Pkd1l2 (polycystin 1 like 2) - Rat Genome Database

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Gene: Pkd1l2 (polycystin 1 like 2) Rattus norvegicus
Analyze
Symbol: Pkd1l2
Name: polycystin 1 like 2
RGD ID: 1588631
Description: Predicted to enable calcium ion binding activity and carbohydrate binding activity. Predicted to be involved in calcium ion transmembrane transport. Predicted to be located in membrane-bounded organelle. Orthologous to human PKD1L2 (polycystin 1 like 2 (gene/pseudogene)); INTERACTS WITH gentamycin; glyphosate; paracetamol.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC691069; polycystic kidney disease 1-like 2; polycystic kidney disease protein 1-like 2; polycystin-1-like protein 2; similar to polycystin 1-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
GRCr81961,958,351 - 62,045,324 (-)NCBIGRCr8
mRatBN7.21945,049,713 - 45,136,503 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1945,049,719 - 45,135,532 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01949,535,122 - 49,624,291 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1949,535,792 - 49,623,758 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01960,326,540 - 60,411,833 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41947,104,964 - 47,187,991 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1944,322,265 - 44,408,508 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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

Genomics

Comparative Map Data
Pkd1l2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81961,958,351 - 62,045,324 (-)NCBIGRCr8
mRatBN7.21945,049,713 - 45,136,503 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1945,049,719 - 45,135,532 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01949,535,122 - 49,624,291 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1949,535,792 - 49,623,758 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01960,326,540 - 60,411,833 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41947,104,964 - 47,187,991 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1944,322,265 - 44,408,508 (-)NCBICelera
Cytogenetic Map19q12NCBI
PKD1L2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381681,100,875 - 81,220,394 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1681,100,875 - 81,220,370 (-)EnsemblGRCh38hg38GRCh38
GRCh371681,134,480 - 81,253,999 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361679,691,985 - 79,811,476 (-)NCBINCBI36Build 36hg18NCBI36
Build 341679,691,991 - 79,811,476NCBI
Celera1665,432,531 - 65,551,310 (-)NCBICelera
Cytogenetic Map16q23.2NCBI
HuRef1666,890,951 - 67,009,177 (-)NCBIHuRef
CHM1_11682,545,869 - 82,665,337 (-)NCBICHM1_1
T2T-CHM13v2.01687,162,065 - 87,281,147 (-)NCBIT2T-CHM13v2.0
Pkd1l2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398117,722,089 - 117,809,227 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8117,722,418 - 117,809,188 (-)EnsemblGRCm39 Ensembl
GRCm388116,995,679 - 117,082,449 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8116,995,679 - 117,082,449 (-)EnsemblGRCm38mm10GRCm38
MGSCv378119,519,579 - 119,606,349 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368119,881,656 - 119,968,426 (-)NCBIMGSCv36mm8
Celera8121,215,068 - 121,301,947 (-)NCBICelera
Cytogenetic Map8E1NCBI
cM Map863.45NCBI
Pkd1l2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555223,877,986 - 3,963,188 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555223,877,806 - 3,963,197 (-)NCBIChiLan1.0ChiLan1.0
LOC100988147
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21890,881,686 - 90,920,784 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11696,770,988 - 96,891,177 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01661,736,153 - 61,770,746 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11681,134,136 - 81,253,092 (-)NCBIpanpan1.1PanPan1.1panPan2
PKD1L2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1570,653,179 - 70,741,134 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl570,653,179 - 70,693,510 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha570,632,005 - 70,689,907 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0570,987,869 - 71,045,831 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1570,930,220 - 70,988,149 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0570,765,417 - 70,823,360 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0571,243,264 - 71,301,235 (+)NCBIUU_Cfam_GSD_1.0
Pkd1l2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934930,742,723 - 30,823,645 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647528,765,609 - 28,846,207 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647528,765,416 - 28,846,310 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PKD1L2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl67,066,912 - 7,166,458 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.167,065,143 - 7,166,620 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PKD1L2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1566,555,686 - 66,662,670 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl566,555,938 - 66,661,802 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660479,174,162 - 9,281,557 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pkd1l2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247466,187,851 - 6,259,586 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pkd1l2
795 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:69
Count of miRNA genes:64
Interacting mature miRNAs:69
Transcripts:ENSRNOT00000071130
Prediction methods: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
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
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
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat

Markers in Region
D19Got48  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21945,099,069 - 45,099,312 (+)MAPPERmRatBN7.2
Rnor_6.01949,584,644 - 49,584,886NCBIRnor6.0
Rnor_5.01960,374,798 - 60,375,040UniSTSRnor5.0
RGSC_v3.41947,151,652 - 47,151,895RGDRGSC3.4
RGSC_v3.41947,151,653 - 47,151,895UniSTSRGSC3.4
RGSC_v3.11947,156,534 - 47,156,776RGD
Celera1944,372,275 - 44,372,517UniSTS
RH 3.4 Map19607.4UniSTS
RH 3.4 Map19607.4RGD
RH 2.0 Map19621.7RGD
Cytogenetic Map19q12UniSTS


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 27 27 3 27 12
Below cutoff 2 29 28 14 14 14 2 3 47 22 27 11 2

Sequence


RefSeq Acc Id: ENSRNOT00000071130   ⟹   ENSRNOP00000064630
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1945,049,719 - 45,135,532 (-)Ensembl
Rnor_6.0 Ensembl1949,535,792 - 49,623,758 (-)Ensembl
RefSeq Acc Id: XM_039098121   ⟹   XP_038954049
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81961,958,351 - 62,045,324 (-)NCBI
mRatBN7.21945,049,713 - 45,136,503 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038954049 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000064630
  ENSRNOP00000064630.3
RefSeq Acc Id: ENSRNOP00000064630   ⟸   ENSRNOT00000071130
RefSeq Acc Id: XP_038954049   ⟸   XM_039098121
- UniProtKB: M0R5G5 (UniProtKB/TrEMBL)
Protein Domains
C-type lectin   PLAT   REJ   SUEL-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R5G5-F1-model_v2 AlphaFold M0R5G5 1-2452 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:1588631 AgrOrtholog
BioCyc Gene G2FUF-5557 BioCyc
Ensembl Genes ENSRNOG00000045626 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071130.3 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.70 UniProtKB/TrEMBL
  2.60.120.740 UniProtKB/TrEMBL
  2.60.220.50 UniProtKB/TrEMBL
  3.10.100.10 UniProtKB/TrEMBL
  PLAT/LH2 domain UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin-like/link_sf UniProtKB/TrEMBL
  CTDL_fold UniProtKB/TrEMBL
  GAIN_dom_sf UniProtKB/TrEMBL
  GPS UniProtKB/TrEMBL
  Lectin_gal-bd_dom UniProtKB/TrEMBL
  Lectin_gal-bd_sf UniProtKB/TrEMBL
  PKD/REJ-like UniProtKB/TrEMBL
  PKD1_2_channel UniProtKB/TrEMBL
  PKD_2 UniProtKB/TrEMBL
  PKD_dom_sf UniProtKB/TrEMBL
  PLAT/LH2_dom UniProtKB/TrEMBL
  PLAT/LH2_dom_sf UniProtKB/TrEMBL
  PLAT_polycystin1 UniProtKB/TrEMBL
  Polycystin_dom UniProtKB/TrEMBL
  REJ_dom UniProtKB/TrEMBL
NCBI Gene 691069 ENTREZGENE
PANTHER POLYCYSTIC KIDNEY DISEASE PROTEIN 1-LIKE 2 UniProtKB/TrEMBL
  POLYCYSTIN FAMILY MEMBER UniProtKB/TrEMBL
Pfam Gal_Lectin UniProtKB/TrEMBL
  GPS UniProtKB/TrEMBL
  Lectin_C UniProtKB/TrEMBL
  PKD_channel UniProtKB/TrEMBL
  PLAT UniProtKB/TrEMBL
  Polycystin_dom UniProtKB/TrEMBL
  REJ UniProtKB/TrEMBL
PhenoGen Pkd1l2 PhenoGen
PRINTS POLYCYSTIN2 UniProtKB/TrEMBL
PROSITE C_TYPE_LECTIN_2 UniProtKB/TrEMBL
  GPS UniProtKB/TrEMBL
  PLAT UniProtKB/TrEMBL
  REJ UniProtKB/TrEMBL
  SUEL_LECTIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000045626 RatGTEx
SMART CLECT UniProtKB/TrEMBL
  GPS UniProtKB/TrEMBL
  LH2 UniProtKB/TrEMBL
Superfamily-SCOP SSF49299 UniProtKB/TrEMBL
  SSF49723 UniProtKB/TrEMBL
  SSF56436 UniProtKB/TrEMBL
UniProt M0R5G5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-02-01 Pkd1l2  polycystin 1 like 2  Pkd1l2  polycystic kidney disease 1-like 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-07-29 Pkd1l2  polycystic kidney disease 1-like 2  LOC691069  similar to polycystin 1-like 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC691069  similar to polycystin 1-like 2  LOC687404  similar to polycystin 1-like 2  Data merged from RGD:1585398 1643240 APPROVED
2006-11-19 LOC691069  similar to polycystin 1-like 2      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC687404  similar to polycystin 1-like 2      Symbol and Name status set to provisional 70820 PROVISIONAL