Pdpn (podoplanin) - Rat Genome Database

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Gene: Pdpn (podoplanin) Rattus norvegicus
Analyze
Symbol: Pdpn
Name: podoplanin
RGD ID: 61819
Description: Predicted to enable chemokine binding activity; protein-folding chaperone 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; positive regulation of cell migration; 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: VALIDATED
Previously 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 Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85160,884,995 - 160,919,112 (-)NCBIGRCr8
mRatBN7.25155,601,691 - 155,635,656 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5155,601,691 - 155,635,656 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5158,285,987 - 158,319,956 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05160,059,293 - 160,093,261 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05160,039,655 - 160,073,636 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05161,947,137 - 161,981,441 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5161,947,137 - 161,981,441 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05165,646,114 - 165,679,595 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45162,142,251 - 162,175,921 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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)
3-Nitrobenzanthrone  (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)
Cuprizon  (EXP)
curcumin  (ISO)
cytarabine  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP)
dichloroacetic acid  (ISO)
dioxygen  (EXP)
diquat  (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)
microcystin-LR  (EXP)
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,ISO)
panobinostat  (ISO)
paracetamol  (EXP)
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)
thiram  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
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

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Detection of lymphovascular invasion in early breast cancer by D2-40 (podoplanin): a clinically useful predictor for axillary lymph node metastases. Braun M, etal., Breast Cancer Res Treat. 2007 Dec 29;.
2. Podoplanin, novel 43-kd membrane protein of glomerular epithelial cells, is down-regulated in puromycin nephrosis. Breiteneder-Geleff S, etal., Am J Pathol 1997 Oct;151(4):1141-52.
3. Coexpression of RTI40 with alveolar epithelial type II cell proteins in lungs following injury: identification of alveolar intermediate cell types. Clegg GR, etal., Am J Physiol Lung Cell Mol Physiol. 2005 Sep;289(3):L382-90. Epub 2005 Apr 22.
4. Low podoplanin expression in pretreatment biopsy material predicts poor prognosis in advanced-stage squamous cell carcinoma of the uterine cervix treated by primary radiation. Dumoff KL, etal., Mod Pathol. 2006 May;19(5):708-16.
5. Low tidal volume reduces epithelial and endothelial injury in acid-injured rat lungs. Frank JA, etal., Am J Respir Crit Care Med. 2002 Jan 15;165(2):242-9.
6. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Intratumoral Lymphatics and Lymphatic Invasion Are Associated with Tumor Aggressiveness and Poor Prognosis in Renal Cell Carcinoma. Horiguchi A, etal., Urology. 2008 Feb 19;.
8. Glomerular hypertrophy precedes albuminuria and segmental loss of podoplanin in podocytes in Munich-Wistar-Fromter rats. Ijpelaar DH, etal., Am J Physiol Renal Physiol. 2008 Apr;294(4):F758-67. Epub 2008 Jan 16.
9. Inhibition of tumor cell-induced platelet aggregation using a novel anti-podoplanin antibody reacting with its platelet-aggregation-stimulating domain. Kato Y, etal., Biochem Biophys Res Commun. 2006 Nov 3;349(4):1301-7. Epub 2006 Sep 7.
10. Molecular identification of Aggrus/T1 alpha as a platelet aggregation-inducing factor expressed in colorectal tumors. Kato Y, etal., J Biol Chem 2003 Dec 19;278(51):51599-605. Epub 2003 Oct 1.
11. Effects of oligohydramnios on lung growth and maturation in the fetal rat. Kitterman JA, etal., Am J Physiol Lung Cell Mol Physiol. 2002 Mar;282(3):L431-9.
12. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
13. A type I cell-specific protein is a biochemical marker of epithelial injury in a rat model of pneumonia. McElroy MC, etal., Am J Physiol. 1995 Feb;268(2 Pt 1):L181-6.
14. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
15. Podoplanin expression in primary central nervous system germ cell tumors: a useful histological marker for the diagnosis of germinoma. Mishima K, etal., Acta Neuropathol. 2006 Jun;111(6):563-8. Epub 2006 May 5.
16. Protein nitration in rat lungs during hyperoxia exposure: a possible role of myeloperoxidase. Narasaraju TA, etal., Am J Physiol Lung Cell Mol Physiol 2003 Nov;285(5):L1037-45. Epub 2003 Aug 15.
17. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. GOA pipeline RGD automated data pipeline
19. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
20. Comprehensive gene review and curation RGD comprehensive gene curation
21. Cloning, characterization, and development expression of a rat lung alveolar type I cell gene in embryonic endodermal and neural derivatives. Rishi AK, etal., Dev Biol 1995 Jan;167(1):294-306.
22. T1alpha/podoplanin deficiency disrupts normal lymphatic vasculature formation and causes lymphedema. Schacht V, etal., EMBO J. 2003 Jul 15;22(14):3546-56.
23. Identity of M2A (D2-40) antigen and gp36 (Aggrus, T1A-2, podoplanin) in human developing testis, testicular carcinoma in situ and germ-cell tumours. Sonne SB, etal., Virchows Arch. 2006 Aug;449(2):200-6. Epub 2006 May 31.
24. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
25. T1 alpha protein is developmentally regulated and expressed by alveolar type I cells, choroid plexus, and ciliary epithelia of adult rats. Williams MC, etal., Am J Respir Cell Mol Biol. 1996 Jun;14(6):577-85.
26. Diffuse membranous immunoreactivity for podoplanin (D2-40) distinguishes primary and metastatic seminomas from other germ cell tumors and metastatic neoplasms. 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
GRCr85160,884,995 - 160,919,112 (-)NCBIGRCr8
mRatBN7.25155,601,691 - 155,635,656 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5155,601,691 - 155,635,656 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5158,285,987 - 158,319,956 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05160,059,293 - 160,093,261 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05160,039,655 - 160,073,636 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05161,947,137 - 161,981,441 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5161,947,137 - 161,981,441 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05165,646,114 - 165,679,595 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45162,142,251 - 162,175,921 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38113,583,757 - 13,617,957 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl113,583,465 - 13,617,957 (+)EnsemblGRCh38hg38GRCh38
GRCh37113,910,252 - 13,944,452 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36113,782,839 - 13,817,039 (+)NCBINCBI36Build 36hg18NCBI36
Celera112,392,151 - 12,426,304 (+)NCBICelera
Cytogenetic Map1p36.21NCBI
HuRef112,427,703 - 12,461,787 (+)NCBIHuRef
CHM1_1113,708,939 - 13,743,119 (+)NCBICHM1_1
T2T-CHM13v2.0113,025,717 - 13,059,901 (+)NCBIT2T-CHM13v2.0
Pdpn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394142,993,979 - 143,026,134 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4142,994,001 - 143,026,134 (-)EnsemblGRCm39 Ensembl
GRCm384143,267,409 - 143,299,564 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4143,267,431 - 143,299,564 (-)EnsemblGRCm38mm10GRCm38
MGSCv374142,857,325 - 142,889,410 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv364142,534,133 - 142,566,099 (-)NCBIMGSCv36mm8
Celera4145,087,916 - 145,122,854 (-)NCBICelera
Cytogenetic Map4E1NCBI
cM Map477.29NCBI
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
NHGRI_mPanPan1-v21213,298,624 - 213,329,916 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11212,551,117 - 212,580,726 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0112,728,569 - 12,759,781 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1113,728,233 - 13,759,584 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl113,728,233 - 13,759,584 (+)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0284,202,661 - 84,231,307 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl284,201,664 - 84,231,418 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1280,955,029 - 80,983,745 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0281,973,249 - 82,001,951 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0283,039,588 - 83,068,230 (-)NCBIUU_Cfam_GSD_1.0
Pdpn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505835,926,390 - 35,954,229 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364741,750,944 - 1,781,156 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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 - 73,049,996 (+)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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20118,644,051 - 118,679,311 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605422,376,384 - 22,421,943 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pdpn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624764163,370 - 192,770 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pdpn
443 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5143608201161165651Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5144358090157869054Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat
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)5128506074166875058Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
1354631Swd2Spike wave discharge measurement QTL 23.640.0002brain electrophysiology trait (VT:0010557)brain total spike-and-wave discharge duration (CMO:0001740)5151113452164465185Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
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)546711509161317411Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5143799107158428037Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5144377876161317411Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
1298090Bp155Blood pressure QTL 1553.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)5151006154161165494Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat

Markers in Region
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


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


Ensembl Acc Id: ENSRNOT00000020316   ⟹   ENSRNOP00000020316
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5155,601,691 - 155,635,656 (-)Ensembl
Rnor_6.0 Ensembl5161,947,137 - 161,981,441 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000093852   ⟹   ENSRNOP00000096212
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5155,603,738 - 155,635,656 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000111603   ⟹   ENSRNOP00000090610
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5155,601,691 - 155,635,656 (-)Ensembl
RefSeq Acc Id: NM_019358   ⟹   NP_062231
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85160,884,995 - 160,918,959 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85160,887,042 - 160,919,112 (-)NCBI
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:
RefSeq Acc Id: NP_062231   ⟸   NM_019358
- Peptide Label: precursor
- UniProtKB: Q64294 (UniProtKB/Swiss-Prot),   O55210 (UniProtKB/Swiss-Prot),   O08731 (UniProtKB/Swiss-Prot),   A0A0G2JSN8 (UniProtKB/TrEMBL),   A6ITZ5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239400   ⟸   XM_006239338
- Peptide Label: isoform X1
- UniProtKB: Q64294 (UniProtKB/Swiss-Prot),   O55210 (UniProtKB/Swiss-Prot),   O08731 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000020316   ⟸   ENSRNOT00000020316
Ensembl Acc Id: ENSRNOP00000090610   ⟸   ENSRNOT00000111603
Ensembl Acc Id: ENSRNOP00000096212   ⟸   ENSRNOT00000093852

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q64294-F1-model_v2 AlphaFold Q64294 1-166 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61819 AgrOrtholog
BioCyc Gene G2FUF-39298 BioCyc
Ensembl Genes ENSRNOG00000014961 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00065026882 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000020316.6 UniProtKB/TrEMBL
  ENSRNOT00000093852.1 UniProtKB/TrEMBL
  ENSRNOT00000111603.1 UniProtKB/TrEMBL
  ENSRNOT00065046427 UniProtKB/Swiss-Prot
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
PANTHER PODOPLANIN UniProtKB/Swiss-Prot
  PODOPLANIN UniProtKB/Swiss-Prot
  PODOPLANIN UniProtKB/TrEMBL
  PODOPLANIN UniProtKB/TrEMBL
Pfam Podoplanin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pdpn PhenoGen
RatGTEx ENSRNOG00000014961 RatGTEx
  ENSRNOG00065026882 RatGTEx
UniProt A0A0G2JSN8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AE24 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AUS3 ENTREZGENE, UniProtKB/TrEMBL
  A6ITZ3_RAT UniProtKB/TrEMBL
  A6ITZ5 ENTREZGENE, UniProtKB/TrEMBL
  O08731 ENTREZGENE
  O55210 ENTREZGENE
  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