Prickle1 (prickle planar cell polarity protein 1) - Rat Genome Database

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Gene: Prickle1 (prickle planar cell polarity protein 1) Rattus norvegicus
Analyze
Symbol: Prickle1
Name: prickle planar cell polarity protein 1
RGD ID: 735090
Description: Exhibits transcription factor binding activity. Involved in protein import into nucleus. Predicted to localize to cytosol and nuclear membrane. Used to study temporal lobe epilepsy. Biomarker of visual epilepsy. Human ortholog(s) of this gene implicated in progressive myoclonus epilepsy 1B. Orthologous to human PRICKLE1 (prickle planar cell polarity protein 1); PARTICIPATES IN Wnt signaling, the planar cell polarity pathway; Wnt signaling pathway; INTERACTS WITH 2,6-dinitrotoluene; 6-propyl-2-thiouracil; all-trans-retinoic acid.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: prickle homolog 1; prickle homolog 1 (Drosophila); prickle-like 1; prickle-like 1 (Drosophila); prickle-like protein 1; REST/NRSF-interacting lim domain protein; REST/NRSF-interacting LIM domain protein 1; Rilp
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
mRatBN7.27124,639,142 - 124,735,027 (-)NCBI
Rnor_6.0 Ensembl7134,702,964 - 134,722,215 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07134,702,964 - 134,799,437 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07134,370,195 - 134,466,674 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47131,967,220 - 131,986,187 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17132,044,813 - 132,052,370 (-)NCBI
Celera7121,036,572 - 121,055,537 (-)NCBICelera
Cytogenetic Map7q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (EXP)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (EXP,ISO)
alpha-pinene  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromobenzene  (EXP)
butan-1-ol  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP)
copper(0)  (EXP)
cylindrospermopsin  (ISO)
cytarabine  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP,ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
flusilazole  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
isobutanol  (ISO)
L-methionine  (ISO)
methyl methanesulfonate  (ISO)
Monobutylphthalate  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
propiconazole  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
torcetrapib  (ISO)
triadimefon  (ISO)
trichostatin A  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytosol  (IEA,ISO)
nuclear membrane  (IEA,ISO)
nucleus  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:16417580   PMID:17030191   PMID:17173866   PMID:18922795   PMID:21199191   PMID:21901791   PMID:22333836   PMID:24312498   PMID:25807483  


Genomics

Comparative Map Data
Prickle1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27124,639,142 - 124,735,027 (-)NCBI
Rnor_6.0 Ensembl7134,702,964 - 134,722,215 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07134,702,964 - 134,799,437 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07134,370,195 - 134,466,674 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47131,967,220 - 131,986,187 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17132,044,813 - 132,052,370 (-)NCBI
Celera7121,036,572 - 121,055,537 (-)NCBICelera
Cytogenetic Map7q35NCBI
PRICKLE1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1242,456,757 - 42,590,355 (-)EnsemblGRCh38hg38GRCh38
GRCh381242,456,757 - 42,589,755 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371242,850,559 - 42,983,548 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361241,139,341 - 41,269,745 (-)NCBINCBI36hg18NCBI36
Build 341241,139,340 - 41,269,745NCBI
Celera1241,653,996 - 41,785,497 (-)NCBI
Cytogenetic Map12q12NCBI
HuRef1239,878,936 - 40,010,599 (-)NCBIHuRef
CHM1_11242,818,791 - 42,950,331 (-)NCBICHM1_1
Prickle1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391593,396,992 - 93,494,147 (-)NCBIGRCm39mm39
GRCm39 Ensembl1593,396,995 - 93,493,772 (-)Ensembl
GRCm381593,499,111 - 93,596,266 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1593,499,114 - 93,595,891 (-)EnsemblGRCm38mm10GRCm38
MGSCv371593,329,545 - 93,426,322 (-)NCBIGRCm37mm9NCBIm37
MGSCv361593,327,294 - 93,424,071 (-)NCBImm8
Celera1595,647,051 - 95,744,081 (-)NCBICelera
Cytogenetic Map15E3NCBI
Prickle1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555001,897,912 - 1,990,875 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555001,897,899 - 1,990,791 (-)NCBIChiLan1.0ChiLan1.0
PRICKLE1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11247,100,352 - 47,126,116 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1247,100,393 - 47,126,102 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01246,127,673 - 46,262,333 (+)NCBIMhudiblu_PPA_v0panPan3
PRICKLE1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12711,327,086 - 11,437,799 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2711,426,647 - 11,437,303 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2734,864,577 - 34,975,269 (-)NCBI
ROS_Cfam_1.02711,522,959 - 11,634,418 (+)NCBI
UMICH_Zoey_3.12711,336,611 - 11,448,200 (+)NCBI
UNSW_CanFamBas_1.02711,366,003 - 11,477,284 (+)NCBI
UU_Cfam_GSD_1.02735,111,079 - 35,222,648 (-)NCBI
Prickle1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494571,894,685 - 71,999,671 (+)NCBI
SpeTri2.0NW_0049365121,165,159 - 1,270,138 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRICKLE1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl573,707,022 - 73,826,431 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1573,707,026 - 73,826,529 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2576,446,397 - 76,452,034 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PRICKLE1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11138,696,771 - 38,819,324 (-)NCBI
ChlSab1.1 Ensembl1138,694,602 - 38,718,519 (-)Ensembl
Vero_WHO_p1.0NW_023666037207,742,821 - 207,865,507 (+)NCBI
Prickle1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462481610,087,866 - 10,185,004 (+)NCBI

Position Markers
AW215793  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27124,639,256 - 124,639,384 (+)MAPPER
Rnor_6.07134,703,079 - 134,703,206NCBIRnor6.0
Rnor_5.07134,370,310 - 134,370,437UniSTSRnor5.0
RGSC_v3.47131,967,335 - 131,967,462UniSTSRGSC3.4
Celera7121,036,687 - 121,036,814UniSTS
Cytogenetic Map7q35UniSTS
BE114974  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27124,696,400 - 124,696,573 (+)MAPPER
Rnor_6.07134,760,686 - 134,760,858NCBIRnor6.0
Rnor_5.07134,427,917 - 134,428,089UniSTSRnor5.0
RGSC_v3.47132,024,474 - 132,024,646UniSTSRGSC3.4
Celera7121,093,972 - 121,094,144UniSTS
RH 3.4 Map71020.7UniSTS
Cytogenetic Map7q35UniSTS
RH143298  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27124,639,200 - 124,639,308 (+)MAPPER
Rnor_6.07134,703,023 - 134,703,130NCBIRnor6.0
Rnor_5.07134,370,254 - 134,370,361UniSTSRnor5.0
RGSC_v3.47131,967,279 - 131,967,386UniSTSRGSC3.4
Celera7121,036,631 - 121,036,738UniSTS
RH 3.4 Map71017.7UniSTS
Cytogenetic Map7q35UniSTS
BE099414  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27124,701,708 - 124,701,907 (+)MAPPER
Rnor_6.07134,766,005 - 134,766,203NCBIRnor6.0
Rnor_5.07134,433,236 - 134,433,434UniSTSRnor5.0
RGSC_v3.47132,029,782 - 132,029,980UniSTSRGSC3.4
Celera7121,099,284 - 121,099,482UniSTS
RH 3.4 Map71019.8UniSTS
Cytogenetic Map7q35UniSTS
RH138805  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map71045.0UniSTS
Cytogenetic Map7q35UniSTS
MARC_13855-13856:1032800061:3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27124,640,929 - 124,641,338 (+)MAPPER
Rnor_6.07134,704,752 - 134,705,160NCBIRnor6.0
Rnor_5.07134,371,983 - 134,372,391UniSTSRnor5.0
RGSC_v3.47131,969,008 - 131,969,416UniSTSRGSC3.4
Celera7121,038,360 - 121,038,768UniSTS
Cytogenetic Map7q35UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)791018361136018361Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)793726906138726906Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)793726906138726906Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)796630946141630946Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)7100160423140335001Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7120746024145692398Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7121654760145729302Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7121986439143965591Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7122421276143965415Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)7126463827137325116Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7129412003145729302Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:182
Count of miRNA genes:129
Interacting mature miRNAs:161
Transcripts:ENSRNOT00000036750
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.


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 36 4 4 4 52 22 33 11
Low 3 7 53 37 19 37 8 11 22 13 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000036750   ⟹   ENSRNOP00000031476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7134,702,964 - 134,722,215 (-)Ensembl
RefSeq Acc Id: NM_199396   ⟹   NP_955428
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27124,639,142 - 124,658,113 (-)NCBI
Rnor_6.07134,702,964 - 134,722,215 (-)NCBI
Rnor_5.07134,370,195 - 134,466,674 (-)NCBI
RGSC_v3.47131,967,220 - 131,986,187 (-)RGD
Celera7121,036,572 - 121,055,537 (-)RGD
Sequence:
RefSeq Acc Id: XM_006242213   ⟹   XP_006242275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27124,639,154 - 124,735,027 (-)NCBI
Rnor_6.07134,702,976 - 134,799,437 (-)NCBI
Rnor_5.07134,370,195 - 134,466,674 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242214   ⟹   XP_006242276
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27124,639,154 - 124,705,022 (-)NCBI
Rnor_6.07134,702,976 - 134,768,432 (-)NCBI
Rnor_5.07134,370,195 - 134,466,674 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242215   ⟹   XP_006242277
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27124,639,154 - 124,673,059 (-)NCBI
Rnor_6.07134,702,976 - 134,737,149 (-)NCBI
Rnor_5.07134,370,195 - 134,466,674 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594887   ⟹   XP_017450376
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07134,702,976 - 134,787,596 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_955428   ⟸   NM_199396
- UniProtKB: G3V8Z4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242275   ⟸   XM_006242213
- Peptide Label: isoform X1
- UniProtKB: G3V8Z4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242276   ⟸   XM_006242214
- Peptide Label: isoform X1
- UniProtKB: G3V8Z4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242277   ⟸   XM_006242215
- Peptide Label: isoform X1
- UniProtKB: G3V8Z4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450376   ⟸   XM_017594887
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000031476   ⟸   ENSRNOT00000036750
Protein Domains
LIM zinc-binding   PET

Transcriptome

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


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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 134372208 134372209 T G snv FHH/EurMcwi (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 134704977 134704978 T G snv FHH/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 131969233 131969234 T G snv FHH/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735090 AgrOrtholog
Ensembl Genes ENSRNOG00000022772 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000031476 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000036750 ENTREZGENE, UniProtKB/TrEMBL
InterPro LIM2_prickle UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM3_prickle UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PET_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PET_prickle UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:315259 UniProtKB/TrEMBL
NCBI Gene 315259 ENTREZGENE
Pfam LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Prickle1 PhenoGen
PROSITE LIM_DOMAIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LIM_DOMAIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PET UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART LIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V8Z4 ENTREZGENE, UniProtKB/TrEMBL
  PRIC1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Prickle1  prickle planar cell polarity protein 1  Prickle1  prickle homolog 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-30 Prickle1  prickle homolog 1  Prickle1  prickle homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-12-15 Prickle1  prickle homolog 1 (Drosophila)  Prickle1  prickle-like 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Prickle1  prickle-like 1 (Drosophila)      Symbol and Name status set to approved 1299863 APPROVED