Pcdh15 (protocadherin related 15) - Rat Genome Database

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Gene: Pcdh15 (protocadherin related 15) Rattus norvegicus
Analyze
Symbol: Pcdh15
Name: protocadherin related 15
RGD ID: 1590969
Description: Exhibits protein N-terminus binding activity. Involved in response to calcium ion. Predicted to localize to several cellular components, including extracellular space; photoreceptor outer segment; and stereocilium. Human ortholog(s) of this gene implicated in Usher syndrome type 1D; Usher syndrome type 1F; and autosomal recessive nonsyndromic deafness 23. Orthologous to human PCDH15 (protocadherin related 15); PARTICIPATES IN auditory mechanotransduction pathway; retinitis pigmentosa pathway; INTERACTS WITH atrazine; bisphenol A; glyphosate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC690865; NEWGENE_1590969; protocadherin 15; protocadherin-15; protocadherin-related 15; similar to protocadherin 15
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   KCI/Kyo  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22013,997,094 - 15,496,446 (-)NCBI
Rnor_6.0 Ensembl2014,952,213 - 15,334,745 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02014,952,213 - 15,334,745 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02018,712,995 - 19,021,206 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.02017,138,580 - 17,521,597 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42014,507,804 - 15,240,479 (-)NCBIRGSC3.4rn4RGSC3.4
Celera2015,459,406 - 16,139,466 (-)NCBICelera
Cytogenetic Map20p12NCBI
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

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:5093631   PMID:9653653   PMID:10430593   PMID:10978835   PMID:11124469   PMID:11138007   PMID:11398101   PMID:11487575   PMID:14570705   PMID:15537665   PMID:15811708   PMID:16369489  
PMID:16481439   PMID:16679490   PMID:16799054   PMID:16887306   PMID:16962269   PMID:18339676   PMID:19151506   PMID:21427143   PMID:23217710   PMID:23376485   PMID:26754646  


Genomics

Comparative Map Data
Pcdh15
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22013,997,094 - 15,496,446 (-)NCBI
Rnor_6.0 Ensembl2014,952,213 - 15,334,745 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02014,952,213 - 15,334,745 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02018,712,995 - 19,021,206 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.02017,138,580 - 17,521,597 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42014,507,804 - 15,240,479 (-)NCBIRGSC3.4rn4RGSC3.4
Celera2015,459,406 - 16,139,466 (-)NCBICelera
Cytogenetic Map20p12NCBI
PCDH15
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1053,802,771 - 55,627,942 (-)EnsemblGRCh38hg38GRCh38
GRCh381053,802,771 - 55,629,182 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371055,562,531 - 57,387,702 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361055,250,866 - 56,231,057 (-)NCBINCBI36hg18NCBI36
Build 341055,250,865 - 56,231,057NCBI
Celera1048,825,500 - 49,824,287 (-)NCBI
Cytogenetic Map10q21.1NCBI
HuRef1049,544,130 - 50,545,244 (-)NCBIHuRef
CHM1_11055,844,015 - 56,842,749 (-)NCBICHM1_1
Pcdh15
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391072,932,003 - 74,485,663 (+)NCBIGRCm39mm39
GRCm39 Ensembl1072,935,174 - 74,485,569 (+)Ensembl
GRCm381073,096,277 - 74,649,831 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1073,099,342 - 74,649,737 (+)EnsemblGRCm38mm10GRCm38
MGSCv371073,284,615 - 74,112,482 (+)NCBIGRCm37mm9NCBIm37
MGSCv361073,667,153 - 74,076,383 (+)NCBImm8
Celera1074,887,647 - 75,712,367 (+)NCBICelera
Cytogenetic Map10B5.3NCBI
cM Map1037.43NCBI
Pcdh15
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554258,428,680 - 8,899,028 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554258,443,523 - 9,203,177 (-)NCBIChiLan1.0ChiLan1.0
PCDH15
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11052,661,035 - 54,456,043 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1052,666,969 - 53,536,611 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01050,452,290 - 52,236,538 (-)NCBIMhudiblu_PPA_v0panPan3
PCDH15
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12633,426,728 - 34,589,208 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2633,719,839 - 34,588,017 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2633,735,217 - 34,473,542 (+)NCBI
ROS_Cfam_1.02635,380,608 - 36,116,590 (+)NCBI
UMICH_Zoey_3.12633,285,817 - 34,023,503 (+)NCBI
UNSW_CanFamBas_1.02632,872,620 - 33,606,715 (+)NCBI
UU_Cfam_GSD_1.02634,074,758 - 34,812,730 (+)NCBI
Pcdh15
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721373,974,985 - 74,439,013 (+)NCBI
SpeTri2.0NW_004936910233,800 - 602,145 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCDH15
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11495,530,168 - 96,388,032 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214103,931,584 - 104,873,398 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PCDH15
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1975,642,985 - 77,415,370 (+)NCBI
ChlSab1.1 Ensembl976,726,627 - 77,398,716 (+)Ensembl
Pcdh15
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247919,042,311 - 9,992,341 (+)NCBI

Position Markers
D20Rat60  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22014,100,894 - 14,101,050 (+)MAPPER
Rnor_6.02015,050,410 - 15,050,565NCBIRnor6.0
Rnor_5.02017,237,299 - 17,237,454UniSTSRnor5.0
RGSC_v3.42014,605,696 - 14,605,852RGDRGSC3.4
RGSC_v3.42014,605,697 - 14,605,852UniSTSRGSC3.4
RGSC_v3.12014,612,602 - 14,612,758RGD
Celera2015,551,025 - 15,551,180UniSTS
FHH x ACI Map206.8999RGD
FHH x ACI Map206.8999UniSTS
Cytogenetic Map20p12UniSTS
D20Got15  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22014,114,102 - 14,114,361 (+)MAPPER
Rnor_6.02015,063,616 - 15,063,874NCBIRnor6.0
Rnor_5.02017,250,507 - 17,250,765UniSTSRnor5.0
RGSC_v3.42014,618,968 - 14,619,227RGDRGSC3.4
RGSC_v3.42014,618,969 - 14,619,227UniSTSRGSC3.4
RGSC_v3.12014,625,874 - 14,626,133RGD
Celera2015,560,527 - 15,560,785UniSTS
RH 2.0 Map20206.1RGD
Cytogenetic Map20p12UniSTS
D20Got14  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22014,041,517 - 14,041,743 (+)MAPPER
Rnor_6.02014,991,035 - 14,991,260NCBIRnor6.0
Rnor_5.02017,177,790 - 17,178,015UniSTSRnor5.0
RGSC_v3.42014,546,135 - 14,546,361RGDRGSC3.4
RGSC_v3.42014,546,136 - 14,546,361UniSTSRGSC3.4
RGSC_v3.12014,553,041 - 14,553,267RGD
RH 2.0 Map20210.6RGD
Cytogenetic Map20p12UniSTS
RH142552  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22014,610,466 - 14,610,747 (-)MAPPER
Rnor_6.02016,616,952 - 16,617,232NCBIRnor6.0
Rnor_5.02018,798,325 - 18,798,605UniSTSRnor5.0
RGSC_v3.42015,120,682 - 15,120,962UniSTSRGSC3.4
Celera2016,050,308 - 16,050,588UniSTS
RH 3.4 Map20180.53UniSTS
Cytogenetic Map20p12UniSTS
RH144278  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22014,265,653 - 14,265,837 (+)MAPPER
Rnor_6.02015,214,790 - 15,214,973NCBIRnor6.0
Rnor_5.02017,401,681 - 17,401,864UniSTSRnor5.0
RGSC_v3.42014,770,572 - 14,770,755UniSTSRGSC3.4
Celera2015,710,436 - 15,710,619UniSTS
RH 3.4 Map20181.74UniSTS
Cytogenetic Map20p12UniSTS
AU048858  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22014,100,889 - 14,100,983 (+)MAPPER
Rnor_6.02015,050,405 - 15,050,498NCBIRnor6.0
Rnor_5.02017,237,294 - 17,237,387UniSTSRnor5.0
RGSC_v3.42014,605,692 - 14,605,785UniSTSRGSC3.4
Celera2015,551,020 - 15,551,113UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20587544818739210Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20865434118872273Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat


Related Rat Strains
The following Strains have been annotated to Pcdh15

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:599
Count of miRNA genes:244
Interacting mature miRNAs:291
Transcripts:ENSRNOT00000000744, ENSRNOT00000065007, ENSRNOT00000065482, ENSRNOT00000065549, ENSRNOT00000066040, ENSRNOT00000066687, ENSRNOT00000067633, ENSRNOT00000067698, ENSRNOT00000068735, ENSRNOT00000074818
Prediction methods:Microtar, 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 8 17 70 4 30
Below cutoff 3 11 13 5 2 5 8 9 2 18 11 7 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067633   ⟹   ENSRNOP00000060829
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2014,952,213 - 15,334,745 (-)Ensembl
RefSeq Acc Id: NM_001271377   ⟹   NP_001258306
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22014,002,696 - 14,700,033 (-)NCBI
Rnor_6.02014,952,213 - 15,334,745 (-)NCBI
Rnor_5.02017,138,580 - 17,521,597 (-)NCBI
Rnor_5.02018,712,995 - 19,021,206 (+)NCBI
Celera2015,459,406 - 16,139,466 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099104   ⟹   XP_038955032
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22014,013,299 - 15,496,446 (-)NCBI
RefSeq Acc Id: XM_039099105   ⟹   XP_038955033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22014,013,299 - 14,826,194 (-)NCBI
RefSeq Acc Id: XM_039099106   ⟹   XP_038955034
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22014,013,299 - 14,954,702 (-)NCBI
RefSeq Acc Id: XM_039099107   ⟹   XP_038955035
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22014,013,299 - 14,826,194 (-)NCBI
RefSeq Acc Id: XM_039099108   ⟹   XP_038955036
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22014,013,299 - 15,496,445 (-)NCBI
RefSeq Acc Id: XM_039099109   ⟹   XP_038955037
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22014,013,299 - 15,496,445 (-)NCBI
RefSeq Acc Id: XM_039099110   ⟹   XP_038955038
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22014,013,299 - 15,496,445 (-)NCBI
RefSeq Acc Id: XM_039099111   ⟹   XP_038955039
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22013,997,094 - 15,496,436 (-)NCBI
RefSeq Acc Id: XM_039099112   ⟹   XP_038955040
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22013,997,094 - 15,496,434 (-)NCBI
RefSeq Acc Id: XM_039099114   ⟹   XP_038955042
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22014,001,386 - 15,496,446 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001258306   ⟸   NM_001271377
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000060829   ⟸   ENSRNOT00000067633
RefSeq Acc Id: XP_038955039   ⟸   XM_039099111
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038955040   ⟸   XM_039099112
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038955042   ⟸   XM_039099114
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038955032   ⟸   XM_039099104
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955038   ⟸   XM_039099110
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038955037   ⟸   XM_039099109
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955036   ⟸   XM_039099108
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955034   ⟸   XM_039099106
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955035   ⟸   XM_039099107
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955033   ⟸   XM_039099105
- Peptide Label: isoform X1
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)
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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)
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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_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 14964789 14964790 G A snv F344/NRrrc (MCW), MR/N (MCW), WN/N (MCW), F344/NCrl (RGD), SS/JrHsdMcwi (RGD), LL/MavRrrc (RGD), SBH/Ygl (RGD), SR/JrHsd (RGD), LH/MavRrrc (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590969 AgrOrtholog
Ensembl Genes ENSRNOG00000000606 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060829 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067633 ENTREZGENE, UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Protocadherin-15 UniProtKB/TrEMBL
NCBI Gene 690865 ENTREZGENE
PANTHER PTHR24028:SF11 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
PhenoGen Pcdh15 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt F1LXN4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Pcdh15  protocadherin related 15  NEWGENE_1590969  protocadherin-related 15  Data Merged 737654 PROVISIONAL
2017-07-18 Pcdh15  protocadherin related 15  Pcdh15  protocadherin 15  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 NEWGENE_1590969  protocadherin-related 15      Symbol and Name status set to provisional 70820 PROVISIONAL
2013-05-24 Pcdh15  protocadherin 15  LOC687745  similar to protocadherin 15  Data Merged 1643240 APPROVED
2008-03-06 Pcdh15  protocadherin 15  LOC690865  similar to protocadherin 15  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC690865  similar to protocadherin 15      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC687745  similar to protocadherin 15      Symbol and Name status set to provisional 70820 PROVISIONAL