Pkd2l2 (polycystin 2 like 2, transient receptor potential cation channel) - Rat Genome Database

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Gene: Pkd2l2 (polycystin 2 like 2, transient receptor potential cation channel) Rattus norvegicus
Analyze
Symbol: Pkd2l2
Name: polycystin 2 like 2, transient receptor potential cation channel
RGD ID: 1310272
Description: Predicted to enable calcium channel activity. Predicted to be involved in detection of mechanical stimulus. Predicted to be active in membrane. Orthologous to human PKD2L2 (polycystin 2 like 2, transient receptor potential cation channel); INTERACTS WITH bisphenol A; cocaine; 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC291683; polycystic kidney disease 2-like 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21826,007,789 - 26,042,428 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1826,007,797 - 26,042,428 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1826,135,200 - 26,169,822 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01826,898,234 - 26,933,379 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01826,233,139 - 26,268,285 (+)NCBIRnor_WKY
Rnor_6.01827,190,661 - 27,225,488 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1827,190,974 - 27,225,488 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01826,904,093 - 26,938,848 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41826,876,459 - 26,911,433 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11826,884,533 - 26,934,194 (+)NCBI
Celera1825,748,845 - 25,782,225 (+)NCBICelera
Cytogenetic Map18p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IBA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Pkd2l2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21826,007,789 - 26,042,428 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1826,007,797 - 26,042,428 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1826,135,200 - 26,169,822 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01826,898,234 - 26,933,379 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01826,233,139 - 26,268,285 (+)NCBIRnor_WKY
Rnor_6.01827,190,661 - 27,225,488 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1827,190,974 - 27,225,488 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01826,904,093 - 26,938,848 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41826,876,459 - 26,911,433 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11826,884,533 - 26,934,194 (+)NCBI
Celera1825,748,845 - 25,782,225 (+)NCBICelera
Cytogenetic Map18p12NCBI
PKD2L2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385137,889,457 - 137,942,747 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl5137,887,968 - 137,942,747 (+)EnsemblGRCh38hg38GRCh38
GRCh375137,225,146 - 137,278,436 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365137,253,024 - 137,304,055 (+)NCBINCBI36Build 36hg18NCBI36
Build 345137,253,056 - 137,304,055NCBI
Celera5133,347,422 - 133,398,422 (+)NCBICelera
Cytogenetic Map5q31.2NCBI
HuRef5132,416,943 - 132,467,932 (+)NCBIHuRef
CHM1_15136,657,755 - 136,708,732 (+)NCBICHM1_1
T2T-CHM13v2.05138,415,893 - 138,469,143 (+)NCBIT2T-CHM13v2.0
Pkd2l2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391834,541,553 - 34,575,842 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1834,541,542 - 34,577,169 (+)EnsemblGRCm39 Ensembl
GRCm381834,408,501 - 34,442,798 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1834,408,489 - 34,444,116 (+)EnsemblGRCm38mm10GRCm38
MGSCv371834,569,077 - 34,602,443 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361834,534,224 - 34,567,599 (+)NCBIMGSCv36mm8
Celera1834,865,542 - 34,898,850 (+)NCBICelera
Cytogenetic Map18B1NCBI
Pkd2l2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554182,439,773 - 2,488,916 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554182,443,557 - 2,488,860 (-)NCBIChiLan1.0ChiLan1.0
PKD2L2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15139,413,548 - 139,466,056 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5139,416,606 - 139,459,732 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05133,276,223 - 133,329,712 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PKD2L2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11125,594,327 - 25,628,262 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1125,594,394 - 25,628,509 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1124,358,304 - 24,392,241 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01126,444,314 - 26,478,229 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1126,444,376 - 26,476,209 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11125,151,973 - 25,185,898 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01124,975,686 - 25,009,595 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01125,638,396 - 25,672,574 (+)NCBIUU_Cfam_GSD_1.0
Pkd2l2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213154,462,731 - 154,495,840 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365317,115,718 - 7,152,010 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PKD2L2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2139,920,583 - 139,956,432 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12139,920,552 - 139,956,509 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22145,643,547 - 145,683,961 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PKD2L2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12340,569,225 - 40,611,967 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2340,569,281 - 40,611,884 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603437,279,173 - 37,320,400 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pkd2l2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474330,743,052 - 30,771,305 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474330,743,052 - 30,770,985 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pkd2l2
214 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:65
Count of miRNA genes:49
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000037690
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
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18130558703Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134291613Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134291613Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135374722Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18142547119Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18420794160377792Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18518585840503530Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181179151863636873Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181179151883218561Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181179151883218561Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194179131393320Rat
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181194179131393320Rat
12904690Cm129Cardiac mass QTL 1290.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)181194427326548295Rat
12904689Cm128Cardiac mass QTL 1280.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)181194427326548295Rat
12904693Am20Aortic mass QTL 200.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)181194427326548295Rat
12904695Kidm73Kidney mass QTL 730.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)181194427326548295Rat
12904691Cm130Cardiac mass QTL 1300.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)181194427326548295Rat
12904680Bw189Body weight QTL 1890.019body mass (VT:0001259)body weight (CMO:0000012)181194427326548295Rat
2301410Bp317Blood pressure QTL 3170.004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181194427326548295Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181194429931359530Rat
61375Bp41Blood pressure QTL 412.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)181194429941122201Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194429952293055Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181194429959330563Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181194454459796478Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181495133759951337Rat
1358193Emca2Estrogen-induced mammary cancer QTL 21.6mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)181800759963571040Rat
1331735Rf44Renal function QTL 442.981total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181823456431359530Rat
1331775Bp235Blood pressure QTL 2353.201arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181823456431359530Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181927890183218561Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182137289383213037Rat
1641923Colcr8Colorectal carcinoma resistance QTL 83.10.0014intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)182206624252293055Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182479697779788953Rat
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182557098570570985Rat

Markers in Region
RH133590  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,041,040 - 26,041,246 (+)MAPPERmRatBN7.2
Rnor_6.01827,224,101 - 27,224,306NCBIRnor6.0
Rnor_5.01826,937,461 - 26,937,666UniSTSRnor5.0
RGSC_v3.41826,910,046 - 26,910,251UniSTSRGSC3.4
Celera1825,780,838 - 25,781,043UniSTS
RH 3.4 Map18364.1UniSTS
Cytogenetic Map18p12UniSTS
AI101820  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,022,809 - 26,023,000 (+)MAPPERmRatBN7.2
Rnor_6.01827,205,954 - 27,206,144NCBIRnor6.0
Rnor_5.01826,919,407 - 26,919,597UniSTSRnor5.0
RGSC_v3.41826,891,129 - 26,891,319UniSTSRGSC3.4
Celera1825,762,348 - 25,762,538UniSTS
RH 3.4 Map18364.5UniSTS
Cytogenetic Map18p12UniSTS
AI101820  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21826,022,845 - 26,023,000 (+)MAPPERmRatBN7.2
Rnor_6.01827,205,990 - 27,206,144NCBIRnor6.0
Rnor_5.01826,919,443 - 26,919,597UniSTSRnor5.0
RGSC_v3.41826,891,165 - 26,891,319UniSTSRGSC3.4
Celera1825,762,384 - 25,762,538UniSTS
RH 3.4 Map18364.5UniSTS
Cytogenetic Map18p12UniSTS


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 6
Low 2 16 19 8 21 28 11
Below cutoff 1 15 17 17 17 8 9 14 14 7 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000037690   ⟹   ENSRNOP00000030483
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1826,007,797 - 26,042,428 (+)Ensembl
Rnor_6.0 Ensembl1827,190,974 - 27,225,488 (+)Ensembl
RefSeq Acc Id: NM_001106156   ⟹   NP_001099626
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21826,007,797 - 26,042,428 (+)NCBI
Rnor_6.01827,190,974 - 27,225,488 (+)NCBI
Rnor_5.01826,904,093 - 26,938,848 (+)NCBI
RGSC_v3.41826,876,459 - 26,911,433 (+)RGD
Celera1825,748,845 - 25,782,225 (+)RGD
Sequence:
RefSeq Acc Id: XM_008772027   ⟹   XP_008770249
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21826,007,789 - 26,039,061 (+)NCBI
Rnor_6.01827,190,661 - 27,222,800 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001099626 (Get FASTA)   NCBI Sequence Viewer  
  XP_008770249 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76225 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099626   ⟸   NM_001106156
- UniProtKB: D4A828 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770249   ⟸   XM_008772027
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000030483   ⟸   ENSRNOT00000037690
Protein Domains
PKD_channel

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A828-F1-model_v2 AlphaFold D4A828 1-621 view protein structure

Transcriptome

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

Promoters
RGD ID:13700692
Promoter ID:EPDNEW_R11216
Type:single initiation site
Name:Pkd2l2_1
Description:polycystin 2 like 2, transient receptor potential cation channel
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_6.01827,190,986 - 27,191,046EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310272 AgrOrtholog
BioCyc Gene G2FUF-7958 BioCyc
Ensembl Genes ENSRNOG00000025489 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000030483 ENTREZGENE
  ENSRNOP00000030483.3 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037690 ENTREZGENE
  ENSRNOT00000037690.4 UniProtKB/TrEMBL
InterPro PKD1_2_channel UniProtKB/TrEMBL
  PKD_2 UniProtKB/TrEMBL
KEGG Report rno:291683 UniProtKB/TrEMBL
NCBI Gene 291683 ENTREZGENE
Pfam PKD_channel UniProtKB/TrEMBL
PhenoGen Pkd2l2 PhenoGen
PRINTS POLYCYSTIN2 UniProtKB/TrEMBL
UniProt D4A828 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-03 Pkd2l2  polycystin 2 like 2, transient receptor potential cation channel  Pkd2l2  polycystic kidney disease 2-like 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Pkd2l2  polycystic kidney disease 2-like 2   Pkd2l2_predicted  polycystic kidney disease 2-like 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pkd2l2_predicted  polycystic kidney disease 2-like 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED