Pdpn (podoplanin) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Pdpn (podoplanin) Rattus norvegicus
Analyze
Symbol: Pdpn
Name: podoplanin
RGD ID: 61819
Description: Predicted to enable chaperone binding activity; chemokine binding activity; and signaling receptor binding activity. Involved in several processes, including lung development; positive regulation of platelet activation; and response to hyperoxia. Acts upstream of or within cell adhesion and tube morphogenesis. Located in apical plasma membrane. Biomarker of adult respiratory distress syndrome; bacterial pneumonia; nephrosis; and oligohydramnios. Orthologous to human PDPN (podoplanin); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: E11; E11 antigen epitope; epithelial cell surface transmembrane protein antigen; glycoprotein 38; Gp38; OTS-8; pulmonary type I alveolar epithelial cell transmembrane differentiation marker; RTI140; RTI40; T1-alpha; T1A; type I cell 40 kDa protein
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
mRatBN7.25155,601,691 - 155,635,656 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl5161,947,137 - 161,981,441 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.05161,947,137 - 161,981,441 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05165,646,114 - 165,679,595 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45162,142,251 - 162,175,921 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15162,152,438 - 162,186,109 (-)NCBI
Celera5153,929,730 - 153,964,026 (-)NCBICelera
RH 3.4 Map51057.9RGD
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1-nitropyrene  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
celecoxib  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
curcumin  (ISO)
cytarabine  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP)
dichloroacetic acid  (ISO)
disulfiram  (ISO)
dorsomorphin  (ISO)
enalapril  (EXP)
entinostat  (ISO)
ethanol  (ISO)
flavonoids  (EXP)
furan  (EXP)
gentamycin  (EXP)
graphite  (EXP)
indometacin  (ISO)
menadione  (ISO)
mercury dibromide  (ISO)
methylmercury chloride  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
nitrofen  (EXP,ISO)
ochratoxin A  (EXP)
orphenadrine  (EXP)
ozone  (EXP)
panobinostat  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
protein kinase inhibitor  (EXP)
SB 431542  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
succimer  (ISO)
sunitinib  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
uranium atom  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
WIN 18446  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
actin-mediated cell contraction  (IBA,ISO,ISS)
amino acid transport  (ISO,ISS)
cell adhesion  (IDA)
cell morphogenesis  (IBA,ISO,ISS)
cell population proliferation  (ISO)
cell-cell adhesion  (IBA,ISO)
folic acid transport  (ISO,ISS)
inflammatory response  (IEP)
lung alveolus development  (ISO)
lung development  (IBA,IEP,ISO,ISS)
lymph node development  (ISO,ISS)
lymphangiogenesis  (ISO,ISS)
lymphatic endothelial cell fate commitment  (ISO,ISS)
negative regulation of apoptotic process  (ISO,ISS)
negative regulation of cell population proliferation  (ISO,ISS)
nervous system development  (IEP)
positive regulation of cell migration  (IBA,IDA,ISO)
positive regulation of cellular component movement  (ISO,ISS)
positive regulation of epithelial to mesenchymal transition  (IBA,ISO,ISS)
positive regulation of extracellular matrix disassembly  (IBA,ISO,ISS)
positive regulation of platelet activation  (IMP)
positive regulation of platelet aggregation  (IBA,ISO,ISS)
prostaglandin metabolic process  (ISO)
regulation of cell adhesion  (ISO,ISS)
regulation of cell shape  (IEA)
regulation of G1/S transition of mitotic cell cycle  (ISO)
regulation of lamellipodium morphogenesis  (IBA,ISO,ISS)
regulation of myofibroblast contraction  (IBA,ISO,ISS)
regulation of substrate adhesion-dependent cell spreading  (IBA,ISO,ISS)
response to hyperoxia  (IBA,IEP)
Rho protein signal transduction  (IBA,ISO,ISS)
signal transduction  (ISO)
tube morphogenesis  (IDA)
water transport  (ISO,ISS)
wound healing, spreading of cells  (ISO,ISS)

Cellular Component

References

References - curated
1. Braun M, etal., Breast Cancer Res Treat. 2007 Dec 29;.
2. Breiteneder-Geleff S, etal., Am J Pathol 1997 Oct;151(4):1141-52.
3. Clegg GR, etal., Am J Physiol Lung Cell Mol Physiol. 2005 Sep;289(3):L382-90. Epub 2005 Apr 22.
4. Dumoff KL, etal., Mod Pathol. 2006 May;19(5):708-16.
5. Frank JA, etal., Am J Respir Crit Care Med. 2002 Jan 15;165(2):242-9.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Horiguchi A, etal., Urology. 2008 Feb 19;.
8. Ijpelaar DH, etal., Am J Physiol Renal Physiol. 2008 Apr;294(4):F758-67. Epub 2008 Jan 16.
9. Kato Y, etal., Biochem Biophys Res Commun. 2006 Nov 3;349(4):1301-7. Epub 2006 Sep 7.
10. Kato Y, etal., J Biol Chem 2003 Dec 19;278(51):51599-605. Epub 2003 Oct 1.
11. Kitterman JA, etal., Am J Physiol Lung Cell Mol Physiol. 2002 Mar;282(3):L431-9.
12. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
13. McElroy MC, etal., Am J Physiol. 1995 Feb;268(2 Pt 1):L181-6.
14. MGD data from the GO Consortium
15. Mishima K, etal., Acta Neuropathol. 2006 Jun;111(6):563-8. Epub 2006 May 5.
16. Narasaraju TA, etal., Am J Physiol Lung Cell Mol Physiol 2003 Nov;285(5):L1037-45. Epub 2003 Aug 15.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. RGD automated data pipeline
19. RGD automated import pipeline for gene-chemical interactions
20. RGD comprehensive gene curation
21. Rishi AK, etal., Dev Biol 1995 Jan;167(1):294-306.
22. Schacht V, etal., EMBO J. 2003 Jul 15;22(14):3546-56.
23. Sonne SB, etal., Virchows Arch. 2006 Aug;449(2):200-6. Epub 2006 May 31.
24. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
25. Williams MC, etal., Am J Respir Cell Mol Biol. 1996 Jun;14(6):577-85.
26. Yu H, etal., Am J Clin Pathol. 2007 Nov;128(5):767-75.
Additional References at PubMed
PMID:8833206   PMID:9632596   PMID:9651190   PMID:9761764   PMID:9920397   PMID:10574709   PMID:12032185   PMID:12654292   PMID:12874451   PMID:14978162   PMID:15489334   PMID:15743802  
PMID:16869965   PMID:17046996   PMID:17222411   PMID:17616532   PMID:18215137   PMID:18541721   PMID:18599604   PMID:20110424   PMID:20962267   PMID:21046115   PMID:21376833   PMID:23180825  
PMID:23541579   PMID:24275092   PMID:25341788   PMID:25347465   PMID:25486435   PMID:26064894   PMID:27039006   PMID:30088964  


Genomics

Comparative Map Data
Pdpn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25155,601,691 - 155,635,656 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl5161,947,137 - 161,981,441 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.05161,947,137 - 161,981,441 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05165,646,114 - 165,679,595 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45162,142,251 - 162,175,921 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15162,152,438 - 162,186,109 (-)NCBI
Celera5153,929,730 - 153,964,026 (-)NCBICelera
RH 3.4 Map51057.9RGD
Cytogenetic Map5q36NCBI
PDPN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl113,583,465 - 13,617,957 (+)EnsemblGRCh38hg38GRCh38
GRCh38113,583,757 - 13,617,957 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37113,910,252 - 13,944,452 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36113,782,839 - 13,817,039 (+)NCBINCBI36hg18NCBI36
Celera112,392,151 - 12,426,304 (+)NCBI
Cytogenetic Map1p36.21NCBI
HuRef112,427,703 - 12,461,787 (+)NCBIHuRef
CHM1_1113,708,939 - 13,743,119 (+)NCBICHM1_1
Pdpn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394142,993,979 - 143,026,134 (-)NCBIGRCm39mm39
GRCm39 Ensembl4142,994,001 - 143,026,134 (-)Ensembl
GRCm384143,267,409 - 143,299,564 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4143,267,431 - 143,299,564 (-)EnsemblGRCm38mm10GRCm38
MGSCv374142,857,325 - 142,889,410 (-)NCBIGRCm37mm9NCBIm37
MGSCv364142,534,133 - 142,566,099 (-)NCBImm8
Celera4145,087,916 - 145,122,854 (-)NCBICelera
Cytogenetic Map4E1NCBI
Pdpn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555274,183,639 - 4,215,200 (-)NCBIChiLan1.0ChiLan1.0
PDPN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1113,728,233 - 13,759,584 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl113,728,233 - 13,759,584 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0112,728,569 - 12,759,781 (+)NCBIMhudiblu_PPA_v0panPan3
PDPN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1283,552,735 - 83,581,375 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl283,552,830 - 83,581,375 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha280,087,666 - 80,116,300 (-)NCBI
ROS_Cfam_1.0284,202,661 - 84,231,307 (-)NCBI
UMICH_Zoey_3.1280,955,029 - 80,983,745 (-)NCBI
UNSW_CanFamBas_1.0281,973,249 - 82,001,951 (-)NCBI
UU_Cfam_GSD_1.0283,039,588 - 83,068,230 (-)NCBI
Pdpn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505835,926,390 - 35,954,229 (+)NCBI
SpeTri2.0NW_0049364741,751,159 - 1,779,011 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDPN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl673,019,057 - 73,049,998 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1673,019,063 - 73,050,000 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2667,223,489 - 67,254,534 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PDPN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120118,644,060 - 118,679,508 (-)NCBI
ChlSab1.1 Ensembl20118,644,051 - 118,679,311 (-)Ensembl
Vero_WHO_p1.0NW_02366605422,376,384 - 22,421,943 (-)NCBI
Pdpn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624764163,370 - 192,770 (+)NCBI

Position Markers
RH142306  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25155,602,043 - 155,602,207 (+)MAPPERmRatBN7.2
Rnor_6.05161,947,490 - 161,947,653NCBIRnor6.0
Rnor_5.05165,646,467 - 165,646,630UniSTSRnor5.0
RGSC_v3.45162,142,604 - 162,142,767UniSTSRGSC3.4
Celera5153,930,083 - 153,930,246UniSTS
RH 3.4 Map51057.9UniSTS
Cytogenetic Map5q36UniSTS
AU048611  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25155,620,384 - 155,620,525 (+)MAPPERmRatBN7.2
Rnor_6.05161,965,831 - 161,965,971NCBIRnor6.0
Rnor_5.05165,664,808 - 165,664,948UniSTSRnor5.0
RGSC_v3.45162,160,945 - 162,161,085UniSTSRGSC3.4
Celera5153,948,424 - 153,948,564UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5149568588167739697Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5149832180164807402Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5142309061173707219Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132551937173707219Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5149029982173687766Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5157212422167739539Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5142307322173707219Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5136354114173707219Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5157319671173707219Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138154677172402610Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5128687766173687766Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133943857173707219Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133943857173707219Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5134197905173707219Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)547745646167946134Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5150340838164298744Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5157319671171194163Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5161084664173707219Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5150360936167946134Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136640731173707219Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5134712342173707219Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5134712342173707219Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5131077716173707219Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:141
Count of miRNA genes:103
Interacting mature miRNAs:123
Transcripts:ENSRNOT00000020316
Prediction methods: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 1
Medium 2 28 1 1 67 29 29 10
Low 1 15 49 34 18 34 8 11 7 6 12 8
Below cutoff 7 7 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020316   ⟹   ENSRNOP00000020316
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5161,947,137 - 161,981,441 (-)Ensembl
RefSeq Acc Id: NM_019358   ⟹   NP_062231
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25155,601,691 - 155,635,656 (-)NCBI
Rnor_6.05161,947,137 - 161,981,441 (-)NCBI
Rnor_5.05165,646,114 - 165,679,595 (-)NCBI
RGSC_v3.45162,142,251 - 162,175,921 (-)RGD
Celera5153,929,730 - 153,964,026 (-)RGD
Sequence:
RefSeq Acc Id: XM_006239338   ⟹   XP_006239400
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25155,603,738 - 155,635,645 (-)NCBI
Rnor_6.05161,949,184 - 161,981,439 (-)NCBI
Rnor_5.05165,646,114 - 165,679,595 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_062231   ⟸   NM_019358
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_006239400   ⟸   XM_006239338
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000020316   ⟸   ENSRNOT00000020316

Transcriptome

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

Promoters
RGD ID:13694241
Promoter ID:EPDNEW_R4766
Type:multiple initiation site
Name:Pdpn_1
Description:podoplanin
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_6.05161,981,405 - 161,981,465EPDNEW

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:61819 AgrOrtholog
Ensembl Genes ENSRNOG00000014961 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020316 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020316 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7097186 IMAGE-MGC_LOAD
KEGG Report rno:54320 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91718 IMAGE-MGC_LOAD
NCBI Gene 54320 ENTREZGENE
PhenoGen Pdpn PhenoGen
UniProt A0A0G2JSN8_RAT UniProtKB/TrEMBL
  PDPN_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O08731 UniProtKB/Swiss-Prot
  O55210 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Pdpn  podoplanin  Gp38  glycoprotein 38  Symbol and Name updated 1299863 APPROVED
2002-06-10 Gp38  glycoprotein 38      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to membrane fraction 632934
gene_expression expressed at high levels in adult and fetal lung and fetal brain, has lower expression in adult brain, kidney, and intestine 61612
gene_expression expressed in glomeruli 632934
gene_protein 43 kD glycoprotein 632934