Pld1 (phospholipase D1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Pld1 (phospholipase D1) Rattus norvegicus
Analyze
Symbol: Pld1
Name: phospholipase D1
RGD ID: 3349
Description: Exhibits phospholipase D activity. Involved in phospholipid metabolic process; positive regulation of cell migration; and response to peptide hormone. Localizes to several cellular components, including Golgi cisterna; lamellipodium; and synapse. Biomarker of visual epilepsy. Human ortholog(s) of this gene implicated in developmental cardiac valvular defect. Orthologous to human PLD1 (phospholipase D1); PARTICIPATES IN mTOR signaling pathway; ceramide signaling pathway; endocytosis pathway; INTERACTS WITH 1-octadec-9-enoylglycero-3-phosphate; 2,2',4,4',5,5'-hexachlorobiphenyl; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: choline phosphatase 1; Phoshpolipase D gene 1; Phoshpolipase D gene 1 probably with two splicing variants A and B; phosphatidylcholine-hydrolyzing phospholipase D1; phospholipase D gene 1; phospholipase D gene 1 probably with two splicing variants A and B; phospholipase D gene 1, probably with two splicing variants A and B; phospholipase D1, phosphatidylcholine-specific; PLD 1; Pld1a; Pld1b; Plda; Pldb; rPLD1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22110,849,205 - 111,047,692 (+)NCBI
Rnor_6.0 Ensembl2113,652,348 - 113,849,403 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02113,651,967 - 113,849,403 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02133,357,235 - 133,554,180 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42115,306,940 - 115,460,518 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12115,251,901 - 115,405,480 (+)NCBI
Celera2106,084,707 - 106,238,116 (+)NCBICelera
Cytogenetic Map2q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-octadec-9-enoylglycero-3-phosphate  (EXP)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,3-bisphospho-D-glyceric acid  (ISO)
2,3-bisphosphoglyceric acid  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-naphthylamine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
8-Br-cAMP  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butan-1-ol  (EXP,ISO)
cadmium atom  (EXP)
cannabidiol  (ISO)
cannabigerol  (ISO)
carbon nanotube  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (ISO)
formaldehyde  (ISO)
furan  (EXP)
ganglioside GM1  (EXP)
genistein  (EXP)
glyphosate  (ISO)
Goe 6976  (EXP,ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (EXP,ISO)
hydroquinone  (ISO)
indometacin  (EXP)
irinotecan  (EXP)
isoprenaline  (ISO)
lithium chloride  (ISO)
lithocholic acid  (ISO)
melanins  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
metformin  (ISO)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
methylmercury(1+)  (EXP)
mifepristone  (ISO)
mono(2-ethylhexyl) phthalate  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
N-acetyl-L-cysteine  (ISO)
N-formyl-L-methionyl-L-leucyl-L-phenylalanine  (EXP,ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (ISO)
nicotine  (ISO)
oleic acid  (ISO)
oxaliplatin  (EXP)
oxycodone  (EXP)
paracetamol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (EXP)
phenobarbital  (ISO)
phenylarsine oxide  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (EXP)
phosphatidic acid  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
prostaglandin E2  (ISO)
quercetin  (ISO)
reactive oxygen species  (EXP,ISO)
resveratrol  (ISO)
rotenone  (EXP)
rottlerin  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
Soman  (EXP)
sulforaphane  (ISO)
testosterone  (ISO)
tetracycline  (ISO)
titanium dioxide  (ISO)
topiramate  (EXP)
topotecan  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vorinostat  (ISO)

References

References - curated
1. Dohke Y, etal., Biochem Biophys Res Commun 2002 Dec 13;299(4):663-8.
2. Freyberg Z, etal., Mol Biol Cell. 2002 Nov;13(11):3930-42.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. GOA data from the GO Consortium
5. Hu J, etal., Oncotarget. 2016 Nov 29;7(48):78557-78565. doi: 10.18632/oncotarget.12447.
6. Hu T and Exton JH, J Biol Chem 2003 Jan 24;278(4):2348-55.
7. Humeau Y, etal., Proc Natl Acad Sci U S A 2001 Dec 18;98(26):15300-5.
8. Jin S, etal., Biochem Biophys Res Commun 2002 Sep 27;297(3):545-51.
9. Kim SY, etal., J Neuropathol Exp Neurol. 2004 Aug;63(8):812-20.
10. Laine J, etal., Pancreas. 2000 May;20(4):323-36.
11. Nagasaki A, etal., Cell Struct Funct. 2008;33(1):27-33. Epub 2008 Mar 13.
12. Nakashima S, etal., Cytogenet Cell Genet 1997;79(1-2):109-13.
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Panupinthu N, etal., J Cell Biol. 2008 Jun 2;181(5):859-71. doi: 10.1083/jcb.200708037.
15. Pipeline to import KEGG annotations from KEGG into RGD
16. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
17. Powner DJ, etal., Mol Biol Cell 2002 Apr;13(4):1252-62.
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Singh AT, etal., Lipids. 2005 Nov;40(11):1135-40.
21. Yoshimura S, etal., Biochem Biophys Res Commun 1996 Aug 14;225(2):494-9.
22. Zhong M, etal., Biochem Biophys Res Commun 2003 Mar 14;302(3):615-9.
Additional References at PubMed
PMID:9188501   PMID:9361006   PMID:9445394   PMID:11121416   PMID:11544318   PMID:11665609   PMID:11812783   PMID:12054584   PMID:12388770   PMID:12429840   PMID:12472177   PMID:12642902  
PMID:12876278   PMID:14660552   PMID:14718562   PMID:14744865   PMID:14769825   PMID:15087463   PMID:15187091   PMID:15199126   PMID:15210717   PMID:15475361   PMID:15601581   PMID:15616193  
PMID:15752728   PMID:15980073   PMID:16339153   PMID:16842757   PMID:17146759   PMID:17540765   PMID:17897319   PMID:18541525   PMID:18550821   PMID:19010519   PMID:19161391   PMID:19261846  
PMID:19741172   PMID:19794068   PMID:19946888   PMID:20965153   PMID:21525000   PMID:21916846   PMID:22544632   PMID:22674271   PMID:22797597   PMID:23932932   PMID:24269608   PMID:24728967  
PMID:24986006   PMID:25361009   PMID:28648601   PMID:28729535   PMID:30207376   PMID:31356881   PMID:32337269  


Genomics

Comparative Map Data
Pld1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22110,849,205 - 111,047,692 (+)NCBI
Rnor_6.0 Ensembl2113,652,348 - 113,849,403 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02113,651,967 - 113,849,403 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02133,357,235 - 133,554,180 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42115,306,940 - 115,460,518 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12115,251,901 - 115,405,480 (+)NCBI
Celera2106,084,707 - 106,238,116 (+)NCBICelera
Cytogenetic Map2q24NCBI
PLD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3171,600,404 - 171,810,950 (-)EnsemblGRCh38hg38GRCh38
GRCh383171,600,404 - 171,810,483 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh373171,318,194 - 171,528,273 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363172,801,339 - 172,938,566 (-)NCBINCBI36hg18NCBI36
Build 343172,801,346 - 172,938,574NCBI
Celera3169,718,435 - 169,928,143 (-)NCBI
Cytogenetic Map3q26.31NCBI
HuRef3168,688,221 - 168,898,341 (-)NCBIHuRef
CHM1_13171,281,084 - 171,491,135 (-)NCBICHM1_1
Pld1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39327,992,636 - 28,187,511 (+)NCBIGRCm39mm39
GRCm39 Ensembl327,992,844 - 28,187,511 (+)Ensembl
GRCm38327,938,459 - 28,133,362 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl327,938,695 - 28,133,362 (+)EnsemblGRCm38mm10GRCm38
MGSCv37327,837,602 - 28,032,284 (+)NCBIGRCm37mm9NCBIm37
MGSCv36328,215,231 - 28,324,307 (+)NCBImm8
Celera327,897,052 - 28,088,894 (+)NCBICelera
Cytogenetic Map3A3NCBI
cM Map311.15NCBI
Pld1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554201,696,751 - 1,892,741 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554201,697,716 - 1,892,741 (-)NCBIChiLan1.0ChiLan1.0
PLD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13176,790,736 - 176,999,974 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3176,790,753 - 176,961,033 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03168,606,342 - 168,816,383 (-)NCBIMhudiblu_PPA_v0panPan3
PLD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13435,917,759 - 36,080,383 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3435,921,058 - 36,121,631 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3444,928,877 - 45,133,990 (-)NCBI
ROS_Cfam_1.03436,000,267 - 36,205,332 (-)NCBI
UMICH_Zoey_3.13435,940,863 - 36,145,600 (-)NCBI
UNSW_CanFamBas_1.03435,903,822 - 36,109,331 (-)NCBI
UU_Cfam_GSD_1.03436,165,953 - 36,370,780 (-)NCBI
Pld1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602102,572,478 - 102,777,840 (-)NCBI
SpeTri2.0NW_004936593844,634 - 1,049,478 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PLD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13110,087,051 - 110,376,319 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113110,152,268 - 110,376,319 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213119,138,285 - 119,362,303 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PLD1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11517,667,079 - 17,871,452 (+)NCBI
ChlSab1.1 Ensembl1517,706,030 - 17,870,266 (+)Ensembl
Pld1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473049,665,432 - 49,885,242 (-)NCBI

Position Markers
RH139663  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22111,046,730 - 111,046,946 (+)MAPPER
Rnor_6.02113,848,442 - 113,848,657NCBIRnor6.0
Rnor_5.02133,553,219 - 133,553,434UniSTSRnor5.0
RGSC_v3.42115,459,557 - 115,459,772UniSTSRGSC3.4
Celera2106,237,155 - 106,237,370UniSTS
RH 3.4 Map2703.0UniSTS
Cytogenetic Map2q23.3-q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)223837491149614623Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491169852800Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491169852800Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)223837719169852670Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)223837719169852670Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226186097135654963Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226186097142053534Rat
12879841Cm87Cardiac mass QTL 870.026heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)227161361148295267Rat
12879842Cm88Cardiac mass QTL 880.042heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)227161361148295267Rat
12879843Am3Aortic mass QTL 30.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)227161361148295267Rat
12879844Kidm62Kidney mass QTL 620.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227161361148295267Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916169852800Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916195645082Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243133606217498545Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243133606217498545Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243141290114164944Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)243141290114164944Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243141290154583160Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243149788198704485Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246537589217498710Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256244671217498710Rat
1558648Smcn1Smooth muscle cell number QTL 10.039blood vessel smooth muscle cell quantity (VT:0010525)aorta smooth muscle cell count per unit vessel length (CMO:0001646)260131410135646395Rat
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)260325352147522851Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828049217498710Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828236243550655Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)268865414169852800Rat
1581578Cm49Cardiac mass QTL 494.90.01heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)268866454149614466Rat
7411551Bw131Body weight QTL 13129.60.001body mass (VT:0001259)body weight gain (CMO:0000420)270132175115132175Rat
2317041Aia14Adjuvant induced arthritis QTL 143.29joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)271495404116495404Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)275687495221880419Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)278321410158159410Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)278321410217498710Rat
2299162Iddm32Insulin dependent diabetes mellitus QTL 322.36blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)280631950149614623Rat
61392Bp6Blood pressure QTL 67arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)282574487127574487Rat
1598865Bp296Blood pressure QTL 2962.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)283656855128656855Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283754907237610852Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283819608239166203Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283819608243901375Rat
1578772Stresp14Stress response QTL 1450.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)284424139132130578Rat
2300165Bmd49Bone mineral density QTL 494.80.0001lumbar vertebra mineral mass (VT:0010511)bone mineral density (CMO:0001226)291664872136664872Rat
2300170Bmd45Bone mineral density QTL 4512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)291664872136664872Rat
2300185Bmd46Bone mineral density QTL 468.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)291664872136664872Rat
7207808Bmd89Bone mineral density QTL 894.1femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)291664872136664872Rat
1558653Prcr1Prostate cancer resistance QTL 15prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)293995316169852800Rat
1598862Glom9Glomerulus QTL 93.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)295946719140946719Rat
1598863Cm65Cardiac mass QTL 652.3heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)295946719140946719Rat
2317886Alcrsp23Alcohol response QTL 232.40.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)296844330141844330Rat
9589093Slep10Serum leptin concentration QTL 103.840.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)2102356980147356980Rat
631566Bp90Blood pressure QTL 900.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2108880910153880910Rat
8662836Vetf8Vascular elastic tissue fragility QTL 80.66thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2110965721155965721Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:953
Count of miRNA genes:299
Interacting mature miRNAs:383
Transcripts:ENSRNOT00000039296, ENSRNOT00000039308
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 2 1 1 6 1 8 27 11 10
Low 41 56 40 13 40 8 11 66 8 30 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039296   ⟹   ENSRNOP00000034466
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2113,652,348 - 113,849,038 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000039308   ⟹   ENSRNOP00000035045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2113,696,154 - 113,849,403 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091545   ⟹   ENSRNOP00000073521
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2113,696,259 - 113,847,533 (+)Ensembl
RefSeq Acc Id: NM_030992   ⟹   NP_112254
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22110,893,623 - 111,047,692 (+)NCBI
Rnor_6.02113,696,154 - 113,849,403 (+)NCBI
Rnor_5.02133,357,235 - 133,554,180 (+)NCBI
RGSC_v3.42115,306,940 - 115,460,518 (+)RGD
Celera2106,084,707 - 106,238,116 (+)RGD
Sequence:
RefSeq Acc Id: XM_006232205   ⟹   XP_006232267
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22110,893,566 - 111,047,304 (+)NCBI
Rnor_6.02113,695,376 - 113,849,015 (+)NCBI
Rnor_5.02133,357,235 - 133,554,180 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006232206   ⟹   XP_006232268
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22110,849,205 - 111,047,304 (+)NCBI
Rnor_6.02113,651,967 - 113,849,015 (+)NCBI
Rnor_5.02133,357,235 - 133,554,180 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760891   ⟹   XP_008759113
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02113,651,968 - 113,849,015 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017590637   ⟹   XP_017446126
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02113,652,429 - 113,849,015 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_112254   ⟸   NM_030992
- Sequence:
RefSeq Acc Id: XP_006232268   ⟸   XM_006232206
- Peptide Label: isoform X1
- UniProtKB: F1LMG4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006232267   ⟸   XM_006232205
- Peptide Label: isoform X1
- UniProtKB: F1LMG4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759113   ⟸   XM_008760891
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017446126   ⟸   XM_017590637
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000073521   ⟸   ENSRNOT00000091545
RefSeq Acc Id: ENSRNOP00000034466   ⟸   ENSRNOT00000039296
RefSeq Acc Id: ENSRNOP00000035045   ⟸   ENSRNOT00000039308
Protein Domains
PH   PLD phosphodiesterase   PX

Transcriptome

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

Promoters
RGD ID:13691272
Promoter ID:EPDNEW_R1790
Type:initiation region
Name:Pld1_2
Description:phospholipase D1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R1791  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02113,652,315 - 113,652,375EPDNEW
RGD ID:13691266
Promoter ID:EPDNEW_R1791
Type:initiation region
Name:Pld1_1
Description:phospholipase D1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R1790  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02113,696,154 - 113,696,214EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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 (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
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)
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
WKY/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
WKY/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
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3349 AgrOrtholog
Ensembl Genes ENSRNOG00000028156 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000034466 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000035045 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073521 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039296 UniProtKB/TrEMBL
  ENSRNOT00000039308 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000091545 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.1520.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro PH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Phox UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLD-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLipase_D/transphosphatidylase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLipase_D_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLipase_D_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PX_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25096 UniProtKB/Swiss-Prot
NCBI Gene 25096 ENTREZGENE
PANTHER PTHR18896 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PF00169 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00787 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLDc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLDc_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pld1 PhenoGen
PIRSF Phospholipase_D_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PH_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PS50195 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PLDc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00233 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00312 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF64268 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K5R0_RAT UniProtKB/TrEMBL
  D4A318_RAT UniProtKB/TrEMBL
  F1LMG4 ENTREZGENE, UniProtKB/TrEMBL
  P70496 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O08959 UniProtKB/Swiss-Prot
  O35856 UniProtKB/Swiss-Prot
  O54765 UniProtKB/Swiss-Prot
  P70497 UniProtKB/Swiss-Prot
  Q9QWJ6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-30 Pld1  phospholipase D1  Pld1  phospholipase D1, phosphatidylcholine-specific  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-05-07 Pld1  phospholipase D1, phosphatidylcholine-specific  Pld1  phospholipase D1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Pld1  Phoshpolipase D gene 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_drugs inhibited by neomycin 628523
gene_expression expressed in neuron plasma membrane 70245
gene_function hydrolyzes phosphatidylcholine to produce choline and phosphatidic acid 70245
gene_function exhibits transphosphatidylation activity 628523
gene_physical_interaction binds PKC-alpha through the N terminus 729596
gene_process involved in cAMP-regulated exocytosis in rat parotid acinar cells 628523
gene_process may have a post-docking role in Ca2+ dependent exocytosis 628523
gene_product member of the phospholipase superfamily 628523
gene_regulation activated by small molecular mass GTP-binding proteins 628523
gene_transcript may have two splice variants, A and B 70245