PDPN (podoplanin) - Rat Genome Database

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Gene: PDPN (podoplanin) Canis lupus familiaris
Analyze
Symbol: PDPN
Name: podoplanin
RGD ID: 12095446
Description: ENCODES a protein that exhibits amino acid transmembrane transporter activity (ortholog); folic acid transmembrane transporter activity (ortholog); water channel activity (ortholog); INVOLVED IN actin-mediated cell contraction (ortholog); amino acid transport (ortholog); cell adhesion (ortholog); ASSOCIATED WITH adult respiratory distress syndrome (ortholog); Albuminuria (ortholog); bacterial pneumonia (ortholog); FOUND IN apical plasma membrane (ortholog); basolateral plasma membrane (ortholog); cell junction (ortholog)
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: glycoprotein 38; gp38; GP40; mucin-type membrane protein gp40
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References
Additional References at PubMed
PMID:9337856   PMID:27380308   PMID:27788030   PMID:27918691   PMID:30032202   PMID:31882481   PMID:32182186   PMID:32380790  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
539 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 5 3 5 6 10 6
Low 2 11 6 12
Below cutoff 6 6 6 6 8

Sequence


RefSeq Acc Id: ENSCAFT00000025944   ⟹   ENSCAFP00000024086
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl283,553,473 - 83,581,375 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000037744   ⟹   ENSCAFP00000033330
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl283,554,483 - 83,561,741 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000046205   ⟹   ENSCAFP00000036264
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl283,552,830 - 83,581,375 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845001867   ⟹   ENSCAFP00845001471
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl284,201,664 - 84,231,418 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845001880   ⟹   ENSCAFP00845001480
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl284,202,282 - 84,231,418 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845001895   ⟹   ENSCAFP00845001490
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl284,204,292 - 84,211,674 (-)Ensembl
RefSeq Acc Id: NM_001003220   ⟹   NP_001003220
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1283,552,735 - 83,581,375 (-)NCBI
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
Sequence:
RefSeq Acc Id: NP_001003220   ⟸   NM_001003220
- Peptide Label: precursor
- UniProtKB: Q95152 (UniProtKB/Swiss-Prot),   A0A8I3MXX5 (UniProtKB/TrEMBL),   A0A8P0PGM8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000024086   ⟸   ENSCAFT00000025944
RefSeq Acc Id: ENSCAFP00000033330   ⟸   ENSCAFT00000037744
RefSeq Acc Id: ENSCAFP00000036264   ⟸   ENSCAFT00000046205
RefSeq Acc Id: ENSCAFP00845001471   ⟸   ENSCAFT00845001867
RefSeq Acc Id: ENSCAFP00845001490   ⟸   ENSCAFT00845001895
RefSeq Acc Id: ENSCAFP00845001480   ⟸   ENSCAFT00845001880

Promoters
RGD ID:13682647
Promoter ID:EPDNEW_C716
Type:single initiation site
Name:PDPN_1
Description:podoplanin precursor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1283,581,395 - 83,581,455EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000016363 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030015564 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSCAFG00040004415 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSCAFG00845001081 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000025944.5 UniProtKB/TrEMBL
  ENSCAFT00000037744.3 UniProtKB/TrEMBL
  ENSCAFT00000046205.4 UniProtKB/TrEMBL
  ENSCAFT00000104156.1 UniProtKB/TrEMBL
  ENSCAFT00030028693.1 UniProtKB/Swiss-Prot
  ENSCAFT00030028775.1 UniProtKB/TrEMBL
  ENSCAFT00030028852.1 UniProtKB/TrEMBL
  ENSCAFT00030028912.1 UniProtKB/TrEMBL
  ENSCAFT00040008380.1 UniProtKB/Swiss-Prot
  ENSCAFT00040008401.1 UniProtKB/Swiss-Prot
  ENSCAFT00040008422.1 UniProtKB/TrEMBL
  ENSCAFT00040008443.1 UniProtKB/TrEMBL
  ENSCAFT00040008457.1 UniProtKB/TrEMBL
  ENSCAFT00845001867 ENTREZGENE
  ENSCAFT00845001867.1 UniProtKB/TrEMBL
  ENSCAFT00845001880.1 UniProtKB/TrEMBL
  ENSCAFT00845001895.1 UniProtKB/TrEMBL
KEGG Report cfa:403886 UniProtKB/Swiss-Prot
NCBI Gene PDPN ENTREZGENE
PANTHER PODOPLANIN UniProtKB/Swiss-Prot
  PODOPLANIN UniProtKB/Swiss-Prot
  PODOPLANIN UniProtKB/TrEMBL
  PODOPLANIN UniProtKB/TrEMBL
Pfam Podoplanin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8C0NKR6_CANLF UniProtKB/TrEMBL
  A0A8C0NNW0_CANLF UniProtKB/TrEMBL
  A0A8C0Q2J4_CANLF UniProtKB/TrEMBL
  A0A8C0QDX3_CANLF UniProtKB/TrEMBL
  A0A8C0QHH8_CANLF UniProtKB/TrEMBL
  A0A8I3MDH5_CANLF UniProtKB/TrEMBL
  A0A8I3MJJ4_CANLF UniProtKB/TrEMBL
  A0A8I3MXX5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0NM74_CANLF UniProtKB/TrEMBL
  A0A8P0PGM8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0SKM9_CANLF UniProtKB/TrEMBL
  PDPN_CANLF UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A0A8P0SRF2 UniProtKB/TrEMBL
VGNC ID VGNC:52226 ENTREZGENE