Prickle3 (prickle planar cell polarity protein 3) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Prickle3 (prickle planar cell polarity protein 3) Rattus norvegicus
Analyze
Symbol: Prickle3
Name: prickle planar cell polarity protein 3
RGD ID: 1359685
Description: Predicted to have zinc ion binding activity. Orthologous to human PRICKLE3 (prickle planar cell polarity protein 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LIM domain only 6; LOC317380; prickle homolog 3; prickle homolog 3 (Drosophila); prickle-like protein 3; similar to Lmo6 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,837,647 - 14,849,305 (-)NCBI
Rnor_6.0 EnsemblX15,682,653 - 15,693,473 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X15,682,652 - 15,693,473 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X16,473,878 - 16,484,448 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,878,508 - 26,889,077 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,931,977 - 26,942,546 (-)NCBI
CeleraX14,920,980 - 14,931,582 (-)NCBICelera
Cytogenetic MapXq12NCBI
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
mitochondrion  (IEA,ISO)

Molecular Function

References


Genomics

Comparative Map Data
Prickle3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,837,647 - 14,849,305 (-)NCBI
Rnor_6.0 EnsemblX15,682,653 - 15,693,473 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X15,682,652 - 15,693,473 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X16,473,878 - 16,484,448 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,878,508 - 26,889,077 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,931,977 - 26,942,546 (-)NCBI
CeleraX14,920,980 - 14,931,582 (-)NCBICelera
Cytogenetic MapXq12NCBI
PRICKLE3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX49,174,802 - 49,186,528 (-)EnsemblGRCh38hg38GRCh38
GRCh38X49,174,802 - 49,186,373 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X49,031,151 - 49,042,826 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,918,850 - 48,929,720 (-)NCBINCBI36hg18NCBI36
Build 34X48,788,276 - 48,799,147NCBI
CeleraX52,621,593 - 52,632,463 (+)NCBI
Cytogenetic MapXp11.23NCBI
HuRefX46,689,176 - 46,699,847 (-)NCBIHuRef
CHM1_1X49,064,231 - 49,075,097 (-)NCBICHM1_1
Prickle3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X7,523,584 - 7,534,425 (+)NCBIGRCm39mm39
GRCm39 EnsemblX7,523,499 - 7,534,425 (+)Ensembl
GRCm38X7,657,379 - 7,668,197 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX7,657,260 - 7,668,186 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X7,235,659 - 7,245,312 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X6,815,492 - 6,825,145 (+)NCBImm8
MGSCv36X3,832,127 - 3,914,808 (+)NCBImm8
CeleraX3,802,719 - 3,812,718 (-)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.45NCBI
Prickle3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955543662,438 - 673,662 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955543662,438 - 673,386 (-)NCBIChiLan1.0ChiLan1.0
PRICKLE3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X49,327,145 - 49,338,613 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX49,327,145 - 49,338,613 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X41,474,569 - 41,486,986 (-)NCBIMhudiblu_PPA_v0panPan3
PRICKLE3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X42,276,316 - 42,285,428 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX42,275,900 - 42,285,321 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX16,655,446 - 16,664,565 (-)NCBI
ROS_Cfam_1.0X42,418,291 - 42,427,520 (-)NCBI
UMICH_Zoey_3.1X42,402,367 - 42,411,486 (-)NCBI
UNSW_CanFamBas_1.0X42,390,018 - 42,399,136 (-)NCBI
UU_Cfam_GSD_1.0X42,484,780 - 42,493,899 (-)NCBI
Prickle3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X34,810,353 - 34,820,245 (-)NCBI
SpeTri2.0NW_0049367211,050,755 - 1,060,603 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRICKLE3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX43,218,271 - 43,230,819 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X43,218,271 - 43,230,368 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X48,066,244 - 48,078,307 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PRICKLE3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X46,271,001 - 46,286,440 (-)NCBI
ChlSab1.1 EnsemblX46,266,985 - 46,283,689 (-)Ensembl
Vero_WHO_p1.0NW_02366607611,835,728 - 11,847,007 (-)NCBI
Prickle3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624893916,340 - 927,128 (-)NCBI

Position Markers
DXWox2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,843,113 - 14,843,484 (+)MAPPER
Rnor_6.0X15,688,119 - 15,688,489NCBIRnor6.0
Rnor_5.0X16,479,345 - 16,479,715UniSTSRnor5.0
RGSC_v3.4X26,883,972 - 26,884,343RGDRGSC3.4
RGSC_v3.4X26,883,973 - 26,884,343UniSTSRGSC3.4
RGSC_v3.1X26,937,442 - 26,937,812RGD
CeleraX14,926,447 - 14,926,817UniSTS
RH 3.4 MapX166.2UniSTS
RH 3.4 MapX166.2RGD
RH 2.0 Map21112.6RGD
Cytogenetic MapXq13UniSTS
DXWox1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,843,116 - 14,843,488 (+)MAPPER
Rnor_6.0X15,688,122 - 15,688,493NCBIRnor6.0
Rnor_5.0X16,479,348 - 16,479,719UniSTSRnor5.0
RGSC_v3.4X26,883,975 - 26,884,348RGDRGSC3.4
RGSC_v3.4X26,883,976 - 26,884,347UniSTSRGSC3.4
CeleraX14,926,450 - 14,926,821UniSTS
RH 3.4 MapX164.1UniSTS
RH 3.4 MapX164.1RGD
RH 2.0 Map21114.6RGD
Cytogenetic MapXq13UniSTS
RH132023  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,849,483 - 14,849,685 (+)MAPPER
Rnor_6.0X15,694,739 - 15,694,940NCBIRnor6.0
Rnor_5.0X16,485,714 - 16,485,915UniSTSRnor5.0
RGSC_v3.4X26,890,343 - 26,890,544UniSTSRGSC3.4
CeleraX14,932,848 - 14,933,049UniSTS
RH 3.4 MapX167.0UniSTS
Cytogenetic MapXq13UniSTS
Cytogenetic MapXq13-q14UniSTS
RH136577  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0X16,473,541 - 16,473,725NCBIRnor5.0
Rnor_5.04188,532,081 - 188,532,265NCBIRnor5.0
Rnor_5.04188,475,121 - 188,475,305NCBIRnor5.0
RGSC_v3.4X26,878,172 - 26,878,355UniSTSRGSC3.4
RGSC_v3.44127,132,356 - 127,132,539UniSTSRGSC3.4
CeleraX14,920,644 - 14,920,827UniSTS
Celera4114,311,849 - 114,312,032UniSTS
Cytogenetic MapXq13UniSTS
Cytogenetic Map4q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X166245321592783Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X183816624331837Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:140
Count of miRNA genes:107
Interacting mature miRNAs:113
Transcripts:ENSRNOT00000013758
Prediction methods:Microtar, Miranda, Pita, 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.


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 3 33 4 4 3 4 1 4 26 28 6 1
Low 10 53 37 16 37 7 7 74 9 12 5 7
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013758   ⟹   ENSRNOP00000013758
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX15,682,653 - 15,693,473 (-)Ensembl
RefSeq Acc Id: NM_001014110   ⟹   NP_001014132
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,837,647 - 14,848,218 (-)NCBI
Rnor_6.0X15,682,652 - 15,693,473 (-)NCBI
Rnor_5.0X16,473,878 - 16,484,448 (-)NCBI
RGSC_v3.4X26,878,508 - 26,889,077 (-)RGD
CeleraX14,920,980 - 14,931,582 (-)RGD
Sequence:
RefSeq Acc Id: XM_017602064   ⟹   XP_017457553
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,837,740 - 14,848,072 (-)NCBI
Rnor_6.0X15,682,745 - 15,692,832 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099791   ⟹   XP_038955719
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,837,740 - 14,849,305 (-)NCBI
RefSeq Acc Id: XM_039099792   ⟹   XP_038955720
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,837,740 - 14,849,305 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001014132 (Get FASTA)   NCBI Sequence Viewer  
  XP_017457553 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955719 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955720 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH85918 (Get FASTA)   NCBI Sequence Viewer  
  EDL83841 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001014132   ⟸   NM_001014110
- UniProtKB: Q5U2Q0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457553   ⟸   XM_017602064
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000013758   ⟸   ENSRNOT00000013758
RefSeq Acc Id: XP_038955720   ⟸   XM_039099792
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955719   ⟸   XM_039099791
- Peptide Label: isoform X1
Protein Domains
LIM zinc-binding   PET

Transcriptome

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

Promoters
RGD ID:13701748
Promoter ID:EPDNEW_R12272
Type:initiation region
Name:Prickle3_1
Description:prickle planar cell polarity protein 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X15,693,449 - 15,693,509EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359685 AgrOrtholog
Ensembl Genes ENSRNOG00000022417 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013758 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013758 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7108577 IMAGE-MGC_LOAD
InterPro LIM1_prickle UniProtKB/TrEMBL
  LIM2_prickle UniProtKB/TrEMBL
  LIM3_prickle UniProtKB/TrEMBL
  PET_domain UniProtKB/TrEMBL
  PET_prickle UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
KEGG Report rno:317380 UniProtKB/TrEMBL
MGC_CLONE MGC:94823 IMAGE-MGC_LOAD
NCBI Gene 317380 ENTREZGENE
Pfam LIM UniProtKB/TrEMBL
  PET UniProtKB/TrEMBL
PhenoGen Prickle3 PhenoGen
PROSITE LIM_DOMAIN_1 UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/TrEMBL
  PET UniProtKB/TrEMBL
SMART LIM UniProtKB/TrEMBL
UniProt Q5U2Q0 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1LPT2 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Prickle3  prickle planar cell polarity protein 3  Prickle3  prickle homolog 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-30 Prickle3  prickle homolog 3  Prickle3  prickle homolog 3 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Prickle3  prickle homolog 3 (Drosophila)  LOC317380  similar to Lmo6 protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 LOC317380  similar to Lmo6 protein      Symbol and Name status set to provisional 70820 PROVISIONAL