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 ciliary membrane and 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 8. 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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81487,766,745 - 87,888,647 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1487,760,208 - 87,852,259 (-)EnsemblGRCr8
mRatBN7.21483,552,964 - 83,670,062 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1483,545,469 - 83,638,498 (-)EnsemblmRatBN7.2
Rnor_6.01489,047,949 - 89,193,579 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1489,060,447 - 89,179,507 (-)Ensemblrn6Rnor6.0
Rnor_5.01488,849,130 - 88,972,494 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41489,228,061 - 89,410,326 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1482,589,392 - 82,724,417 (-)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1487,760,208 - 87,852,259 (-)EnsemblGRCr8
mRatBN7.21483,552,964 - 83,670,062 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1483,545,469 - 83,638,498 (-)EnsemblmRatBN7.2
Rnor_6.01489,047,949 - 89,193,579 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1489,060,447 - 89,179,507 (-)Ensemblrn6Rnor6.0
Rnor_5.01488,849,130 - 88,972,494 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41489,228,061 - 89,410,326 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
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 (-)Ensemblhg38GRCh38
GRCh37747,814,212 - 47,988,063 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36747,780,815 - 47,954,562 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm38118,825,696 - 8,974,709 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl118,826,708 - 8,973,266 (-)Ensemblmm10GRCm38
MGSCv37118,726,711 - 8,881,423 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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
ChiLan1.0 EnsemblNW_0049554565,510,654 - 5,573,399 (+)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01697,085 - 177,041 (+)NCBIROS_Cfam_1.0ROS_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 (-)EnsemblSpeTri2.0 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 1.0HetGla 1.0hetGla2
Pkd1l1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11177,866,738 - 78,043,077 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pkd1l1
940 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1459848686104848686Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147764007196755654Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)1484164970100078267Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1477914838104348525Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1433424686102238540Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1474255551109089856Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147764007196755654Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1462398852107398852Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1477640071100078267Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1460854936105854936Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1474255551109089856Rat
4889951Bss92Bone structure and strength QTL 923.9tibia area (VT:1000281)tibia-fibula cortical bone total cross-sectional area (CMO:0001721)1486271332100078267Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147764007196755654Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1459848686104848686Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147764007196755654Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144261625899224555Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)146592028399224555Rat

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
GRCr81487,674,410 - 87,674,605 (+)Marker Load Pipeline
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_v3.41489,301,667 - 89,301,862RGDRGSC3.4
RGSC_v3.41489,301,668 - 89,301,862UniSTSRGSC3.4
Celera1482,498,754 - 82,498,948UniSTS
RGSC_v3.11489,320,813 - 89,321,007RGD
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
Celera1482,509,281 - 82,509,422UniSTS
RGSC_v3.11489,331,432 - 89,331,573RGD
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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
6 6 58 119 59 56 27 54 27 5 232 139 8 98 55 89 29 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000006498   ⟹   ENSRNOP00000006498
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1487,760,208 - 87,852,259 (-)Ensembl
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
Ensembl Acc Id: ENSRNOP00000006498   ⟸   ENSRNOT00000006498
RefSeq Acc Id: XP_063129791   ⟸   XM_063273721
Protein Domains
GAIN-B   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 ENSRNOT00000006498.9 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  PLAT/LH2 domain UniProtKB/TrEMBL
InterPro GAIN_B UniProtKB/TrEMBL
  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 GAIN_B UniProtKB/TrEMBL
  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