Pln (phospholamban) - Rat Genome Database

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Gene: Pln (phospholamban) Rattus norvegicus
Analyze
Symbol: Pln
Name: phospholamban
RGD ID: 619894
Description: Enables ATPase inhibitor activity and identical protein binding activity. Involved in several processes, including response to insulin; response to testosterone; and response to zinc ion. Located in sarcoplasmic reticulum and vesicle. Part of protein-containing complex. Used to study congestive heart failure; heart disease; and myocardial infarction. Biomarker of type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in dilated cardiomyopathy 1P and hypertrophic cardiomyopathy 18. Orthologous to human PLN (phospholamban); PARTICIPATES IN acebutolol pharmacodynamics pathway; adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway; amiodarone pharmacodynamics pathway; INTERACTS WITH 1,2-dimethylhydrazine; 3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: cardiac phospholamban; PLB; Plm
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
mRatBN7.22032,629,537 - 32,639,559 (+)NCBImRatBN7.2
Rnor_6.02034,633,157 - 34,642,904 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2034,633,157 - 34,642,904 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02036,390,879 - 36,400,626 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42032,000,371 - 32,008,559 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12032,014,170 - 32,022,359 (+)NCBI
Celera2034,009,102 - 34,018,849 (+)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aconitine  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
anthracen-2-amine  (EXP)
astragaloside IV  (EXP)
benzo[a]pyrene  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
candesartan  (EXP)
cilostazol  (EXP)
cisplatin  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
Cuprizon  (EXP)
cycloheximide  (ISO)
decabromodiphenyl ether  (EXP)
dibutyl phthalate  (EXP)
diethyldithiocarbamic acid  (EXP)
dioxygen  (ISO)
diuron  (EXP)
dobutamine  (ISO)
doxorubicin  (EXP,ISO)
endosulfan  (EXP)
ethanol  (ISO)
flavonoids  (EXP)
isoprenaline  (EXP)
lead diacetate  (EXP)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (EXP,ISO)
mercury dichloride  (EXP)
methapyrilene  (EXP)
methotrexate  (ISO)
mifepristone  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
nickel atom  (ISO)
nitrofen  (EXP)
oxaliplatin  (EXP)
ozone  (EXP)
paraquat  (EXP)
PCB138  (ISO)
pioglitazone  (ISO)
progesterone  (EXP)
propofol  (EXP)
propranolol  (EXP)
resveratrol  (EXP,ISO)
sarpogrelate  (EXP)
streptozocin  (ISO)
sulforaphane  (ISO)
tamoxifen  (ISO)
tebuconazole  (EXP)
thioacetamide  (EXP)
Tiron  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (ISO)
triclosan  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
wortmannin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process  (ISO)
calcium ion transport  (IMP,NAS)
cardiac muscle tissue development  (ISO)
cellular calcium ion homeostasis  (ISO)
negative regulation of ATPase activity  (ISO)
negative regulation of ATPase-coupled calcium transmembrane transporter activity  (IBA,ISO,ISS)
negative regulation of calcium ion binding  (ISO)
negative regulation of calcium ion import into sarcoplasmic reticulum  (IBA,ISO,ISS)
negative regulation of calcium ion transmembrane transporter activity  (ISO)
negative regulation of calcium ion transport  (ISO)
negative regulation of catalytic activity  (IEA)
negative regulation of heart contraction  (ISO)
negative regulation of heart rate  (IBA,ISO)
Notch signaling pathway  (ISO)
regulation of ATPase-coupled calcium transmembrane transporter activity  (ISO)
regulation of calcium ion import  (ISO)
regulation of calcium ion transport  (ISO,ISS)
regulation of cardiac muscle cell contraction  (ISO)
regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion  (ISO)
regulation of heart contraction  (ISO)
regulation of relaxation of muscle  (ISO)
regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum  (ISO)
regulation of ryanodine-sensitive calcium-release channel activity  (ISO)
regulation of the force of heart contraction  (ISO)
regulation of the force of heart contraction by cardiac conduction  (ISO)
response to insulin  (IEP)
response to testosterone  (IDA)
response to zinc ion  (IDA)

Cellular Component

Molecular Function

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)
calcium/calcium-mediated signaling pathway  (IEA)
calcium/calmodulin dependent kinase 2 signaling pathway  (ISO)
carvedilol pharmacodynamics pathway  (ISO)
dilated cardiomyopathy pathway  (IEA)
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. Babick A, etal., J Cell Mol Med. 2012 Dec;16(12):2958-67. doi: 10.1111/j.1582-4934.2012.01623.x.
2. Fang F, etal., Pharmacology. 2011;88(3-4):149-58. doi: 10.1159/000330068. Epub 2011 Sep 16.
3. Fang Y, etal., Nan Fang Yi Ke Da Xue Xue Bao. 2013 Feb;33(2):177-81.
4. Ferrington DA, etal., Biochemistry 2002 Nov 5;41(44):13289-96.
5. Fredersdorf S, etal., Cardiovasc Diabetol. 2012 May 23;11:57.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Haghighi K, etal., Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1388-93. Epub 2006 Jan 23.
8. Hwang KS and Nadal-Ginard B, Adv Exp Med Biol 1991;304:387-95.
9. Johns DC and Feldman AM, Biochem Biophys Res Commun 1992 Oct 30;188(2):927-33.
10. Kagota S, etal., Can J Physiol Pharmacol. 2013 Feb;91(2):124-33. doi: 10.1139/cjpp-2012-0226. Epub 2013 Feb 15.
11. Le Douairon Lahaye S, etal., Appl Physiol Nutr Metab. 2012 Feb;37(1):53-62. doi: 10.1139/h11-127. Epub 2011 Dec 20.
12. Li D, etal., Hypertension. 2012 Mar;59(3):642-9. doi: 10.1161/HYPERTENSIONAHA.111.186460. Epub 2012 Jan 17.
13. Lygren B, etal., EMBO Rep. 2007 Nov;8(11):1061-7. Epub 2007 Sep 28.
14. MGD data from the GO Consortium
15. NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. OMIM Disease Annotation Pipeline
17. Pipeline to import KEGG annotations from KEGG into RGD
18. Pipeline to import SMPDB annotations from SMPDB into RGD
19. Qiu Z, etal., J Cell Mol Med. 2012 Dec;16(12):3052-61. doi: 10.1111/j.1582-4934.2012.01632.x.
20. RGD automated data pipeline
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. Rokita AG and Anderson ME, Circulation. 2012 Oct 23;126(17):2125-39. doi: 10.1161/CIRCULATIONAHA.112.124990.
24. Shanahan CM, etal., Circ Res 1993 Jul;73(1):193-204.
25. Shenoy R, etal., Am J Physiol Heart Circ Physiol 2001 Oct;281(4):H1690-6.
26. Vittone L, etal., J Mol Cell Cardiol 2002 Jan;34(1):39-50.
27. Witayavanitkul N, etal., Am J Physiol Heart Circ Physiol. 2013 Feb 1;304(3):H465-72. doi: 10.1152/ajpheart.00555.2012. Epub 2012 Nov 30.
28. Wu LL, etal., Shock 2002 May;17(5):389-93.
29. Xing Y, etal., Evid Based Complement Alternat Med. 2013;2013:464508. doi: 10.1155/2013/464508. Epub 2013 May 28.
30. Yi T, etal., Am J Physiol Heart Circ Physiol. 2013 Sep;305(5):H706-15. doi: 10.1152/ajpheart.00025.2013. Epub 2013 Jun 28.
Additional References at PubMed
PMID:8062415   PMID:8349590   PMID:8620604   PMID:8831698   PMID:9038922   PMID:9118481   PMID:10024311   PMID:10471356   PMID:10555147   PMID:10603936   PMID:10644605   PMID:12763747  
PMID:12881214   PMID:12933346   PMID:15231818   PMID:15524173   PMID:15598648   PMID:15637115   PMID:15801907   PMID:16648178   PMID:17239900   PMID:18838385   PMID:19074672   PMID:19278978  
PMID:19708671   PMID:20833797   PMID:21876643   PMID:22427649   PMID:23117660   PMID:23907041   PMID:25020913   PMID:26027516   PMID:26316108   PMID:26816378   PMID:27206677   PMID:27923914  
PMID:29045568   PMID:29913456   PMID:30299255   PMID:33220932  


Genomics

Comparative Map Data
Pln
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22032,629,537 - 32,639,559 (+)NCBImRatBN7.2
Rnor_6.02034,633,157 - 34,642,904 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2034,633,157 - 34,642,904 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02036,390,879 - 36,400,626 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42032,000,371 - 32,008,559 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12032,014,170 - 32,022,359 (+)NCBI
Celera2034,009,102 - 34,018,849 (+)NCBICelera
Cytogenetic Map20q11NCBI
PLN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6118,548,296 - 118,561,716 (+)EnsemblGRCh38hg38GRCh38
GRCh386118,548,296 - 118,561,716 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376118,869,459 - 118,882,879 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366118,976,165 - 118,988,280 (+)NCBINCBI36hg18NCBI36
Build 346118,976,164 - 118,988,279NCBI
Celera6119,612,768 - 119,624,905 (+)NCBI
Cytogenetic Map6q22.31NCBI
HuRef6116,451,106 - 116,463,257 (+)NCBIHuRef
CHM1_16119,133,487 - 119,145,628 (+)NCBICHM1_1
Pln
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391053,213,782 - 53,222,095 (+)NCBIGRCm39mm39
GRCm39 Ensembl1053,213,763 - 53,222,083 (+)Ensembl
GRCm381053,337,686 - 53,345,999 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1053,337,667 - 53,345,987 (+)EnsemblGRCm38mm10GRCm38
MGSCv371053,057,492 - 53,065,805 (+)NCBIGRCm37mm9NCBIm37
MGSCv361053,026,122 - 53,034,396 (+)NCBImm8
Celera1054,164,488 - 54,172,801 (+)NCBICelera
Cytogenetic Map10B3NCBI
Pln
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554361,439,098 - 1,447,070 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554361,439,098 - 1,447,070 (+)NCBIChiLan1.0ChiLan1.0
PLN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16120,498,943 - 120,511,969 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6120,509,510 - 120,509,668 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06116,357,335 - 116,370,382 (+)NCBIMhudiblu_PPA_v0panPan3
PLN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1158,579,095 - 58,590,541 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl158,579,145 - 58,590,535 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha159,381,980 - 59,393,371 (+)NCBI
ROS_Cfam_1.0158,763,549 - 58,775,010 (+)NCBI
UMICH_Zoey_3.1158,664,392 - 58,675,778 (+)NCBI
UNSW_CanFamBas_1.0158,505,736 - 58,517,122 (+)NCBI
UU_Cfam_GSD_1.0159,137,737 - 59,149,128 (+)NCBI
Pln
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946109,336,904 - 109,346,907 (+)NCBI
SpeTri2.0NW_0049366581,443,626 - 1,453,770 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1143,449,354 - 43,458,925 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2148,678,936 - 48,688,510 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PLN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11355,316,962 - 55,332,502 (-)NCBI
ChlSab1.1 Ensembl1355,318,326 - 55,318,481 (-)Ensembl
Vero_WHO_p1.0NW_02366604027,627,687 - 27,641,160 (-)NCBI
Pln
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479811,522,245 - 11,528,741 (-)NCBI

Position Markers
RH133632  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22032,637,611 - 32,637,811 (+)MAPPERmRatBN7.2
Rnor_6.02034,640,957 - 34,641,156NCBIRnor6.0
Rnor_5.02036,398,679 - 36,398,878UniSTSRnor5.0
RGSC_v3.42032,008,164 - 32,008,363UniSTSRGSC3.4
Celera2034,016,902 - 34,017,101UniSTS
RH 3.4 Map20332.11UniSTS
Cytogenetic Map20q11UniSTS
RH140536  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22032,637,624 - 32,637,868 (+)MAPPERmRatBN7.2
Rnor_6.02034,640,970 - 34,641,213NCBIRnor6.0
Rnor_5.02036,398,692 - 36,398,935UniSTSRnor5.0
RGSC_v3.42032,008,177 - 32,008,420UniSTSRGSC3.4
Celera2034,016,915 - 34,017,158UniSTS
RH 3.4 Map20332.63UniSTS
Cytogenetic Map20q11UniSTS
BE100029  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22032,631,348 - 32,631,498 (+)MAPPERmRatBN7.2
Rnor_6.02034,634,695 - 34,634,844NCBIRnor6.0
Rnor_5.02036,392,417 - 36,392,566UniSTSRnor5.0
RGSC_v3.42032,001,902 - 32,002,051UniSTSRGSC3.4
Celera2034,010,640 - 34,010,789UniSTS
RH 3.4 Map20332.52UniSTS
Cytogenetic Map20q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203161428444396023Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:34
Count of miRNA genes:34
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000000469
Prediction methods: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 25
Medium 3 24 2 2 6 8 2
Low 34 18 19 18 6 9 27 22 27 3 6
Below cutoff 23 23 23 20 13 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000469   ⟹   ENSRNOP00000000469
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2034,633,157 - 34,642,904 (+)Ensembl
RefSeq Acc Id: NM_022707   ⟹   NP_073198
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22032,629,811 - 32,639,559 (+)NCBI
Rnor_6.02034,633,157 - 34,642,904 (+)NCBI
Rnor_5.02036,390,879 - 36,400,626 (+)NCBI
RGSC_v3.42032,000,371 - 32,008,559 (+)RGD
Celera2034,009,102 - 34,018,849 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099053   ⟹   XP_038954981
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22032,629,537 - 32,639,198 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_073198   ⟸   NM_022707
- UniProtKB: P61016 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000469   ⟸   ENSRNOT00000000469
RefSeq Acc Id: XP_038954981   ⟸   XM_039099053
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13701626
Promoter ID:EPDNEW_R12150
Type:initiation region
Name:Pln_1
Description:phospholamban
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02034,633,171 - 34,633,231EPDNEW

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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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)
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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)
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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (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)
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)
SS/JrHsdMcwi (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
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:619894 AgrOrtholog
Ensembl Genes ENSRNOG00000000413 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000000469 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000000469 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro PLB UniProtKB/Swiss-Prot
KEGG Report rno:64672 UniProtKB/Swiss-Prot
NCBI Gene 64672 ENTREZGENE
PANTHER PTHR21194 UniProtKB/Swiss-Prot
Pfam Phospholamban UniProtKB/Swiss-Prot
PharmGKB PLN RGD
PhenoGen Pln PhenoGen
PIRSF PLB UniProtKB/Swiss-Prot
TIGRFAMs P_lamban UniProtKB/Swiss-Prot
UniProt P61016 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P20006 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Pln  phospholamban  Plm    Symbol updated 1299863 APPROVED
2002-08-07 Plm  phospholamban      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in heart atria and ventricles 631306
gene_process may regulate function of Atp2a2, a cardiac muscle, Ca++ transporting, slow twitch ATPase 2 631306