PKD2 (polycystin 2, transient receptor potential cation channel) - Rat Genome Database

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Gene: PKD2 (polycystin 2, transient receptor potential cation channel) Canis lupus familiaris
Analyze
Symbol: PKD2
Name: polycystin 2, transient receptor potential cation channel
RGD ID: 12219657
Description: ENCODES a protein that exhibits alpha-actinin binding (ortholog); calcium channel activity (ortholog); muscle alpha-actinin binding (ortholog); INVOLVED IN calcium ion transport (ortholog); cell surface receptor signaling pathway (ortholog); cell surface receptor signaling pathway via JAK-STAT (ortholog); ASSOCIATED WITH acute kidney failure (ortholog); autosomal dominant polycystic kidney disease (ortholog); autosomal recessive polycystic kidney disease (ortholog); FOUND IN microtubule cytoskeleton (ortholog); polycystin complex (ortholog); spindle microtubule (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: PC2; polycystin-2
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
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13211,383,441 - 11,437,603 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3211,383,424 - 11,435,438 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3230,517,045 - 30,571,324 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03211,435,888 - 11,490,399 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3211,435,683 - 11,490,397 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13211,519,719 - 11,571,825 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03211,345,806 - 11,399,834 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03228,555,188 - 28,609,469 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aorta development  (IEA)
branching involved in ureteric bud morphogenesis  (IEA)
calcium ion transmembrane transport  (IEA)
calcium ion transport  (IEA,ISO)
calcium-mediated signaling  (IEA)
cell surface receptor signaling pathway  (ISO)
cell surface receptor signaling pathway via JAK-STAT  (IEA,ISO)
cellular response to calcium ion  (IEA)
cellular response to cAMP  (IEA)
cellular response to fluid shear stress  (IEA)
cellular response to hydrostatic pressure  (IEA)
cellular response to osmotic stress  (IEA)
cilium organization  (IEA,ISO)
detection of mechanical stimulus  (IEA,ISO)
detection of nodal flow  (IEA)
determination of left/right symmetry  (IEA,ISO)
determination of liver left/right asymmetry  (IEA)
embryonic placenta development  (IEA,ISO)
establishment of localization in cell  (IEA,ISO)
heart development  (IEA,ISO)
heart looping  (IEA)
inorganic cation transmembrane transport  (IEA)
intracellular calcium ion homeostasis  (IEA,ISO)
kidney development  (IEA,ISO)
liver development  (IEA,ISO)
mesonephric duct development  (IEA)
mesonephric tubule development  (IEA)
metanephric ascending thin limb development  (IEA)
metanephric cortex development  (IEA)
metanephric cortical collecting duct development  (IEA)
metanephric distal tubule development  (IEA)
metanephric mesenchyme development  (IEA)
metanephric part of ureteric bud development  (IEA)
metanephric S-shaped body morphogenesis  (IEA)
metanephric smooth muscle tissue development  (IEA)
negative regulation of G1/S transition of mitotic cell cycle  (IEA,ISO)
neural tube development  (IEA)
placenta blood vessel development  (IEA)
positive regulation of cytosolic calcium ion concentration  (ISO)
positive regulation of gene expression  (IEA)
positive regulation of nitric oxide biosynthetic process  (IEA)
positive regulation of transcription by RNA polymerase II  (IEA)
potassium ion transmembrane transport  (IEA)
protein heterotetramerization  (IEA)
protein homotetramerization  (IEA)
protein tetramerization  (IEA)
regulation of calcium ion import  (IEA)
regulation of cell cycle  (IEA,ISO)
regulation of cell population proliferation  (IEA)
release of sequestered calcium ion into cytosol  (IEA,ISO)
renal artery morphogenesis  (IEA)
renal tubule morphogenesis  (IEA)
sodium ion transmembrane transport  (IEA)
spinal cord development  (IEA)
Wnt signaling pathway  (IEA)

References
Additional References at PubMed
PMID:16978192   PMID:17283055   PMID:19726544   PMID:19801576   PMID:20881056   PMID:22301074   PMID:23390129   PMID:24116661   PMID:24459142   PMID:30032202  


Genomics

Comparative Map Data
PKD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13211,383,441 - 11,437,603 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3211,383,424 - 11,435,438 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3230,517,045 - 30,571,324 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03211,435,888 - 11,490,399 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3211,435,683 - 11,490,397 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13211,519,719 - 11,571,825 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03211,345,806 - 11,399,834 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03228,555,188 - 28,609,469 (-)NCBIUU_Cfam_GSD_1.0
PKD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38488,007,635 - 88,077,777 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl488,007,635 - 88,077,777 (+)EnsemblGRCh38hg38GRCh38
GRCh37488,928,787 - 88,998,929 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36489,147,844 - 89,217,953 (+)NCBINCBI36Build 36hg18NCBI36
Build 34489,285,998 - 89,356,107NCBI
Celera486,220,746 - 86,290,863 (+)NCBICelera
Cytogenetic Map4q22.1NCBI
HuRef484,675,256 - 84,745,398 (+)NCBIHuRef
CHM1_1488,905,594 - 88,975,728 (+)NCBICHM1_1
T2T-CHM13v2.0491,334,123 - 91,404,269 (+)NCBIT2T-CHM13v2.0
Pkd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395104,599,379 - 104,653,685 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5104,607,316 - 104,653,685 (+)EnsemblGRCm39 Ensembl
GRCm385104,453,982 - 104,505,819 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5104,459,450 - 104,505,819 (+)EnsemblGRCm38mm10GRCm38
MGSCv375104,888,476 - 104,934,838 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365104,699,856 - 104,746,118 (+)NCBIMGSCv36mm8
Celera5101,769,092 - 101,817,838 (+)NCBICelera
Cytogenetic Map5E5NCBI
cM Map550.68NCBI
Pkd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8145,541,821 - 5,585,140 (-)NCBIGRCr8
mRatBN7.2145,237,135 - 5,280,455 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl145,237,135 - 5,280,825 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx145,198,260 - 5,241,484 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0146,498,456 - 6,541,680 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0145,192,618 - 5,233,125 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0146,602,004 - 6,645,257 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl146,602,004 - 6,645,257 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0146,581,342 - 6,624,595 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4146,349,519 - 6,392,988 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera145,376,651 - 5,418,198 (-)NCBICelera
Cytogenetic Map14p22NCBI
Pkd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554741,833,701 - 1,868,817 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554741,831,221 - 1,868,170 (-)NCBIChiLan1.0ChiLan1.0
PKD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2386,009,202 - 86,079,254 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1486,271,612 - 86,341,660 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0480,295,243 - 80,365,271 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1491,019,739 - 91,088,858 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl491,019,734 - 91,086,775 (+)Ensemblpanpan1.1panPan2
Pkd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244052851,657,007 - 1,709,229 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493690576,781 - 128,995 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PKD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8131,005,407 - 131,058,932 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18131,002,973 - 131,058,932 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28140,233,075 - 140,289,084 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PKD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1736,369,226 - 36,445,713 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl736,369,524 - 36,443,612 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603715,121,642 - 15,193,435 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pkd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248724,539,847 - 4,594,793 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248724,539,965 - 4,592,004 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in PKD2
674 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 4 16 3 6 12 10 6
Low 1 5 6 6 3 6 6 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000015243   ⟹   ENSCAFP00000014105
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl3211,383,424 - 11,435,438 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845028895   ⟹   ENSCAFP00845022734
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl3211,435,683 - 11,490,397 (+)Ensembl
RefSeq Acc Id: XM_022413656   ⟹   XP_022269364
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.13211,383,441 - 11,437,603 (+)NCBI
Dog10K_Boxer_Tasha3230,517,045 - 30,571,324 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038444090   ⟹   XP_038300018
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.03211,435,888 - 11,490,399 (+)NCBI
RefSeq Acc Id: XM_038518483   ⟹   XP_038374411
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.13211,519,719 - 11,571,825 (+)NCBI
RefSeq Acc Id: XM_038582181   ⟹   XP_038438109
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.03228,555,188 - 28,609,469 (-)NCBI
RefSeq Acc Id: XM_038646419   ⟹   XP_038502347
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.03211,345,806 - 11,399,834 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_022269364   ⟸   XM_022413656
- UniProtKB: A0A8I3NZH4 (UniProtKB/TrEMBL),   A0A8P0SEP7 (UniProtKB/TrEMBL),   A0A8C0PIY8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000014105   ⟸   ENSCAFT00000015243
RefSeq Acc Id: XP_038374411   ⟸   XM_038518483
RefSeq Acc Id: XP_038502347   ⟸   XM_038646419
RefSeq Acc Id: XP_038300018   ⟸   XM_038444090
- UniProtKB: A0A8I3NZH4 (UniProtKB/TrEMBL),   A0A8P0SEP7 (UniProtKB/TrEMBL),   A0A8C0PIY8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038438109   ⟸   XM_038582181
- UniProtKB: A0A8C0PIY8 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845022734   ⟸   ENSCAFT00845028895
Protein Domains
EF-hand


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000009595 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030025852 UniProtKB/TrEMBL
  ENSCAFG00845016245 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000015243.5 UniProtKB/TrEMBL
  ENSCAFT00030047736.1 UniProtKB/TrEMBL
  ENSCAFT00845028895 ENTREZGENE
  ENSCAFT00845028895.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.70 UniProtKB/TrEMBL
  1.20.120.350 UniProtKB/TrEMBL
  1.20.5.340 UniProtKB/TrEMBL
  EF-hand UniProtKB/TrEMBL
InterPro EF-hand-dom_pair UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/TrEMBL
  PKD1_2_channel UniProtKB/TrEMBL
  PKD_2 UniProtKB/TrEMBL
  Polycystin_dom UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/TrEMBL
NCBI Gene PKD2 ENTREZGENE
PANTHER POLYCYSTIN FAMILY MEMBER UniProtKB/TrEMBL
  POLYCYSTIN-2 UniProtKB/TrEMBL
Pfam Fer4_24 UniProtKB/TrEMBL
  PKD_channel UniProtKB/TrEMBL
  Polycystin_dom UniProtKB/TrEMBL
PRINTS POLYCYSTIN2 UniProtKB/TrEMBL
PROSITE EF_HAND_2 UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/TrEMBL
  Voltage-gated potassium channels UniProtKB/TrEMBL
UniProt A0A8C0PIY8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NZH4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0SEP7 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:44600 ENTREZGENE