Pard6a (par-6 family cell polarity regulator alpha) - Rat Genome Database

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Gene: Pard6a (par-6 family cell polarity regulator alpha) Rattus norvegicus
Analyze
Symbol: Pard6a
Name: par-6 family cell polarity regulator alpha
RGD ID: 1303273
Description: Predicted to have GTP-dependent protein binding activity; protein kinase C binding activity; and small GTPase binding activity. Involved in regulation of cellular localization. Localizes to axonal growth cone; neuronal cell body; and protein-containing complex. Orthologous to human PARD6A (par-6 family cell polarity regulator alpha); PARTICIPATES IN adenosine signaling pathway; insulin signaling pathway; protein kinase C (PKC) signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: par-6 (partitioning defective 6,) homolog alpha; par-6 (partitioning defective 6,) homolog alpha (C. elegans); PAR-6 alpha; Par-6a; Par6a; partitioning defective 6 homolog alpha; partitioning defective protein 6A
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
mRatBN7.21933,589,583 - 33,591,900 (+)NCBI
Rnor_6.0 Ensembl1937,668,133 - 37,672,729 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01937,668,133 - 37,670,450 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01948,534,837 - 48,537,154 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41935,533,395 - 35,535,711 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11935,538,275 - 35,540,592 (+)NCBI
Celera1933,017,530 - 33,019,847 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:10954424   PMID:12813044   PMID:14685273   PMID:15028215   PMID:15723051   PMID:16510873   PMID:18267090   PMID:19620967   PMID:20719959   PMID:21262463   PMID:24305805   PMID:24312324  
PMID:25948265   PMID:27044754   PMID:28848997   PMID:29155179  


Genomics

Comparative Map Data
Pard6a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21933,589,583 - 33,591,900 (+)NCBI
Rnor_6.0 Ensembl1937,668,133 - 37,672,729 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01937,668,133 - 37,670,450 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01948,534,837 - 48,537,154 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41935,533,395 - 35,535,711 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11935,538,275 - 35,540,592 (+)NCBI
Celera1933,017,530 - 33,019,847 (+)NCBICelera
Cytogenetic Map19q12NCBI
PARD6A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1667,660,946 - 67,662,774 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1667,660,946 - 67,662,778 (+)EnsemblGRCh38hg38GRCh38
GRCh381667,660,956 - 67,662,774 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371667,694,863 - 67,696,677 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361666,252,352 - 66,254,182 (+)NCBINCBI36hg18NCBI36
Build 341666,252,362 - 66,254,177NCBI
Celera1652,203,341 - 52,205,171 (+)NCBI
Cytogenetic Map16q22.1NCBI
HuRef1653,567,763 - 53,569,593 (+)NCBIHuRef
CHM1_11669,102,564 - 69,104,394 (+)NCBICHM1_1
Pard6a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398106,427,780 - 106,430,126 (+)NCBIGRCm39mm39
GRCm39 Ensembl8106,427,780 - 106,430,128 (+)Ensembl
GRCm388105,701,148 - 105,703,494 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8105,701,148 - 105,703,496 (+)EnsemblGRCm38mm10GRCm38
MGSCv378108,225,054 - 108,227,394 (+)NCBIGRCm37mm9NCBIm37
MGSCv368108,590,812 - 108,592,595 (+)NCBImm8
Celera8109,926,072 - 109,928,412 (+)NCBICelera
Cytogenetic Map8D3NCBI
Pard6a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554849,019,929 - 9,021,995 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554849,019,929 - 9,022,561 (-)NCBIChiLan1.0ChiLan1.0
PARD6A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11667,394,252 - 67,395,991 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1667,394,252 - 67,395,991 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01648,004,822 - 48,006,656 (+)NCBIMhudiblu_PPA_v0panPan3
PARD6A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1581,787,424 - 81,789,833 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl581,787,553 - 81,790,324 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha581,777,186 - 81,779,574 (-)NCBI
ROS_Cfam_1.0582,222,592 - 82,224,980 (-)NCBI
UMICH_Zoey_3.1582,048,921 - 82,051,309 (-)NCBI
UNSW_CanFamBas_1.0581,730,456 - 81,732,843 (-)NCBI
UU_Cfam_GSD_1.0582,373,005 - 82,375,393 (-)NCBI
Pard6a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934941,533,814 - 41,536,924 (-)NCBI
SpeTri2.0NW_00493647518,052,768 - 18,054,620 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PARD6A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl628,280,502 - 28,283,760 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1628,280,502 - 28,282,923 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PARD6A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1559,781,890 - 59,783,990 (-)NCBI
Pard6a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474618,686,916 - 18,688,739 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19138221845Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19138221845Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19138221845Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19138221845Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19500757143907843Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191130392747879277Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191593952838798459Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192445572643907843Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)193119430141686140Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)193119430141686140Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)193119430141686140Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:43
Count of miRNA genes:40
Interacting mature miRNAs:43
Transcripts:ENSRNOT00000044971
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 2
Low 2 16 19 72 29 30 11
Below cutoff 1 43 41 41 41 8 11 6 11 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044971   ⟹   ENSRNOP00000043456
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1937,668,133 - 37,670,449 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084970   ⟹   ENSRNOP00000069044
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1937,668,693 - 37,672,729 (+)Ensembl
RefSeq Acc Id: NM_001003653   ⟹   NP_001003653
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21933,590,122 - 33,591,900 (+)NCBI
Rnor_6.01937,668,672 - 37,670,450 (+)NCBI
Rnor_5.01948,534,837 - 48,537,154 (+)NCBI
RGSC_v3.41935,533,395 - 35,535,711 (+)RGD
Celera1933,018,069 - 33,019,847 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001003654   ⟹   NP_001003654
RefSeq Status: REVIEWED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21933,589,583 - 33,591,900 (+)NCBI
Rnor_6.01937,668,133 - 37,670,450 (+)NCBI
Rnor_5.01948,534,837 - 48,537,154 (+)NCBI
RGSC_v3.41935,533,395 - 35,535,711 (+)RGD
Celera1933,017,530 - 33,019,847 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006255490   ⟹   XP_006255552
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21933,589,754 - 33,591,900 (+)NCBI
Rnor_6.01937,668,599 - 37,670,450 (+)NCBI
Rnor_5.01948,534,837 - 48,537,154 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001003654   ⟸   NM_001003654
- Peptide Label: isoform 2
- UniProtKB: F1LPM7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001003653   ⟸   NM_001003653
- Peptide Label: isoform 1
- UniProtKB: A0A0G2JUC3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255552   ⟸   XM_006255490
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000069044   ⟸   ENSRNOT00000084970
RefSeq Acc Id: ENSRNOP00000043456   ⟸   ENSRNOT00000044971
Protein Domains
PB1   PDZ   Pseudo-CRIB

Transcriptome

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

Promoters
RGD ID:13701084
Promoter ID:EPDNEW_R11608
Type:single initiation site
Name:Pard6a_1
Description:par-6 family cell polarity regulator alpha
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_6.01937,668,738 - 37,668,798EPDNEW

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)
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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)
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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
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
19 48536935 48536936 T A snv ACI/EurMcwi (MCW), BDIX.Cg-Tal/NemOda (KyushuU), SBH/Ygl (MCW), SBN/Ygl (MCW), ACI/N (KNAW), ACI/EurMcwi (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), DA/BklArbNsi (KNAW), GK/Ox (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), SDLEF7/Barth (UDEL), LE/Stm (KyushuU), BDIX/NemOda (KyushuU), DOB/Oda (KyushuU), COP/CrCrl (MCW & UW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 37670231 37670232 T A snv ACI/EurMcwi (MCW), WKY/NHsd (RGD), SBH/Ygl (MCW), SBN/Ygl (MCW), ACI/N (MCW), WKY/N (MCW), ACI/EurMcwi (RGD), GK/Ox (RGD), LE/Stm (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), COP/CrCrl (MCW & UW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 35535493 35535494 T A snv SHR/OlaIpcv (ICL), DA/BklArbNsi (ICAHN), LE/Stm (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (ICL), LE/Stm (ICL), GK/Ox (ICL), SBH/Ygl (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), ACI/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303273 AgrOrtholog
Ensembl Genes ENSRNOG00000017746 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000043456 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069044 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044971 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000084970 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.30.42.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro PAR-6_a UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PB1_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PB1_Par6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:307799 UniProtKB/TrEMBL
NCBI Gene 307799 ENTREZGENE
PANTHER PTHR14102:SF9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PB1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Pard6a PhenoGen
PROSITE PB1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PB1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50156 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JUC3 ENTREZGENE, UniProtKB/TrEMBL
  F1LPM7 ENTREZGENE, UniProtKB/TrEMBL
  PAR6A_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q4U4X0 UniProtKB/Swiss-Prot
  Q6B4M6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-19 Pard6a  par-6 family cell polarity regulator alpha  Pard6a  par-6 (partitioning defective 6,) homolog alpha (C. elegans)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Pard6a  par-6 (partitioning defective 6,) homolog alpha (C. elegans)  Par-6a    Symbol updated 1299863 APPROVED
2005-09-30 Par-6a        Symbol and Name status set to provisional 70820 PROVISIONAL