Pcdhga3 (protocadherin gamma subfamily A, 3) - Rat Genome Database
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Gene: Pcdhga3 (protocadherin gamma subfamily A, 3) Rattus norvegicus
Analyze
Symbol: Pcdhga3
Name: protocadherin gamma subfamily A, 3
RGD ID: 1598664
Description: Predicted to have calcium ion binding activity. Predicted to be involved in endosome to lysosome transport and lipid tube assembly involved in organelle fusion. Predicted to localize to membrane. Orthologous to human PCDHGA3 (protocadherin gamma subfamily A, 3); INTERACTS WITH bisphenol A; doxorubicin; furan.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: protocadherin gamma-A3
RGD Orthologs
Human
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21829,499,148 - 29,667,865 (+)NCBI
Rnor_6.0 Ensembl1830,820,321 - 30,822,735 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01830,820,151 - 30,971,113 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01830,514,378 - 30,662,065 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,580,301 - 30,754,205 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1829,145,644 - 29,311,954 (+)NCBICelera
Cytogenetic Map18p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:10650949   PMID:14672974   PMID:15347688   PMID:15744052   PMID:17110050   PMID:21917590  


Genomics

Comparative Map Data
Pcdhga3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21829,499,148 - 29,667,865 (+)NCBI
Rnor_6.0 Ensembl1830,820,321 - 30,822,735 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01830,820,151 - 30,971,113 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01830,514,378 - 30,662,065 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41830,580,301 - 30,754,205 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1829,145,644 - 29,311,954 (+)NCBICelera
Cytogenetic Map18p11NCBI
PCDHGA3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5141,343,829 - 141,512,975 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl5141,343,829 - 141,512,979 (+)EnsemblGRCh38hg38GRCh38
GRCh385141,343,829 - 141,512,975 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh375140,723,396 - 140,892,542 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh375140,723,601 - 140,892,546 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365140,703,785 - 140,872,730 (+)NCBINCBI36hg18NCBI36
Build 345140,703,784 - 140,706,274NCBI
Celera5136,800,426 - 136,969,282 (+)NCBI
Cytogenetic Map5q31.3NCBI
HuRef5135,868,672 - 136,037,386 (+)NCBIHuRef
CHM1_15140,156,808 - 140,325,823 (+)NCBICHM1_1
Pcdhga3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391837,807,388 - 37,974,926 (+)NCBIGRCm39mm39
GRCm381837,674,335 - 37,841,873 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1837,674,307 - 37,841,873 (+)EnsemblGRCm38mm10GRCm38
MGSCv371837,833,989 - 38,001,527 (+)NCBIGRCm37mm9NCBIm37
MGSCv361837,861,242 - 38,028,850 (+)NCBImm8
MGSCv361837,800,309 - 37,967,847 (+)NCBImm8
Celera1839,168,490 - 39,185,352 (+)NCBICelera
Cytogenetic Map18B3NCBI

Position Markers
D18Rat100  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01830,928,541 - 30,928,753NCBIRnor6.0
Rnor_5.01830,622,699 - 30,622,911UniSTSRnor5.0
RGSC_v3.41830,688,754 - 30,688,967RGDRGSC3.4
RGSC_v3.41830,688,755 - 30,688,967UniSTSRGSC3.4
RGSC_v3.11830,715,400 - 30,715,613RGD
Celera1829,253,446 - 29,253,658UniSTS
SHRSP x BN Map1813.7599UniSTS
SHRSP x BN Map1813.7599RGD
Cytogenetic Map18p11UniSTS
D18Wox21  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01830,969,617 - 30,969,695NCBIRnor6.0
Rnor_5.01830,660,569 - 30,660,647UniSTSRnor5.0
RGSC_v3.41830,752,709 - 30,752,787UniSTSRGSC3.4
Celera1829,310,458 - 29,310,536UniSTS
Cytogenetic Map18p11UniSTS
BF403187  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01830,828,762 - 30,828,882NCBIRnor6.0
Rnor_5.01830,522,989 - 30,523,109UniSTSRnor5.0
RGSC_v3.41830,588,912 - 30,589,032UniSTSRGSC3.4
Celera1829,154,255 - 29,154,375UniSTS
RH 3.4 Map18428.1UniSTS
Cytogenetic Map18p11UniSTS
RH129840  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01830,953,941 - 30,954,108NCBIRnor6.0
Rnor_5.01830,648,099 - 30,648,266UniSTSRnor5.0
RGSC_v3.41830,713,933 - 30,714,100UniSTSRGSC3.4
Celera1829,279,250 - 29,279,417UniSTS
Cytogenetic Map18p11UniSTS
BF398325  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01830,900,106 - 30,900,255NCBIRnor6.0
Rnor_5.01830,594,333 - 30,594,482UniSTSRnor5.0
RGSC_v3.41830,660,266 - 30,660,415UniSTSRGSC3.4
Celera1829,225,604 - 29,225,753UniSTS
RH 3.4 Map8610.9UniSTS
Cytogenetic Map18p11UniSTS
RH138098  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01830,907,536 - 30,907,687NCBIRnor6.0
Rnor_5.01830,601,763 - 30,601,914UniSTSRnor5.0
RGSC_v3.41830,667,696 - 30,667,847UniSTSRGSC3.4
Celera1829,233,034 - 29,233,185UniSTS
RH 3.4 Map18426.4UniSTS
Cytogenetic Map18p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135097280Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18138195967Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18138195967Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18138753381Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18371954732487870Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18440751362570466Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18543013441781619Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181467885259678852Rat
631264Scl22Serum cholesterol level QTL 226.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)181553296332704022Rat
61382Bp46Blood pressure QTL 4618.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181553296332704022Rat
1331766Bp236Blood pressure QTL 2363.022arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181553942732670473Rat
1331753Bp231Blood pressure QTL 2313.643arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181553942753861431Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181553942761499684Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181553967161985648Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181569587268524999Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181569587287080053Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181569587287080053Rat
1358193Emca2Estrogen-induced mammary cancer QTL 21.6mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)181903103068436105Rat
1331775Bp235Blood pressure QTL 2353.201arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)181925171732670473Rat
1331735Rf44Renal function QTL 442.981total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181925171732670473Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)182028575887080053Rat
7387267Uae42Urinary albumin excretion QTL 420.61urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)142163949166639491Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182260373687074531Rat
6903353Bp353Blood pressure QTL 3532.8arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182260476461985648Rat
1641923Colcr8Colorectal carcinoma resistance QTL 83.10.0014intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)182318422753861431Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182596102681761656Rat
2325839Bp348Blood pressure QTL 3480.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182674340443659626Rat
2301413Bp318Blood pressure QTL 3180.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182774302448499517Rat
12904673Cm127Cardiac mass QTL 1270.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)182774302448499517Rat
12904675Am19Aortic mass QTL 190.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)182774302448499517Rat
12904677Kidm72Kidney mass QTL 720.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)182774302448499517Rat
12904668Bw188Body weight QTL 1880.03body mass (VT:0001259)body weight (CMO:0000012)182774302448499517Rat
12904669Cm125Cardiac mass QTL 1250.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)182774302448499517Rat
12904670Cm126Cardiac mass QTL 1260.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)182774302448499517Rat
2300157Bmd66Bone mineral density QTL 6613.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)183053361475533614Rat
2300177Bmd65Bone mineral density QTL 6519.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)183053361475533614Rat
2293704Bss35Bone structure and strength QTL 354.590.0002femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)183053361475533614Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:20
Count of miRNA genes:17
Interacting mature miRNAs:20
Transcripts:ENSRNOT00000060472
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 33 1 2
Low 40 27 11 18 11 8 8 41 29 36 9 8
Below cutoff 3 3 26 26 1 26 3 6 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000060472   ⟹   ENSRNOP00000057216
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1830,820,321 - 30,822,735 (+)Ensembl
RefSeq Acc Id: NM_001037154   ⟹   NP_001032231
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21829,499,148 - 29,667,865 (+)NCBI
Rnor_6.01830,820,151 - 30,971,113 (+)NCBI
Rnor_5.01830,514,378 - 30,662,065 (+)NCBI
RGSC_v3.41830,580,301 - 30,754,205 (+)RGD
Celera1829,145,644 - 29,311,954 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001032231 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT77596 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001032231   ⟸   NM_001037154
- Peptide Label: precursor
- UniProtKB: I6LBX2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000057216   ⟸   ENSRNOT00000060472
Protein Domains
Cadherin

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)
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)
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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)
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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
18 30564042 30564043 C T snv ZF (KyushuU), BUF/MNa (KyushuU), LEC/Tj (KyushuU), ZFDM (KyushuU), RCS/Kyo (KyushuU)
18 30564971 30564972 G T snv IS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU)
18 30585338 30585339 C G snv HWY/Slc (KyushuU), F344/Jcl (KyushuU), F344/Stm (KyushuU), F344/NSlc (KyushuU), LE/Stm (KyushuU), F344/DuCrlCrlj (KyushuU), SBN/Ygl (MCW), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW)
18 30586362 30586363 A T snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), IS/Kyo (KyushuU), BUF/MNa (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), DOB/Oda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), ZFDM (KyushuU)
18 30587400 30587401 T C snv DOB/Oda (KyushuU)
18 30587503 30587504 C T snv F344/Jcl (KyushuU), LEC/Tj (KyushuU), HWY/Slc (KyushuU), F344/Stm (KyushuU), IS-Tlk/Kyo (KyushuU), FHH/EurMcwi (MCW), COP/CrCrl (MCW & UW), F344/NSlc (KyushuU), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), KFRS3B/Kyo (KyushuU), SS/JrHsdMcwi (MCW), ACI/EurMcwi (MCW), IS/Kyo (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), DOB/Oda (KyushuU), FHL/EurMcwi (MCW)
18 30587578 30587579 C T snv SS/JrHsdMcwi (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), SBH/Ygl (MCW), COP/CrCrl (MCW & UW), ACI/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1598664 AgrOrtholog
Ensembl Genes ENSRNOG00000039461 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000057216 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060472 UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_C UniProtKB/TrEMBL
  Cadherin_CBD UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
  PCDHGA2 UniProtKB/TrEMBL
KEGG Report rno:498847 UniProtKB/TrEMBL
NCBI Gene 498847 ENTREZGENE
PANTHER PTHR24028:SF134 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Cadherin_C_2 UniProtKB/TrEMBL
  Cadherin_tail UniProtKB/TrEMBL
PhenoGen Pcdhga3 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt D4ACT8_RAT UniProtKB/TrEMBL
  I6LBX2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-12-10 Pcdhga3  protocadherin gamma subfamily A, 3      Symbol and Name status set to provisional 70820 PROVISIONAL