PKD1L2 (polycystin 1 like 2) - Rat Genome Database

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Gene: PKD1L2 (polycystin 1 like 2) Canis lupus familiaris
Analyze
Symbol: PKD1L2
Name: polycystin 1 like 2
RGD ID: 12056784
Description: ENCODES a protein that exhibits carbohydrate binding (inferred); ASSOCIATED WITH genetic disease (ortholog); giant axonal neuropathy 1 (ortholog); long QT syndrome (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: polycystic kidney disease protein 1-like 2
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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
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

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
1081 total Variants

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 nervous system reproductive system respiratory system adipose tissue
High
Medium
Low
Below cutoff 4 2 13 6 5 6 6 9 8 4 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000031848   ⟹   ENSCAFP00000029653
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl570,653,179 - 70,693,510 (+)Ensembl
RefSeq Acc Id: XM_022419447   ⟹   XP_022275155
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1570,653,179 - 70,741,134 (+)NCBI
Dog10K_Boxer_Tasha570,632,005 - 70,689,907 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038477026   ⟹   XP_038332954
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1570,930,220 - 70,988,149 (+)NCBI
RefSeq Acc Id: XM_038538211   ⟹   XP_038394139
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0571,243,264 - 71,301,235 (+)NCBI
RefSeq Acc Id: XM_038602338   ⟹   XP_038458266
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0570,765,417 - 70,823,360 (+)NCBI
RefSeq Acc Id: XM_038666945   ⟹   XP_038522873
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0570,987,869 - 71,045,831 (+)NCBI
Protein Sequences
Protein RefSeqs XP_022275155 (Get FASTA)   NCBI Sequence Viewer  
  XP_038332954 (Get FASTA)   NCBI Sequence Viewer  
  XP_038394139 (Get FASTA)   NCBI Sequence Viewer  
  XP_038458266 (Get FASTA)   NCBI Sequence Viewer  
  XP_038522873 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCAFP00000029653.5
Reference Protein Sequences
RefSeq Acc Id: XP_022275155   ⟸   XM_022419447
- Sequence:
RefSeq Acc Id: ENSCAFP00000029653   ⟸   ENSCAFT00000031848
RefSeq Acc Id: XP_038332954   ⟸   XM_038477026
RefSeq Acc Id: XP_038458266   ⟸   XM_038602338
RefSeq Acc Id: XP_038522873   ⟸   XM_038666945
RefSeq Acc Id: XP_038394139   ⟸   XM_038538211
Protein Domains
C-type lectin   REJ   SUEL-type lectin


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000020012 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000031848.5 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.740 UniProtKB/TrEMBL
  3.10.100.10 UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin-like/link_sf UniProtKB/TrEMBL
  CTDL_fold UniProtKB/TrEMBL
  Lectin_gal-bd_dom UniProtKB/TrEMBL
  Lectin_gal-bd_sf UniProtKB/TrEMBL
  PKD/REJ-like UniProtKB/TrEMBL
  REJ_dom UniProtKB/TrEMBL
NCBI Gene PKD1L2 ENTREZGENE
PANTHER L-RHAMNOSE-BINDING LECTIN CSL2-RELATED UniProtKB/TrEMBL
  PROTEIN EVA-1 UniProtKB/TrEMBL
Pfam Gal_Lectin UniProtKB/TrEMBL
  Lectin_C UniProtKB/TrEMBL
  REJ UniProtKB/TrEMBL
PROSITE C_TYPE_LECTIN_2 UniProtKB/TrEMBL
  REJ UniProtKB/TrEMBL
  SUEL_LECTIN UniProtKB/TrEMBL
SMART CLECT UniProtKB/TrEMBL
Superfamily-SCOP C-type lectin-like UniProtKB/TrEMBL
UniProt A0A8P0NLA1_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:56013 ENTREZGENE