22462 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017450150   ⟸   XM_017594661
- Peptide Label: isoform X2
- UniProtKB: P22462 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017450149   ⟸   XM_017594660
- Peptide Label: isoform X1
- UniProtKB: P22462 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000005690   ⟸   ENSRNOT00000005690
RefSeq Acc Id: ENSRNOP00000005773   ⟸   ENSRNOT00000005773
RefSeq Acc Id: XP_038934340   ⟸   XM_039078412
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038934341   ⟸   XM_039078413
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038934344   ⟸   XM_039078416
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038934339   ⟸   XM_039078411
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038934342   ⟸   XM_039078414
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000088724   ⟸   ENSRNOT00000105247
RefSeq Acc Id: ENSRNOP00000084708   ⟸   ENSRNOT00000099049

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)
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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
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)
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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
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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
BN/SsN (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
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (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
BXH2/CubMcwi (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
BXH3/CubMcwi (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
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
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)
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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
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)
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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
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
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)
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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/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
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
LL/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
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)
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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 (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
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
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)
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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
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)
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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
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 (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)
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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 (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
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
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)
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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 (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
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 (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)
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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 (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
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:628829 AgrOrtholog
Ensembl Genes ENSRNOG00000004077 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000005690 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000005773 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000084708 ENTREZGENE
  ENSRNOP00000088724 ENTREZGENE
Ensembl Transcript ENSRNOT00000005690 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000005773 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000099049 ENTREZGENE
  ENSRNOT00000105247 ENTREZGENE
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot
InterPro BTB/POZ_dom UniProtKB/Swiss-Prot
  Ion_trans_dom UniProtKB/Swiss-Prot
  K_chnl_volt-dep_Kv UniProtKB/Swiss-Prot
  K_chnl_volt-dep_Kv3 UniProtKB/Swiss-Prot
  SKP1/BTB/POZ_sf UniProtKB/Swiss-Prot
  T1-type_BTB UniProtKB/Swiss-Prot
  VG_K_chnl UniProtKB/Swiss-Prot
  Volt_channel_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:246153 UniProtKB/Swiss-Prot
NCBI Gene 246153 ENTREZGENE
PANTHER PTHR11537 UniProtKB/Swiss-Prot
Pfam BTB_2 UniProtKB/Swiss-Prot
  Ion_trans UniProtKB/Swiss-Prot
PhenoGen Kcnc2 PhenoGen
PRINTS KVCHANNEL UniProtKB/Swiss-Prot
  SHAWCHANNEL UniProtKB/Swiss-Prot
SMART BTB UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54695 UniProtKB/Swiss-Prot
UniProt KCNC2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P22461 UniProtKB/Swiss-Prot
  P22463 UniProtKB/Swiss-Prot
  Q63735 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Kcnc2  potassium voltage-gated channel subfamily C member 2  Kcnc2  potassium channel, voltage gated Shaw-related subfamily C, member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-01-26 Kcnc2  potassium channel, voltage gated Shaw-related subfamily C, member 2  Kcnc2  potassium voltage gated channel, Shaw-related subfamily, member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Kcnc2  potassium voltage gated channel, Shaw-related subfamily, member 2      Symbol and Name status set to approved 625702 APPROVED
2003-02-27 Kcnc2  potassium voltage gated channel, Shaw-related subfamily, member 2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression prominantly expressed in dorsal thalamus 729132