Pkd1l3 (polycystin 1 like 3, transient receptor potential channel interacting) - Rat Genome Database

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Gene: Pkd1l3 (polycystin 1 like 3, transient receptor potential channel interacting) Rattus norvegicus
Analyze
Symbol: Pkd1l3
Name: polycystin 1 like 3, transient receptor potential channel interacting
RGD ID: 2324490
Description: Predicted to enable calcium channel activity and transmembrane transporter binding activity. Predicted to contribute to monoatomic cation channel activity and sour taste receptor activity. Predicted to be involved in several processes, including cellular response to acidic pH; detection of chemical stimulus involved in sensory perception of sour taste; and detection of mechanical stimulus. Predicted to be located in plasma membrane. Predicted to be part of cation channel complex and receptor complex. Predicted to be active in membrane. Predicted to colocalize with cell surface. Orthologous to human PKD1L3 (polycystin 1 like 3, transient receptor potential channel interacting); INTERACTS WITH aflatoxin B1; 4,4'-sulfonyldiphenol (ortholog); aristolochic acid A (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC100362565; polycystic kidney disease 1 like 3; polycystic kidney disease 1 like 3-like; polycystic kidney disease 1-like 3; polycystic kidney disease protein 1-like 3; polycystin-1-like protein 3
RGD Orthologs
Human
Mouse
Bonobo
Dog
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
GRCr81954,494,529 - 54,559,596 (+)NCBIGRCr8
mRatBN7.21937,585,564 - 37,650,083 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1937,585,725 - 37,650,155 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01941,990,249 - 42,054,390 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1941,989,650 - 42,054,018 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01952,814,619 - 52,879,420 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41939,489,363 - 39,555,398 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1936,990,385 - 37,053,340 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16891422   PMID:19056867   PMID:19812697   PMID:20538909   PMID:20605874  


Genomics

Comparative Map Data
Pkd1l3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81954,494,529 - 54,559,596 (+)NCBIGRCr8
mRatBN7.21937,585,564 - 37,650,083 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1937,585,725 - 37,650,155 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01941,990,249 - 42,054,390 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1941,989,650 - 42,054,018 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01952,814,619 - 52,879,420 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41939,489,363 - 39,555,398 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1936,990,385 - 37,053,340 (+)NCBICelera
Cytogenetic Map19q12NCBI
PKD1L3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381671,929,538 - 72,000,402 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1671,929,538 - 72,000,402 (-)EnsemblGRCh38hg38GRCh38
GRCh371671,963,441 - 72,034,301 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361670,520,395 - 70,591,378 (-)NCBINCBI36Build 36hg18NCBI36
Build 341670,520,941 - 70,591,378NCBI
Celera1656,277,357 - 56,347,989 (-)NCBICelera
Cytogenetic Map16q22.2NCBI
HuRef1657,730,623 - 57,800,692 (-)NCBIHuRef
CHM1_11673,376,773 - 73,447,194 (-)NCBICHM1_1
T2T-CHM13v2.01677,746,662 - 77,818,469 (-)NCBIT2T-CHM13v2.0
Pkd1l3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398110,340,828 - 110,399,305 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8110,341,149 - 110,401,018 (+)EnsemblGRCm39 Ensembl
GRCm388109,614,190 - 109,672,673 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8109,614,517 - 109,674,386 (+)EnsemblGRCm38mm10GRCm38
MGSCv378112,138,417 - 112,196,492 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368112,503,646 - 112,559,850 (+)NCBIMGSCv36mm8
Celera8113,840,135 - 113,898,231 (+)NCBICelera
Cytogenetic Map8D3NCBI
cM Map857.14NCBI
PKD1L3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21882,151,287 - 82,230,522 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11688,078,954 - 88,158,318 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01653,002,427 - 53,081,964 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11671,764,791 - 71,845,674 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1671,764,791 - 71,845,674 (-)Ensemblpanpan1.1panPan2
PKD1L3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1577,690,991 - 77,756,355 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl577,692,200 - 77,754,474 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha577,648,165 - 77,718,071 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0578,126,411 - 78,195,695 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl578,131,520 - 78,193,816 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1577,946,493 - 78,015,756 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0577,769,182 - 77,838,638 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0578,268,517 - 78,337,780 (-)NCBIUU_Cfam_GSD_1.0
PKD1L3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1555,063,602 - 55,155,171 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl555,064,355 - 55,154,736 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604717,863,767 - 17,950,243 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pkd1l3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474614,191,382 - 14,243,579 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pkd1l3
453 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:165
Count of miRNA genes:109
Interacting mature miRNAs:114
Transcripts:ENSRNOT00000041395, ENSRNOT00000063840, ENSRNOT00000071179
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
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192481797839654489Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)192753020737947399Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)192753020737947399Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)192753020737947399Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat


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
Low 3 16 19 1 2 11 7 20 11 1
Below cutoff 23 13 13 13 7 9 25 16 20 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000082380   ⟹   ENSRNOP00000073135
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1937,585,725 - 37,650,155 (+)Ensembl
Rnor_6.0 Ensembl1941,989,650 - 42,054,018 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089134   ⟹   ENSRNOP00000069332
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1937,585,725 - 37,650,155 (+)Ensembl
Rnor_6.0 Ensembl1941,989,650 - 42,054,018 (-)Ensembl
RefSeq Acc Id: XM_039098288   ⟹   XP_038954216
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81954,494,529 - 54,559,596 (+)NCBI
mRatBN7.21937,585,564 - 37,650,083 (+)NCBI
RefSeq Acc Id: XM_039098289   ⟹   XP_038954217
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81954,494,529 - 54,559,596 (+)NCBI
mRatBN7.21937,585,564 - 37,650,083 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038954216 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954217 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000069332
  ENSRNOP00000069332.2
  ENSRNOP00000073135
  ENSRNOP00000073135.2
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000069332   ⟸   ENSRNOT00000089134
RefSeq Acc Id: ENSRNOP00000073135   ⟸   ENSRNOT00000082380
RefSeq Acc Id: XP_038954216   ⟸   XM_039098288
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JV34 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954217   ⟸   XM_039098289
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K4Q7 (UniProtKB/TrEMBL)
Protein Domains
PLAT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K4Q7-F1-model_v2 AlphaFold A0A0G2K4Q7 1-2181 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:2324490 AgrOrtholog
BioCyc Gene G2FUF-5728 BioCyc
Ensembl Genes ENSRNOG00000052310 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000082380.2 UniProtKB/TrEMBL
  ENSRNOT00000089134.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.70 UniProtKB/TrEMBL
  3.10.100.10 UniProtKB/TrEMBL
  PLAT/LH2 domain UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
  GPS_dom UniProtKB/TrEMBL
  LipOase_LH2 UniProtKB/TrEMBL
  PKD1_2_channel UniProtKB/TrEMBL
  PKD_2 UniProtKB/TrEMBL
  PLAT/LH2_dom_sf UniProtKB/TrEMBL
  PLAT_polycystin1 UniProtKB/TrEMBL
  Polycystin_dom UniProtKB/TrEMBL
NCBI Gene 100362565 ENTREZGENE
PANTHER POLYCYSTIC KIDNEY DISEASE PROTEIN 1-LIKE 3 UniProtKB/TrEMBL
  POLYCYSTIN FAMILY MEMBER UniProtKB/TrEMBL
Pfam GPS UniProtKB/TrEMBL
  PKD_channel UniProtKB/TrEMBL
  PLAT UniProtKB/TrEMBL
  Polycystin_dom UniProtKB/TrEMBL
PhenoGen Pkd1l3 PhenoGen
PRINTS POLYCYSTIN2 UniProtKB/TrEMBL
PROSITE GPS UniProtKB/TrEMBL
  PLAT UniProtKB/TrEMBL
RatGTEx ENSRNOG00000052310 RatGTEx
SMART GPS UniProtKB/TrEMBL
  LH2 UniProtKB/TrEMBL
Superfamily-SCOP C-type_lectin_fold UniProtKB/TrEMBL
  Lipase_LipOase UniProtKB/TrEMBL
UniProt A0A0G2JV34 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K4Q7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-03 Pkd1l3  polycystin 1 like 3, transient receptor potential channel interacting  Pkd1l3  polycystic kidney disease 1-like 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-08-29 Pkd1l3  polycystic kidney disease 1-like 3  LOC100362565  polycystic kidney disease 1 like 3-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100362565  polycystic kidney disease 1 like 3-like      Symbol and Name status set to provisional 70820 PROVISIONAL