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

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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 enable zinc ion binding activity. Predicted to be located in mitochondrion. Orthologous to human PRICKLE3 (prickle planar cell polarity protein 3); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X17,509,551 - 17,520,157 (-)NCBIGRCr8
mRatBN7.2X14,837,647 - 14,849,305 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX14,837,650 - 14,848,218 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX19,651,793 - 19,662,569 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X20,420,565 - 20,431,339 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X16,685,708 - 16,696,482 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X15,682,652 - 15,693,473 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,682,653 - 15,693,473 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X16,473,878 - 16,484,448 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,878,508 - 26,889,077 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. null JRS Domain-based curation
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Genomics

Comparative Map Data
Prickle3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X17,509,551 - 17,520,157 (-)NCBIGRCr8
mRatBN7.2X14,837,647 - 14,849,305 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX14,837,650 - 14,848,218 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX19,651,793 - 19,662,569 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X20,420,565 - 20,431,339 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X16,685,708 - 16,696,482 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X15,682,652 - 15,693,473 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,682,653 - 15,693,473 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X16,473,878 - 16,484,448 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,878,508 - 26,889,077 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38X49,174,802 - 49,186,373 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX49,174,802 - 49,186,528 (-)EnsemblGRCh38hg38GRCh38
GRCh37X49,031,151 - 49,042,826 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,918,850 - 48,929,720 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X48,788,276 - 48,799,147NCBI
CeleraX52,621,593 - 52,632,463 (+)NCBICelera
Cytogenetic MapXp11.23NCBI
HuRefX46,689,176 - 46,699,847 (-)NCBIHuRef
CHM1_1X49,064,231 - 49,075,097 (-)NCBICHM1_1
T2T-CHM13v2.0X48,586,552 - 48,598,227 (-)NCBIT2T-CHM13v2.0
Prickle3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X7,523,616 - 7,535,086 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX7,523,499 - 7,534,425 (+)EnsemblGRCm39 Ensembl
GRCm38X7,657,379 - 7,668,197 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX7,657,260 - 7,668,186 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X7,235,659 - 7,245,312 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X6,815,492 - 6,825,145 (+)NCBIMGSCv36mm8
MGSCv36X3,832,127 - 3,914,808 (+)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v2X50,666,421 - 50,678,526 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X50,670,220 - 50,681,916 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X41,474,569 - 41,486,986 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X49,327,145 - 49,338,613 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX49,327,145 - 49,338,613 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X42,418,291 - 42,427,520 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX42,418,294 - 42,427,517 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X42,402,367 - 42,411,486 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X42,390,018 - 42,399,136 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X42,484,780 - 42,493,899 (-)NCBIUU_Cfam_GSD_1.0
Prickle3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X34,810,353 - 34,820,245 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367211,050,801 - 1,060,574 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367211,050,755 - 1,060,603 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRICKLE3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX43,218,277 - 43,230,367 (-)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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX46,266,985 - 46,283,689 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607611,835,728 - 11,847,007 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Prickle3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624893913,755 - 927,122 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624893916,340 - 927,128 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Prickle3
47 total Variants
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.


QTLs in Region (mRatBN7.2)
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)X143491017Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat

Markers in Region
DXWox2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,843,113 - 14,843,484 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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


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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,837,650 - 14,848,218 (-)Ensembl
Rnor_6.0 EnsemblX15,682,653 - 15,693,473 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096373   ⟹   ENSRNOP00000083394
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,837,650 - 14,847,471 (-)Ensembl
RefSeq Acc Id: NM_001014110   ⟹   NP_001014132
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X17,509,551 - 17,520,122 (-)NCBI
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_039099791   ⟹   XP_038955719
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X17,509,644 - 17,520,149 (-)NCBI
mRatBN7.2X14,837,740 - 14,849,305 (-)NCBI
RefSeq Acc Id: XM_039099792   ⟹   XP_038955720
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X17,509,644 - 17,520,157 (-)NCBI
mRatBN7.2X14,837,740 - 14,849,305 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001014132 (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  
Ensembl Protein ENSRNOP00000013758
  ENSRNOP00000013758.6
  ENSRNOP00000083394.1
Reference Protein Sequences
RefSeq Acc Id: NP_001014132   ⟸   NM_001014110
- UniProtKB: Q5U2Q0 (UniProtKB/TrEMBL),   F1LPT2 (UniProtKB/TrEMBL),   A0A8I5ZZA9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000013758   ⟸   ENSRNOT00000013758
RefSeq Acc Id: XP_038955720   ⟸   XM_039099792
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZZA9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038955719   ⟸   XM_039099791
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZZA9 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000083394   ⟸   ENSRNOT00000096373
Protein Domains
LIM zinc-binding   PET

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5U2Q0-F1-model_v2 AlphaFold Q5U2Q0 1-623 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359685 AgrOrtholog
BioCyc Gene G2FUF-2910 BioCyc
Ensembl Genes ENSRNOG00000022417 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013758 ENTREZGENE
  ENSRNOT00000013758.7 UniProtKB/TrEMBL
  ENSRNOT00000096373.1 UniProtKB/TrEMBL
Gene3D-CATH Cysteine Rich Protein 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
  Pk/Esn/Tes UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
KEGG Report rno:317380 UniProtKB/TrEMBL
MGC_CLONE MGC:94823 IMAGE-MGC_LOAD
NCBI Gene 317380 ENTREZGENE
PANTHER LIM DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
  PRICKLE PLANAR CELL POLARITY PROTEIN 3 UniProtKB/TrEMBL
Pfam LIM UniProtKB/TrEMBL
  PET UniProtKB/TrEMBL
PhenoGen Prickle3 PhenoGen
PROSITE LIM_DOMAIN_1 UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/TrEMBL
  PET UniProtKB/TrEMBL
RatGTEx ENSRNOG00000022417 RatGTEx
SMART LIM UniProtKB/TrEMBL
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/TrEMBL
UniProt A0A8I5ZZA9 ENTREZGENE, UniProtKB/TrEMBL
  F1LPT2 ENTREZGENE
  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