Kcnd2 (potassium voltage-gated channel subfamily D member 2) - Rat Genome Database

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Gene: Kcnd2 (potassium voltage-gated channel subfamily D member 2) Rattus norvegicus
Analyze
Symbol: Kcnd2
Name: potassium voltage-gated channel subfamily D member 2
RGD ID: 68393
Description: Enables A-type (transient outward) potassium channel activity and voltage-gated ion channel activity involved in regulation of postsynaptic membrane potential. Involved in several processes, including cellular response to drug; cellular response to mechanical stimulus; and potassium ion transmembrane transport. Located in several cellular components, including T-tubule; neuronal cell body membrane; and perinuclear endoplasmic reticulum. Is integral component of plasma membrane. Part of voltage-gated potassium channel complex. Is active in glutamatergic synapse. Is integral component of postsynaptic membrane. Orthologous to human KCND2 (potassium voltage-gated channel subfamily D member 2); PARTICIPATES IN excitatory synaptic transmission pathway; alfentanil pharmacodynamics pathway; bupivacaine pharmacodynamics pathway; INTERACTS WITH 1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Kv4.2; potassium channel, voltage-gated Shal-related subfamily D, member 2; potassium voltage gated channel, Shal-related family, member 2; potassium voltage-gated channel, Shal-related subfamily, member 2; RK5; Shal1; voltage-gated potassium channel subunit Kv4.2
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
mRatBN7.2449,775,812 - 50,277,746 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl449,776,246 - 50,277,728 (+)Ensembl
Rnor_6.0448,309,283 - 48,816,804 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0448,099,455 - 48,609,215 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4447,541,787 - 48,047,924 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1447,772,679 - 48,277,046 (+)NCBI
Celera444,984,114 - 45,483,230 (+)NCBICelera
Cytogenetic Map4q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

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)
excitatory synaptic transmission pathway  (IMP)
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)
long term potentiation  (TAS)
mepivacaine pharmacodynamics pathway  (ISO)
methadone pharmacodynamics pathway  (ISO)
nalbuphine pharmacodynamics pathway  (ISO)
naloxone pharmacodynamics pathway  (ISO)
naltrexone pharmacodynamics pathway  (ISO)
nicotine pharmacodynamics pathway  (ISO)
oxybuprocaine pharmacodynamics pathway  (ISO)
oxycodone pharmacodynamics pathway  (ISO)
oxymorphone pharmacodynamics pathway  (ISO)
pentazocine pharmacodynamics pathway  (ISO)
prilocaine pharmacodynamics pathway  (ISO)
procaine pharmacodynamics pathway  (ISO)
remifentanil pharmacodynamics pathway  (ISO)
ropivacaine pharmacodynamics pathway  (ISO)
tramadol pharmacodynamics pathway  (ISO)

References

References - curated
1. Alday A, etal., Channels (Austin). 2010 May-Jun;4(3):168-78.
2. Alonso G and Widmer H, Neuroscience. 1997 Apr;77(3):617-21.
3. Blair TA, etal., FEBS Lett 1991 Dec 16;295(1-3):211-3.
4. Chavira-Suarez E, etal., Biochem Biophys Res Commun. 2011 Jan 14;404(2):678-83. doi: 10.1016/j.bbrc.2010.12.041. Epub 2010 Dec 11.
5. Dabrowska J and Rainnie DG, Neuroscience. 2010 Dec 15;171(3):721-33. doi: 10.1016/j.neuroscience.2010.09.011. Epub 2010 Sep 16.
6. Deschenes I, etal., J Mol Cell Cardiol. 2008 Sep;45(3):336-46. Epub 2008 May 12.
7. Gardoni F, etal., J Biol Chem. 2007 Sep 28;282(39):28691-9. Epub 2007 Jul 16.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. GOA data from the GO Consortium
10. Holmqvist MH, etal., Proc Natl Acad Sci U S A 2002 Jan 22;99(2):1035-40.
11. Jerng HH, etal., J Physiol. 2005 Nov 1;568(Pt 3):767-88. Epub 2005 Aug 25.
12. Kim J, etal., J Physiol. 2005 Nov 15;569(Pt 1):41-57. Epub 2005 Sep 1.
13. Kim J, etal., Neuron. 2007 Jun 21;54(6):933-47.
14. Kobayashi T, etal., J Mol Cell Cardiol. 2003 Sep;35(9):1073-82.
15. Liu YQ, etal., Front Cell Neurosci. 2014 Oct 14;8:329. doi: 10.3389/fncel.2014.00329. eCollection 2014.
16. MGD data from the GO Consortium
17. Nadal MS, etal., Neuron. 2003 Feb 6;37(3):449-61.
18. NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Nishiyama A, etal., Am J Physiol Heart Circ Physiol 2001 Oct;281(4):H1800-7.
20. Pipeline to import SMPDB annotations from SMPDB into RGD
21. RGD automated data pipeline
22. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
23. RGD automated import pipeline for gene-chemical interactions
24. Rhodes KJ, etal., J Neurosci. 2004 Sep 8;24(36):7903-15.
25. Roberds SL and Tamkun MM, Proc Natl Acad Sci U S A 1991 Mar 1;88(5):1798-802.
26. Rudakova E, etal., Pflugers Arch. 2015 Feb;467(2):299-309. doi: 10.1007/s00424-014-1521-3. Epub 2014 May 6.
27. Sanguinetti MC, etal., Mol Pharmacol. 1997 Mar;51(3):491-8.
28. Saygili E, etal., Am J Physiol Heart Circ Physiol. 2007 Jun;292(6):H2898-905. Epub 2007 Feb 9.
29. Strassle BW, etal., J Comp Neurol. 2005 Apr 4;484(2):144-55.
30. Takeuchi S, etal., J Mol Cell Cardiol. 2000 Jul;32(7):1361-9.
31. Tseng GN Cardiovasc Res 1999 Jan;41(1):16-8.
32. Wickenden AD, etal., Am J Physiol 1999 May;276(5 Pt 2):H1599-607.
33. Yeola SW and Snyders DJ, Cardiovasc Res. 1997 Mar;33(3):540-7.
34. Zhou W, etal., Neuron. 2004 Feb 19;41(4):573-86.
35. Zobel C, etal., Circulation 2002 Oct 29;106(18):2385-91.
Additional References at PubMed
PMID:1840649   PMID:10676964   PMID:11040264   PMID:11606724   PMID:11847232   PMID:11923279   PMID:12592409   PMID:12626328   PMID:12754210   PMID:12829703   PMID:12835418   PMID:12843309  
PMID:14551056   PMID:14613857   PMID:14980207   PMID:15454437   PMID:15485870   PMID:15671030   PMID:15946675   PMID:16176357   PMID:16271805   PMID:16553778   PMID:16636498   PMID:16648177  
PMID:16820361   PMID:17026528   PMID:17122053   PMID:17475505   PMID:17725325   PMID:18045912   PMID:18088376   PMID:18363830   PMID:18371079   PMID:18463498   PMID:18513371   PMID:18515646  
PMID:18603586   PMID:18815185   PMID:19213956   PMID:19261906   PMID:19267230   PMID:19453640   PMID:19713751   PMID:19857555   PMID:20573902   PMID:20920553   PMID:21034530   PMID:21252158  
PMID:21273417   PMID:21451062   PMID:21472817   PMID:21511008   PMID:21895522   PMID:21943606   PMID:22098631   PMID:22245500   PMID:22511771   PMID:22700470   PMID:22815518   PMID:23066017  
PMID:24037673   PMID:24404150   PMID:24486512   PMID:24811166   PMID:25043828   PMID:25756524   PMID:26179130   PMID:27259067   PMID:27322747   PMID:28566490   PMID:29996472   PMID:31935048  
PMID:32554946  


Genomics

Comparative Map Data
Kcnd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2449,775,812 - 50,277,746 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl449,776,246 - 50,277,728 (+)Ensembl
Rnor_6.0448,309,283 - 48,816,804 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0448,099,455 - 48,609,215 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4447,541,787 - 48,047,924 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1447,772,679 - 48,277,046 (+)NCBI
Celera444,984,114 - 45,483,230 (+)NCBICelera
Cytogenetic Map4q22NCBI
KCND2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7120,273,175 - 120,750,337 (+)EnsemblGRCh38hg38GRCh38
GRCh387120,273,175 - 120,750,337 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh377119,913,229 - 120,390,391 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 367119,700,958 - 120,177,623 (+)NCBINCBI36hg18NCBI36
Build 347119,507,672 - 119,984,338NCBI
Celera7114,723,245 - 115,199,902 (+)NCBI
Cytogenetic Map7q31.31NCBI
HuRef7114,276,961 - 114,753,560 (+)NCBIHuRef
CHM1_17119,847,044 - 120,323,690 (+)NCBICHM1_1
CRA_TCAGchr7v27119,308,832 - 119,785,474 (+)NCBI
Kcnd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39621,212,101 - 21,729,804 (+)NCBIGRCm39mm39
GRCm39 Ensembl621,215,502 - 21,729,804 (+)Ensembl
GRCm38621,215,346 - 21,729,805 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl621,215,503 - 21,729,805 (+)EnsemblGRCm38mm10GRCm38
MGSCv37621,166,109 - 21,679,805 (+)NCBIGRCm37mm9NCBIm37
MGSCv36621,166,110 - 21,679,806 (+)NCBImm8
Celera621,270,473 - 21,783,671 (+)NCBICelera
Cytogenetic Map6A2- A3.1NCBI
cM Map68.49NCBI
Kcnd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554792,062,608 - 2,543,125 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554792,062,607 - 2,545,576 (+)NCBIChiLan1.0ChiLan1.0
KCND2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17124,965,851 - 125,439,913 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7124,966,816 - 125,437,430 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07112,277,018 - 112,751,896 (+)NCBIMhudiblu_PPA_v0panPan3
LOC607881
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha1460,421,540 - 60,422,657 (+)NCBI
ROS_Cfam_1.014126,284 - 155,942 (+)NCBI
UNSW_CanFamBas_1.01468,634 - 98,256 (+)NCBI
UU_Cfam_GSD_1.01449,808 - 79,444 (+)NCBI
Kcnd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511847,376,410 - 47,833,708 (+)NCBI
SpeTri2.0NW_0049366054,370,222 - 4,828,972 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KCND2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1826,141,506 - 26,623,034 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11826,139,457 - 26,624,210 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21827,744,043 - 27,759,304 (-)NCBISscrofa10.2Sscrofa10.2susScr3
KCND2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12189,091,939 - 89,575,464 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604214,004,421 - 14,488,070 (-)NCBIVero_WHO_p1.0
Kcnd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478315,349,416 - 15,892,011 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D4Rat15  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2450,119,848 - 50,119,996 (+)MAPPERmRatBN7.2
Rnor_6.0448,656,252 - 48,656,399NCBIRnor6.0
Rnor_6.0446,898,276 - 46,898,423NCBIRnor6.0
Rnor_5.0446,704,280 - 46,704,427UniSTSRnor5.0
Rnor_5.0448,448,661 - 48,448,808UniSTSRnor5.0
RGSC_v3.4447,889,730 - 47,890,193RGDRGSC3.4
RGSC_v3.4447,890,039 - 47,890,186UniSTSRGSC3.4
RGSC_v3.1448,120,304 - 48,120,767RGD
Celera445,326,958 - 45,327,119UniSTS
RH 2.0 Map4373.2RGD
SHRSP x BN Map429.41RGD
Cytogenetic Map4q22UniSTS
D4Got29  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2449,943,823 - 49,944,098 (+)MAPPERmRatBN7.2
Rnor_6.0448,477,569 - 48,477,843NCBIRnor6.0
Rnor_5.0448,269,332 - 48,269,606UniSTSRnor5.0
RGSC_v3.4447,709,493 - 47,709,768RGDRGSC3.4
RGSC_v3.4447,709,494 - 47,709,768UniSTSRGSC3.4
RGSC_v3.1447,940,068 - 47,940,342RGD
Celera445,151,415 - 45,151,680UniSTS
RH 3.4 Map4284.9UniSTS
RH 3.4 Map4284.9RGD
RH 2.0 Map4346.3RGD
Cytogenetic Map4q22UniSTS
RH144078  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2450,158,389 - 50,158,622 (+)MAPPERmRatBN7.2
Rnor_6.0448,696,267 - 48,696,499NCBIRnor6.0
Rnor_6.0446,937,142 - 46,937,374NCBIRnor6.0
Rnor_5.0448,488,676 - 48,488,908UniSTSRnor5.0
Rnor_5.0446,743,146 - 46,743,378UniSTSRnor5.0
RGSC_v3.4447,928,578 - 47,928,810UniSTSRGSC3.4
Celera445,364,025 - 45,364,257UniSTS
RH 3.4 Map4300.42UniSTS
Cytogenetic Map4q22UniSTS
RH138133  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2450,277,545 - 50,277,730 (+)MAPPERmRatBN7.2
Rnor_6.0448,816,604 - 48,816,788NCBIRnor6.0
Rnor_5.0448,609,015 - 48,609,199UniSTSRnor5.0
RGSC_v3.4448,047,724 - 48,047,908UniSTSRGSC3.4
Celera445,483,030 - 45,483,214UniSTS
RH 3.4 Map4285.6UniSTS
Cytogenetic Map4q22UniSTS
BF390067  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2450,020,194 - 50,020,385 (+)MAPPERmRatBN7.2
Rnor_6.0448,555,300 - 48,555,490NCBIRnor6.0
Rnor_5.0448,346,327 - 48,346,517UniSTSRnor5.0
RGSC_v3.4447,786,311 - 47,786,501UniSTSRGSC3.4
Celera445,227,735 - 45,227,925UniSTS
RH 3.4 Map4300.52UniSTS
Cytogenetic Map4q22UniSTS
UniSTS:498320  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2450,274,908 - 50,276,068 (+)MAPPERmRatBN7.2
Rnor_6.0448,813,967 - 48,815,126NCBIRnor6.0
Rnor_5.0448,606,378 - 48,607,537UniSTSRnor5.0
RGSC_v3.4448,045,087 - 48,046,246UniSTSRGSC3.4
Celera445,480,393 - 45,481,552UniSTS
Cytogenetic Map4q22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
11530004Niddm71Non-insulin dependent diabetes mellitus QTL 710.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43258419952754138Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43950527573892441Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43952426474726312Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
10450818Scl76Serum cholesterol level QTL 763.60.01blood VLDL cholesterol amount (VT:0005144)blood high density lipoprotein cholesterol level (CMO:0000052)44917811657114705Rat
10450821Scl77Serum cholesterol level QTL 774.10.01blood VLDL cholesterol amount (VT:0005144)blood high density lipoprotein cholesterol level (CMO:0000052)44917811657114705Rat
10450825Scl78Serum cholesterol level QTL 783.70.01blood VLDL cholesterol amount (VT:0005144)blood low density lipoprotein cholesterol level (CMO:0000053)44917811657114705Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:25
Count of miRNA genes:24
Interacting mature miRNAs:25
Transcripts:ENSRNOT00000051611
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


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000112178   ⟹   ENSRNOP00000095226
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl449,776,246 - 50,277,728 (+)Ensembl
RefSeq Acc Id: NM_031730   ⟹   NP_113918
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2449,776,702 - 50,277,746 (+)NCBI
Rnor_6.0448,309,283 - 48,816,804 (+)NCBI
Rnor_5.0448,099,455 - 48,609,215 (+)NCBI
RGSC_v3.4447,541,787 - 48,047,924 (+)RGD
Celera444,984,114 - 45,483,230 (+)RGD
Sequence:
RefSeq Acc Id: XM_039108326   ⟹   XP_038964254
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2449,775,812 - 49,877,551 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_113918   ⟸   NM_031730
- Peptide Label: precursor
- UniProtKB: Q63881 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_038964254   ⟸   XM_039108326
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000095226   ⟸   ENSRNOT00000112178

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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)
DA/OlaHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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
F344/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
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/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
FXLE18/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
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/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
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/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
LEXF1A/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
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)
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
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
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (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
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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:68393 AgrOrtholog
Ensembl Genes ENSRNOG00000067416 Ensembl
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot
  3.30.710.10 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_Kv4 UniProtKB/Swiss-Prot
  K_chnl_volt-dep_Kv4.2 UniProtKB/Swiss-Prot
  K_chnl_volt-dep_Kv4_C UniProtKB/Swiss-Prot
  Shal-type_N 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:65180 UniProtKB/Swiss-Prot
NCBI Gene 65180 ENTREZGENE
PANTHER PTHR11537 UniProtKB/Swiss-Prot
Pfam BTB_2 UniProtKB/Swiss-Prot
  DUF3399 UniProtKB/Swiss-Prot
  Ion_trans UniProtKB/Swiss-Prot
  Shal-type UniProtKB/Swiss-Prot
PhenoGen Kcnd2 PhenoGen
PRINTS KV42CHANNEL UniProtKB/Swiss-Prot
  KVCHANNEL UniProtKB/Swiss-Prot
  SHALCHANNEL UniProtKB/Swiss-Prot
SMART BTB UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54695 UniProtKB/Swiss-Prot
UniProt KCND2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q00090 UniProtKB/Swiss-Prot
  Q99249 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Kcnd2  potassium voltage-gated channel subfamily D member 2  Kcnd2  potassium channel, voltage-gated Shal-related subfamily D, member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-01-26 Kcnd2  potassium channel, voltage-gated Shal-related subfamily D, member 2  Kcnd2  potassium voltage-gated channel, Shal-related subfamily, member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-04-20 Kcnd2  potassium voltage-gated channel, Shal-related subfamily, member 2  Kcnd2  potassium voltage gated channel, Shal-related family, member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Kcnd2  potassium voltage gated channel, Shal-related family, member 2      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease reduced expression is seen in diabetes mellitus 68269
gene_disease reduced expression is seen in diabetes mellitus 628458
gene_disease reduced expression is seen in diabetes mellitus 628469
gene_disease reduced expression is seen in diabetes mellitus 628470
gene_disease reduced expression is seen in diabetes mellitus 628471
gene_domains contains 6 hydrophobic domains, the putative voltage sensing domain has only 5 basic residues 68269
gene_domains contains 6 hydrophobic domains, the putative voltage sensing domain has only 5 basic residues 628458
gene_domains contains 6 hydrophobic domains, the putative voltage sensing domain has only 5 basic residues 628469
gene_domains contains 6 hydrophobic domains, the putative voltage sensing domain has only 5 basic residues 628470
gene_domains contains 6 hydrophobic domains, the putative voltage sensing domain has only 5 basic residues 628471
gene_expression mRNA expressed in the brain and also in the cardiac atrium and ventricle 68269
gene_expression mRNA expressed in the brain and also in the cardiac atrium and ventricle 628458
gene_expression mRNA expressed in the brain and also in the cardiac atrium and ventricle 628469
gene_expression mRNA expressed in the brain and also in the cardiac atrium and ventricle 628470
gene_expression mRNA expressed in the brain and also in the cardiac atrium and ventricle 628471
gene_function forms voltage-gated outward current during repolarization in cardiac myocytes 68269
gene_mutations_overexpression overexpression preventes the AP duration prolongation as well as the increases in Ca2+ influx and Ca2+-transient amplitude induced by phenylephrine 633152
gene_other in stretozin-induced diabetic rats ventricular mRNA level decreased 68269
gene_other in stretozin-induced diabetic rats ventricular mRNA level decreased 628458
gene_other in stretozin-induced diabetic rats ventricular mRNA level decreased 628469
gene_other in stretozin-induced diabetic rats ventricular mRNA level decreased 628470
gene_other in stretozin-induced diabetic rats ventricular mRNA level decreased 628471
gene_physical_interaction forms heteromultimer channels with Kcnd4 which helps in increasing the rate of recovery from inactivation 68269
gene_physical_interaction forms heteromultimer channels with Kcnd4 which helps in increasing the rate of recovery from inactivation 628458
gene_physical_interaction forms heteromultimer channels with Kcnd4 which helps in increasing the rate of recovery from inactivation 628469
gene_physical_interaction forms heteromultimer channels with Kcnd4 which helps in increasing the rate of recovery from inactivation 628470
gene_physical_interaction forms heteromultimer channels with Kcnd4 which helps in increasing the rate of recovery from inactivation 628471
gene_process in the left ventricle the mRNA level displays transmural gradient of the voltage-gated transient outward current density which impacts on cardiac functions such as contractility and impulse conduction 68269
gene_process in the left ventricle the mRNA level displays transmural gradient of the voltage-gated transient outward current density which impacts on cardiac functions such as contractility and impulse conduction 628458
gene_process in the left ventricle the mRNA level displays transmural gradient of the voltage-gated transient outward current density which impacts on cardiac functions such as contractility and impulse conduction 628469
gene_process in the left ventricle the mRNA level displays transmural gradient of the voltage-gated transient outward current density which impacts on cardiac functions such as contractility and impulse conduction 628470
gene_process in the left ventricle the mRNA level displays transmural gradient of the voltage-gated transient outward current density which impacts on cardiac functions such as contractility and impulse conduction 628471
gene_process contributes to the calcium independent voltage-gated transient outward current density in the right wall and septum of the ventricle 68269
gene_process contributes to the calcium independent voltage-gated transient outward current density in the right wall and septum of the ventricle 628458
gene_process contributes to the calcium independent voltage-gated transient outward current density in the right wall and septum of the ventricle 628469
gene_process contributes to the calcium independent voltage-gated transient outward current density in the right wall and septum of the ventricle 628470
gene_process contributes to the calcium independent voltage-gated transient outward current density in the right wall and septum of the ventricle 628471
gene_protein 490 amino acids in size 68269