Abcc9 (ATP binding cassette subfamily C member 9) - Rat Genome Database

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Gene: Abcc9 (ATP binding cassette subfamily C member 9) Rattus norvegicus
Analyze
Symbol: Abcc9
Name: ATP binding cassette subfamily C member 9
RGD ID: 3787
Description: Enables several functions, including identical protein binding activity; sulfonylurea receptor activity; and syntaxin binding activity. Contributes to cation channel activity. Involved in potassium ion import across plasma membrane; response to ATP; and response to xenobiotic stimulus. Located in T-tubule; acrosomal vesicle; and mitochondrion. Part of inward rectifying potassium channel. Biomarker of Parkinsonism; hypertension; and sciatic neuropathy. Human ortholog(s) of this gene implicated in dilated cardiomyopathy; dilated cardiomyopathy 1O; familial atrial fibrillation; and hypertrichotic osteochondrodysplasia Cantu type. Orthologous to human ABCC9 (ATP binding cassette subfamily C member 9); PARTICIPATES IN acebutolol pharmacodynamics pathway; adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway; amiodarone pharmacodynamics pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ATP-binding cassette sub-family C member 9; ATP-binding cassette transporter sub-family C member 9; ATP-binding cassette, sub-family C (CFTR/MRP), member 9; ATP-binding cassette, sub-family C, member 9-like; ATP-binding cassette, subfamily C (CFTR/MRP), member 9; LOC100360403; Sulfonylurea receptor 2; Sur2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Abcc9_v1   Abcc9_v2  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24175,531,854 - 175,655,849 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4175,532,547 - 175,655,356 (-)Ensembl
Rnor_6.04176,806,098 - 176,928,540 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4176,805,431 - 176,922,424 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04241,019,980 - 241,139,051 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44180,165,979 - 180,236,791 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11533,877,146 - 33,883,992NCBI
Celera4164,064,977 - 164,186,502 (-)NCBICelera
Cytogenetic Map4q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2-deoxy-D-glucose  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acetamide  (EXP)
adenosine 5'-monophosphate  (ISO)
aflatoxin B1  (EXP,ISO)
aflatoxin M1  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
ATP  (EXP,ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
captan  (ISO)
carbon nanotube  (ISO)
cisplatin  (ISO)
cocaine  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
creatine  (ISO)
cyclosporin A  (ISO)
dextran sulfate  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
endosulfan  (ISO)
folic acid  (ISO)
genistein  (EXP,ISO)
glyburide  (ISO)
ivermectin  (ISO)
kojic acid  (ISO)
MeIQx  (ISO)
metformin  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
nicorandil  (ISO)
O-methyleugenol  (ISO)
oxidopamine  (EXP)
paracetamol  (ISO)
paraquat  (EXP)
phenobarbital  (ISO)
phenylephrine  (EXP)
Pinacidil  (EXP,ISO)
pioglitazone  (ISO)
pirinixic acid  (EXP,ISO)
progesterone  (EXP,ISO)
resveratrol  (ISO)
riddelliine  (EXP)
rubidium atom  (EXP,ISO)
sodium arsenate  (ISO)
sunitinib  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
toluene  (EXP)
trichloroethene  (EXP)
triclosan  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP)
vinclozolin  (EXP)
zinc sulfate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
acebutolol pharmacodynamics pathway  (ISO)
adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway  (ISO)
amiodarone pharmacodynamics pathway  (ISO)
amlodipine pharmacodynamics pathway  (ISO)
atenolol pharmacodynamics pathway  (ISO)
betaxolol pharmacodynamics pathway  (ISO)
bisoprolol pharmacodynamics pathway  (ISO)
bupranolol drug pathway  (ISO)
bupranolol pharmacodynamics pathway  (ISO)
carvedilol pharmacodynamics pathway  (ISO)
diltiazem pharmacodynamics pathway  (ISO)
disopyramide pharmacodynamics pathway  (ISO)
dobutamine pharmacodynamics pathway  (ISO)
esmolol pharmacodynamics pathway  (ISO)
flecainde pharmacodynamics pathway  (ISO)
fosphenytoin pharmacodynamics pathway  (ISO)
ibutilide pharmacodynamics pathway  (ISO)
isoprenaline pharmacodynamics pathway  (ISO)
isradipine pharmacodynamics pathway  (ISO)
levobunolol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
metoprolol pharmacodynamics pathway  (ISO)
mexiletine pharmacodynamics pathway  (ISO)
nadolol pharmacodynamics pathway  (ISO)
nebivolol pharmacodynamics pathway  (ISO)
nifedipine pharmacodynamics pathway  (ISO)
nimodipine pharmacodynamics pathway  (ISO)
nisoldipine pharmacodynamics pathway  (ISO)
nitrendipine pharmacodynamics pathway  (ISO)
penbutolol pharmacodynamics pathway  (ISO)
phenytoin pharmacodynamics pathway  (ISO)
pindolol pharmacodynamics pathway  (ISO)
procainamide pharmacodynamics pathway  (ISO)
propranolol pharmacodynamics pathway  (ISO)
quinidine pharmacodynamics pathway  (ISO)
sotalol pharmacodynamics pathway  (ISO)
timolol pharmacodynamics pathway  (ISO)
verapamil pharmacodynamics pathway  (ISO)

References

References - curated
1. Bienengraeber M, etal., Nat Genet 2004 Apr;36(4):382-7. Epub 2004 Mar 21.
2. Blanco-Rivero J, etal., Eur J Pharmacol. 2008 Jun 10;587(1-3):204-8. Epub 2008 Mar 30.
3. Cao K, etal., Biochem Biophys Res Commun 2002 Aug 16;296(2):463-9.
4. Chen ZC, etal., Cardiovasc Diabetol. 2012 Jan 18;11:8. doi: 10.1186/1475-2840-11-8.
5. Cooper PE, etal., J Biol Chem. 2017 Oct 20;292(42):17387-17398. doi: 10.1074/jbc.M117.804971. Epub 2017 Aug 23.
6. Cooper PE, etal., J Gen Physiol. 2015 Dec;146(6):527-40. doi: 10.1085/jgp.201511495.
7. Cuong DV, etal., Mitochondrion. 2005 Apr;5(2):121-33.
8. Dong K, etal., J Biol Chem 2001 Nov 23;276(47):44347-53.
9. Dorschner H, etal., Mol Pharmacol. 1999 Jun;55(6):1060-6.
10. Fotinou C, etal., FEBS J. 2013 Feb;280(4):1051-63. doi: 10.1111/febs.12097. Epub 2013 Jan 27.
11. Gao M, etal., Life Sci. 2005 Oct 14;77(22):2743-51.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. GOA data from the GO Consortium
14. Horinaka S, etal., Cardiovasc Drugs Ther. 2004 Jan;18(1):13-22.
15. Inagaki N, etal., Neuron. 1996 May;16(5):1011-7.
16. Kang Y, etal., J Biol Chem. 2004 Nov 5;279(45):47125-31. Epub 2004 Aug 31.
17. Lodwick D, etal., Biochem J. 2014 Dec 15;464(3):343-54. doi: 10.1042/BJ20140273.
18. Lybaert P, etal., Placenta. 2013 Jun;34(6):467-73. doi: 10.1016/j.placenta.2013.03.006. Epub 2013 Apr 13.
19. López-Alonso JP, etal., Biochemistry. 2012 Nov 13;51(45):9211-22. doi: 10.1021/bi301019e. Epub 2012 Nov 1.
20. MGD data from the GO Consortium
21. Morrissey A, etal., BMC Physiol. 2005 Jan 12;5(1):1.
22. NCBI rat LocusLink and RefSeq merged data July 26, 2002
23. OMIM Disease Annotation Pipeline
24. Pipeline to import SMPDB annotations from SMPDB into RGD
25. Purves GI, etal., J Physiol. 2009 Jul 15;587(Pt 14):3639-50. doi: 10.1113/jphysiol.2009.173534.
26. Rainbow RD, etal., Biochem J. 2004 Apr 1;379(Pt 1):173-81.
27. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
28. RGD automated import pipeline for gene-chemical interactions
29. Santa N, etal., Stroke 2003 May;34(5):1276-80.
30. Szamosfalvi B, etal., Kidney Int 2002 May;61(5):1739-49.
31. Wang S, etal., Neuropharmacology. 2005 Jun;48(7):984-92.
32. Wu XF, etal., Pain. 2011 Nov;152(11):2605-15. doi: 10.1016/j.pain.2011.08.003. Epub 2011 Sep 9.
33. Zhou M, etal., Anat Rec (Hoboken). 2011 Apr;294(4):729-37. doi: 10.1002/ar.21348. Epub 2011 Feb 15.
Additional References at PubMed
PMID:11927600   PMID:14724757   PMID:16085792   PMID:16672225   PMID:16820413   PMID:17294036   PMID:17395632   PMID:17438353   PMID:17510180   PMID:17596331   PMID:17656102   PMID:17855752  
PMID:17942071   PMID:18026101   PMID:18198173   PMID:18323694   PMID:19224154   PMID:19464385   PMID:20123112   PMID:20332621   PMID:20456845   PMID:20553499   PMID:20610380   PMID:20656890  
PMID:21479273   PMID:21527399   PMID:21714514   PMID:22144717   PMID:22960600   PMID:23085378   PMID:24035941   PMID:24439875   PMID:25073062   PMID:25599573   PMID:26181369   PMID:26198630  
PMID:27035370   PMID:29275331   PMID:30074836  


Genomics

Comparative Map Data
Abcc9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24175,531,854 - 175,655,849 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4175,532,547 - 175,655,356 (-)Ensembl
Rnor_6.04176,806,098 - 176,928,540 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4176,805,431 - 176,922,424 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04241,019,980 - 241,139,051 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44180,165,979 - 180,236,791 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11533,877,146 - 33,883,992NCBI
Celera4164,064,977 - 164,186,502 (-)NCBICelera
Cytogenetic Map4q44NCBI
ABCC9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1221,797,389 - 21,942,543 (-)EnsemblGRCh38hg38GRCh38
GRCh381221,797,389 - 21,941,863 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371221,950,323 - 22,094,360 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361221,841,590 - 21,980,895 (-)NCBINCBI36hg18NCBI36
Build 341221,849,374 - 21,980,875NCBI
Celera1227,105,336 - 27,244,581 (-)NCBI
Cytogenetic Map12p12.1NCBI
HuRef1221,723,876 - 21,863,675 (-)NCBIHuRef
CHM1_11221,915,604 - 22,054,751 (-)NCBICHM1_1
Abcc9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396142,533,588 - 142,648,472 (-)NCBIGRCm39mm39
GRCm39 Ensembl6142,533,588 - 142,648,041 (-)Ensembl
GRCm386142,587,862 - 142,702,766 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6142,587,862 - 142,702,315 (-)EnsemblGRCm38mm10GRCm38
MGSCv376142,536,382 - 142,650,794 (-)NCBIGRCm37mm9NCBIm37
MGSCv366142,546,355 - 142,659,495 (-)NCBImm8
Celera6145,649,701 - 145,764,495 (-)NCBICelera
Cytogenetic Map6G2NCBI
cM Map674.35NCBI
Abcc9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541317,382,564 - 17,510,132 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541317,385,966 - 17,510,220 (-)NCBIChiLan1.0ChiLan1.0
ABCC9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11266,960,888 - 67,102,496 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1266,960,888 - 67,102,496 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01264,357,176 - 64,500,358 (+)NCBIMhudiblu_PPA_v0panPan3
ABCC9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12725,199,580 - 25,352,637 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2725,200,418 - 25,388,477 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2721,008,307 - 21,161,033 (-)NCBI
ROS_Cfam_1.02725,419,340 - 25,572,249 (+)NCBI
UMICH_Zoey_3.12725,218,211 - 25,370,572 (+)NCBI
UNSW_CanFamBas_1.02725,241,668 - 25,394,276 (+)NCBI
UU_Cfam_GSD_1.02721,179,155 - 21,329,671 (-)NCBI
Abcc9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494587,079,120 - 87,187,785 (+)NCBI
SpeTri2.0NW_0049365484,983,461 - 5,110,693 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCC9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl551,536,526 - 51,673,583 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1551,536,531 - 51,673,583 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2554,818,859 - 54,944,118 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ABCC9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11121,658,804 - 21,797,851 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1121,658,794 - 21,797,263 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606913,343,449 - 13,484,437 (+)NCBIVero_WHO_p1.0
Abcc9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475216,792,202 - 16,926,552 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D4Got140  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,734,862 - 176,735,053 (+)MAPPERmRatBN7.2
Rnor_6.04178,015,760 - 178,015,950NCBIRnor6.0
Rnor_5.04242,219,183 - 242,219,373UniSTSRnor5.0
RGSC_v3.44180,347,915 - 180,348,106RGDRGSC3.4
RGSC_v3.44180,347,916 - 180,348,106UniSTSRGSC3.4
RGSC_v3.14180,593,040 - 180,593,230RGD
Celera4165,262,255 - 165,262,445UniSTS
RH 3.4 Map41060.3RGD
RH 3.4 Map41060.3UniSTS
Cytogenetic Map4q44UniSTS
BE108803  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,860,248 - 176,860,432 (+)MAPPERmRatBN7.2
Rnor_6.04178,141,125 - 178,141,308NCBIRnor6.0
Rnor_5.04242,344,099 - 242,344,282UniSTSRnor5.0
RGSC_v3.44180,472,699 - 180,472,882UniSTSRGSC3.4
Celera4165,387,487 - 165,387,670UniSTS
RH 3.4 Map41057.9UniSTS
Cytogenetic Map4q44UniSTS
RH134712  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,786,011 - 176,786,169 (+)MAPPERmRatBN7.2
Rnor_6.04178,066,907 - 178,067,064NCBIRnor6.0
Rnor_5.04242,270,935 - 242,271,092UniSTSRnor5.0
RGSC_v3.44180,399,064 - 180,399,221UniSTSRGSC3.4
Celera4165,313,400 - 165,313,557UniSTS
RH 3.4 Map41057.9UniSTS
Cytogenetic Map4q44UniSTS
RH139436  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,781,873 - 176,782,078 (+)MAPPERmRatBN7.2
Rnor_6.04178,062,769 - 178,062,973NCBIRnor6.0
Rnor_5.04242,266,797 - 242,267,001UniSTSRnor5.0
RGSC_v3.44180,394,926 - 180,395,130UniSTSRGSC3.4
Celera4165,309,262 - 165,309,466UniSTS
RH 3.4 Map41057.1UniSTS
Cytogenetic Map4q44UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:119
Count of miRNA genes:94
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000055540, ENSRNOT00000067489
Prediction methods:Microtar, Miranda, Rnahybrid
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 43 16 6 4 6 8 11 25 18 24 11 8
Low 3 41 35 15 35 43 17 17
Below cutoff 6

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_013040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107119 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107120 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107121 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107123 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039107124 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB045281 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC130778 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF019628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF087838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH006903 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D83598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000055540   ⟹   ENSRNOP00000052402
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4176,807,804 - 176,922,424 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000067489   ⟹   ENSRNOP00000063326
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4175,532,547 - 175,655,356 (-)Ensembl
Rnor_6.0 Ensembl4176,805,431 - 176,909,075 (-)Ensembl
RefSeq Acc Id: NM_013040   ⟹   NP_037172
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,532,509 - 175,655,356 (-)NCBI
Rnor_6.04176,806,098 - 176,928,540 (-)NCBI
Rnor_5.04241,019,980 - 241,139,051 (-)NCBI
Celera4164,064,977 - 164,186,502 (-)RGD
Sequence:
RefSeq Acc Id: XM_039107117   ⟹   XP_038963045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,534,211 - 175,655,299 (-)NCBI
RefSeq Acc Id: XM_039107118   ⟹   XP_038963046
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,531,854 - 175,655,299 (-)NCBI
RefSeq Acc Id: XM_039107119   ⟹   XP_038963047
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,534,046 - 175,655,849 (-)NCBI
RefSeq Acc Id: XM_039107120   ⟹   XP_038963048
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,534,046 - 175,655,548 (-)NCBI
RefSeq Acc Id: XM_039107121   ⟹   XP_038963049
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,534,211 - 175,655,356 (-)NCBI
RefSeq Acc Id: XM_039107122   ⟹   XP_038963050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,534,212 - 175,655,452 (-)NCBI
RefSeq Acc Id: XM_039107123   ⟹   XP_038963051
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,534,211 - 175,655,451 (-)NCBI
RefSeq Acc Id: XM_039107124   ⟹   XP_038963052
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24175,534,212 - 175,655,451 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_037172   ⟸   NM_013040
- UniProtKB: Q63563 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000052402   ⟸   ENSRNOT00000055540
RefSeq Acc Id: ENSRNOP00000063326   ⟸   ENSRNOT00000067489
RefSeq Acc Id: XP_038963046   ⟸   XM_039107118
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038963047   ⟸   XM_039107119
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038963048   ⟸   XM_039107120
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038963051   ⟸   XM_039107123
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038963049   ⟸   XM_039107121
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963045   ⟸   XM_039107117
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963050   ⟸   XM_039107122
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038963052   ⟸   XM_039107124
- Peptide Label: isoform X5
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)
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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)
ACI/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
ACI/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
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)
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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
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)
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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
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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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:3787 AgrOrtholog
Ensembl Genes ENSRNOG00000036960 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000052402 UniProtKB/TrEMBL
  ENSRNOP00000063326 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055540 UniProtKB/TrEMBL
  ENSRNOT00000067489 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.1560.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AAA+_ATPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC1_TM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC1_TM_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_transporter-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_transporter_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABCC9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sulphorea_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25560 UniProtKB/Swiss-Prot
NCBI Gene 25560 ENTREZGENE
PANTHER PTHR24223:SF173 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam ABC_membrane UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_tran UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB ABCC9 RGD
PhenoGen Abcc9 PhenoGen
PRINTS SULFNYLUR2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SULFNYLUREAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ABC_TM1F UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_TRANSPORTER_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_TRANSPORTER_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF90123 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt ABCC9_RAT UniProtKB/Swiss-Prot
  D3ZZ00_RAT UniProtKB/TrEMBL
  F1M9Q2_RAT UniProtKB/TrEMBL
  Q63563 ENTREZGENE
UniProt Secondary O89115 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-09 Abcc9  ATP binding cassette subfamily C member 9  Abcc9  ATP-binding cassette, subfamily C (CFTR/MRP), member 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-29 Abcc9  ATP-binding cassette, subfamily C (CFTR/MRP), member 9  LOC100360403  ATP-binding cassette, sub-family C, member 9-like  Data Merged 737654 PROVISIONAL
2010-11-16 Abcc9  ATP-binding cassette, subfamily C (CFTR/MRP), member 9  Abcc9  ATP-binding cassette, sub-family C (CFTR/MRP), member 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100360403  ATP-binding cassette, sub-family C, member 9-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-02-27 Abcc9  ATP-binding cassette, sub-family C (CFTR/MRP), member 9      Symbol and Name updated to reflect Human and Mouse nomenclature 70292 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function can form cardiac and smooth muscle-type K(ATP) channels with Kir6.2. Kir6.2 forms the channel pore while Sur2 is required for activation and regulation 724707
gene_function subunit of ATP-sensitve potassium channels (KATP). 724707