Pkd1l1 (polycystin 1 like 1, transient receptor potential channel interacting) - Rat Genome Database

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Gene: Pkd1l1 (polycystin 1 like 1, transient receptor potential channel interacting) Rattus norvegicus
Analyze
Symbol: Pkd1l1
Name: polycystin 1 like 1, transient receptor potential channel interacting
RGD ID: 1564724
Description: Predicted to enable calcium channel activity. Predicted to be involved in detection of mechanical stimulus; detection of nodal flow; and left/right axis specification. Predicted to act upstream of or within determination of left/right symmetry and heart development. Predicted to be located in non-motile cilium. Predicted to be part of calcium channel complex. Predicted to be active in membrane. Human ortholog(s) of this gene implicated in visceral heterotaxy. Orthologous to human PKD1L1 (polycystin 1 like 1, transient receptor potential channel interacting); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC289796; polycystic kidney disease 1 like 1; polycystic kidney disease protein 1-like 1; polycystin-1-like protein 1; RGD1564724; RGD1566034; similar to polycystic kidney disease 1 like 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
GRCr81487,766,745 - 87,888,647 (-)NCBIGRCr8
mRatBN7.21483,552,964 - 83,670,062 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1483,545,469 - 83,638,498 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01489,047,949 - 89,193,579 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1489,060,447 - 89,179,507 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01488,849,130 - 88,972,494 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41489,228,061 - 89,410,326 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1482,589,392 - 82,724,417 (-)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Situs inversus in Dpcd/Poll-/-, Nme7-/- , and Pkd1l1-/- mice. Vogel P, etal., Vet Pathol. 2010 Jan;47(1):120-31. doi: 10.1177/0300985809353553.
5. Genetic risk for ischemic and hemorrhagic stroke. Yamada Y, etal., Arterioscler Thromb Vasc Biol. 2006 Aug;26(8):1920-5. doi: 10.1161/01.ATV.0000229694.97827.38. Epub 2006 Jun 1.
Additional References at PubMed
PMID:21307093   PMID:24336289   PMID:25807483  


Genomics

Comparative Map Data
Pkd1l1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81487,766,745 - 87,888,647 (-)NCBIGRCr8
mRatBN7.21483,552,964 - 83,670,062 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1483,545,469 - 83,638,498 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01489,047,949 - 89,193,579 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1489,060,447 - 89,179,507 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01488,849,130 - 88,972,494 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41489,228,061 - 89,410,326 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1482,589,392 - 82,724,417 (-)NCBICelera
Cytogenetic Map14q21NCBI
PKD1L1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38747,774,614 - 47,960,906 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl747,740,202 - 47,948,466 (-)EnsemblGRCh38hg38GRCh38
GRCh37747,814,212 - 47,988,063 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36747,780,815 - 47,954,562 (-)NCBINCBI36Build 36hg18NCBI36
Build 34747,587,529 - 47,761,277NCBI
Celera747,912,632 - 48,087,291 (-)NCBICelera
Cytogenetic Map7p12.3NCBI
HuRef747,698,276 - 47,873,587 (-)NCBIHuRef
CHM1_1747,818,258 - 47,991,724 (-)NCBICHM1_1
T2T-CHM13v2.0747,937,113 - 48,116,591 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2747,854,508 - 48,027,995 (-)NCBI
Pkd1l1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39118,782,025 - 8,924,365 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl118,776,708 - 8,938,709 (-)EnsemblGRCm39 Ensembl
GRCm38118,825,696 - 8,974,709 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl118,826,708 - 8,973,266 (-)EnsemblGRCm38mm10GRCm38
MGSCv37118,726,711 - 8,881,423 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36118,726,711 - 8,881,423 (-)NCBIMGSCv36mm8
MGSCv36118,736,930 - 8,767,599 (-)NCBIMGSCv36mm8
Celera119,268,831 - 9,406,931 (-)NCBICelera
Cytogenetic Map11A1NCBI
cM Map115.57NCBI
Pkd1l1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554565,497,126 - 5,582,342 (+)NCBIChiLan1.0ChiLan1.0
PKD1L1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2652,578,177 - 52,841,380 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan17100,903,063 - 101,166,113 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0748,451,329 - 48,596,991 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1748,527,430 - 48,705,584 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl748,545,432 - 48,701,736 (-)Ensemblpanpan1.1panPan2
PKD1L1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.116119,639 - 199,418 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha16893,327 - 958,041 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01697,085 - 177,041 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl16101,949 - 177,151 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11696,459 - 170,974 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01630,109 - 106,117 (+)NCBIUNSW_CanFamBas_1.0
Pkd1l1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118103,047,006 - 103,171,182 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647822,262,017 - 22,347,643 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647822,255,887 - 22,389,477 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PKD1L1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12110,850,618 - 11,030,099 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606211,146,495 - 11,367,241 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pkd1l1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247405,619,253 - 5,703,032 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pkd1l1
673 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:80
Interacting mature miRNAs:87
Transcripts:ENSRNOT00000006498
Prediction methods:Microtar, Miranda, Rnahybrid, 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
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)147995092195876975Rat
4889951Bss92Bone structure and strength QTL 923.9tibia area (VT:1000281)tibia-fibula cortical bone total cross-sectional area (CMO:0001721)148205747195876975Rat

Markers in Region
D14Mit15  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21483,610,680 - 83,610,873 (+)MAPPERmRatBN7.2
Rnor_6.01489,117,072 - 89,117,264NCBIRnor6.0
Rnor_5.01488,913,990 - 88,914,182UniSTSRnor5.0
Celera1482,646,677 - 82,646,869UniSTS
Cytogenetic Map14q21UniSTS
D14Rat51  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21483,460,635 - 83,460,830 (+)MAPPERmRatBN7.2
Rnor_6.01488,963,427 - 88,963,621NCBIRnor6.0
Rnor_5.01488,762,363 - 88,762,557UniSTSRnor5.0
RGSC_v3.41489,301,668 - 89,301,862UniSTSRGSC3.4
RGSC_v3.41489,301,667 - 89,301,862RGDRGSC3.4
RGSC_v3.11489,320,813 - 89,321,007RGD
Celera1482,498,754 - 82,498,948UniSTS
RH 3.4 Map14610.8UniSTS
RH 3.4 Map14610.8RGD
RH 2.0 Map14727.0RGD
SHRSP x BN Map1449.49RGD
FHH x ACI Map1464.88RGD
Cytogenetic Map14q21UniSTS
D14Rat67  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21483,471,255 - 83,471,397 (+)MAPPERmRatBN7.2
Rnor_6.01488,974,044 - 88,974,185NCBIRnor6.0
Rnor_5.01488,772,980 - 88,773,121UniSTSRnor5.0
RGSC_v3.41489,312,286 - 89,312,428RGDRGSC3.4
RGSC_v3.41489,312,287 - 89,312,428UniSTSRGSC3.4
RGSC_v3.11489,331,432 - 89,331,573RGD
Celera1482,509,281 - 82,509,422UniSTS
RH 3.4 Map14623.3RGD
RH 3.4 Map14623.3UniSTS
RH 2.0 Map14742.7RGD
FHH x ACI Map1464.8499RGD
Cytogenetic Map14q21UniSTS
BE119538  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21483,582,772 - 83,582,953 (+)MAPPERmRatBN7.2
Rnor_6.01489,089,176 - 89,089,356NCBIRnor6.0
Rnor_5.01488,886,241 - 88,886,421UniSTSRnor5.0
RGSC_v3.41489,373,593 - 89,373,773UniSTSRGSC3.4
Celera1482,619,035 - 82,619,215UniSTS
RH 3.4 Map14620.5UniSTS
Cytogenetic Map14q21UniSTS
G46230  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21483,493,012 - 83,493,246 (+)MAPPERmRatBN7.2
Rnor_6.01488,995,722 - 88,995,955NCBIRnor6.0
Rnor_5.01488,792,532 - 88,792,765UniSTSRnor5.0
RGSC_v3.41489,332,661 - 89,332,894UniSTSRGSC3.4
Celera1482,529,621 - 82,529,872UniSTS
Cytogenetic Map14q21UniSTS


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

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
Low 13 2 6
Below cutoff 27 30 14 17 14 5 5 53 26 33 9 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006498   ⟹   ENSRNOP00000006498
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1483,545,469 - 83,638,498 (-)Ensembl
Rnor_6.0 Ensembl1489,060,447 - 89,179,507 (-)Ensembl
RefSeq Acc Id: XM_063273721   ⟹   XP_063129791
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81487,766,745 - 87,888,647 (-)NCBI
Protein Sequences
Protein RefSeqs XP_063129791 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL76032 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006498.8
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000006498   ⟸   ENSRNOT00000006498
RefSeq Acc Id: XP_063129791   ⟸   XM_063273721
Protein Domains
PLAT   REJ

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M1X0-F1-model_v2 AlphaFold F1M1X0 1-2605 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564724 AgrOrtholog
BioCyc Gene G2FUF-15027 BioCyc
Ensembl Genes ENSRNOG00000004865 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006498.8 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  PLAT/LH2 domain UniProtKB/TrEMBL
InterPro Ig-like_fold UniProtKB/TrEMBL
  LipOase_LH2 UniProtKB/TrEMBL
  PKD/REJ-like UniProtKB/TrEMBL
  PLAT/LH2_dom_sf UniProtKB/TrEMBL
  PLAT_polycystin1 UniProtKB/TrEMBL
  Polycystin_dom UniProtKB/TrEMBL
  REJ-like UniProtKB/TrEMBL
NCBI Gene 289796 ENTREZGENE
PANTHER POLYCYSTIC KIDNEY DISEASE PROTEIN 1-LIKE 1 UniProtKB/TrEMBL
  POLYCYSTIN-1 UniProtKB/TrEMBL
Pfam PLAT UniProtKB/TrEMBL
  Polycystin_dom UniProtKB/TrEMBL
  REJ UniProtKB/TrEMBL
PhenoGen Pkd1l1 PhenoGen
PROSITE PLAT UniProtKB/TrEMBL
  REJ UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004865 RatGTEx
SMART LH2 UniProtKB/TrEMBL
Superfamily-SCOP Lipase_LipOase UniProtKB/TrEMBL
UniProt F1M1X0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-03 Pkd1l1  polycystin 1 like 1, transient receptor potential channel interacting  Pkd1l1  polycystic kidney disease 1 like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Pkd1l1  polycystic kidney disease 1 like 1  RGD1564724_predicted  similar to polycystic kidney disease 1 like 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1564724_predicted  similar to polycystic kidney disease 1 like 1 (predicted)  LOC289796  similar to polycystic kidney disease 1 like 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC289796  similar to polycystic kidney disease 1 like 1      Symbol and Name status set to provisional 70820 PROVISIONAL