Pcdh9 (protocadherin 9) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Pcdh9 (protocadherin 9) Rattus norvegicus
Analyze
Symbol: Pcdh9
Name: protocadherin 9
RGD ID: 1306348
Description: Predicted to enable calcium ion binding activity. Involved in forebrain development. Predicted to be located in cell-cell contact zone and growth cone. Orthologous to human PCDH9 (protocadherin 9); INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC306091; protocadherin-9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81575,748,472 - 76,646,644 (-)NCBIGRCr8
mRatBN7.21569,340,108 - 70,237,531 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1569,340,645 - 70,237,538 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1573,385,787 - 74,283,083 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01574,471,032 - 75,368,337 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01571,367,999 - 72,310,028 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01576,787,108 - 77,738,668 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1577,733,402 - 77,736,892 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01580,956,263 - 81,286,488 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01580,341,840 - 80,658,843 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41575,827,180 - 76,739,147 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11575,842,960 - 76,753,010 (-)NCBI
Celera1568,728,387 - 69,614,167 (-)NCBICelera
Cytogenetic Map15q21NCBI
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
1,2-dimethylhydrazine  (EXP)
15-acetyldeoxynivalenol  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2-palmitoylglycerol  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
cefaloridine  (EXP)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
crocidolite asbestos  (ISO)
CU-O LINKAGE  (ISO)
cyclosporin A  (ISO)
DDT  (EXP)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
fenvalerate  (EXP)
formaldehyde  (ISO)
genistein  (ISO)
ketoconazole  (ISO)
maneb  (ISO)
mercury dibromide  (ISO)
methapyrilene  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel atom  (ISO)
ozone  (ISO)
paracetamol  (EXP)
paraquat  (EXP,ISO)
PCB138  (ISO)
pentanal  (ISO)
permethrin  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
tert-butyl hydroperoxide  (ISO)
trichostatin A  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Spatiotemporal expression pattern of non-clustered protocadherin family members in the developing rat brain. Kim SY, etal., Neuroscience. 2007 Jul 29;147(4):996-1021. Epub 2007 Jul 5.
3. Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts. Loh KH, etal., Cell. 2016 Aug 25;166(5):1295-1307.e21. doi: 10.1016/j.cell.2016.07.041.
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:22982106  


Genomics

Comparative Map Data
Pcdh9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81575,748,472 - 76,646,644 (-)NCBIGRCr8
mRatBN7.21569,340,108 - 70,237,531 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1569,340,645 - 70,237,538 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1573,385,787 - 74,283,083 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01574,471,032 - 75,368,337 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01571,367,999 - 72,310,028 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01576,787,108 - 77,738,668 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1577,733,402 - 77,736,892 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01580,956,263 - 81,286,488 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01580,341,840 - 80,658,843 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41575,827,180 - 76,739,147 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11575,842,960 - 76,753,010 (-)NCBI
Celera1568,728,387 - 69,614,167 (-)NCBICelera
Cytogenetic Map15q21NCBI
PCDH9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381366,302,834 - 67,230,336 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1366,302,834 - 67,230,445 (-)EnsemblGRCh38hg38GRCh38
GRCh371366,876,966 - 67,804,468 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361365,774,967 - 66,702,464 (-)NCBINCBI36Build 36hg18NCBI36
Build 341365,774,967 - 66,702,464NCBI
Celera1347,778,636 - 48,706,116 (-)NCBICelera
Cytogenetic Map13q21.32NCBI
HuRef1347,575,260 - 48,502,804 (-)NCBIHuRef
CHM1_11366,844,545 - 67,771,982 (-)NCBICHM1_1
T2T-CHM13v2.01365,522,767 - 66,450,396 (-)NCBIT2T-CHM13v2.0
Pcdh9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391493,251,136 - 94,132,619 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1493,250,846 - 94,128,115 (-)EnsemblGRCm39 Ensembl
GRCm381493,013,700 - 93,892,834 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1493,013,410 - 93,890,679 (-)EnsemblGRCm38mm10GRCm38
MGSCv371493,412,920 - 94,287,951 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361491,896,835 - 92,773,764 (-)NCBIMGSCv36mm8
MGSCv361484,158,372 - 85,033,109 (-)NCBIMGSCv36mm8
Celera1490,651,091 - 91,529,532 (-)NCBICelera
Cytogenetic Map14E2.1NCBI
cM Map1445.8NCBI
Pcdh9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540438,667,015 - 39,532,423 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540438,666,480 - 39,534,211 (+)NCBIChiLan1.0ChiLan1.0
PCDH9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21467,859,201 - 68,775,102 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11366,450,616 - 67,366,559 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01347,512,960 - 48,430,521 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11366,308,482 - 67,224,143 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1366,310,212 - 67,222,134 (-)Ensemblpanpan1.1panPan2
PCDH9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12221,326,040 - 22,212,847 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2221,327,856 - 22,213,083 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2221,176,900 - 22,063,212 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02221,577,598 - 22,465,466 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2221,579,414 - 22,465,684 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12221,278,289 - 22,165,850 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02221,365,500 - 22,246,733 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02221,419,187 - 22,313,542 (-)NCBIUU_Cfam_GSD_1.0
Pcdh9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945138,092,918 - 138,942,759 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936553424,988 - 1,272,450 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936553424,425 - 971,388 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCDH9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1138,523,033 - 39,453,741 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11138,522,221 - 39,455,166 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21141,808,073 - 42,265,226 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PCDH9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1345,256,171 - 46,194,724 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660461,136,960 - 2,056,266 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pcdh9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474827,606,224 - 28,543,269 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474827,604,426 - 28,543,256 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pcdh9
6145 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:160
Count of miRNA genes:125
Interacting mature miRNAs:133
Transcripts:ENSRNOT00000057924
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
724545Niddm54Non-insulin dependent diabetes mellitus QTL 540.02blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)155079449473699215Rat
2317050Aia24Adjuvant induced arthritis QTL 242.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)155284790873690657Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)155380615298806152Rat
61477Aia4Adjuvant induced arthritis QTL 43joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)155559608991365858Rat
631516Gluco31Glucose level QTL 317blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)155559608995018120Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1558156477101769107Rat
2313080Bss65Bone structure and strength QTL 653.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)156099046873690657Rat
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1567588667101769107Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1568327165100062518Rat
724548Niddm55Non-insulin dependent diabetes mellitus QTL 550.02blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)156832736073699069Rat

Markers in Region
D15Rat94  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21569,625,793 - 69,625,966 (+)MAPPERmRatBN7.2
Rnor_6.01577,072,146 - 77,072,316NCBIRnor6.0
Rnor_5.01580,627,077 - 80,627,247UniSTSRnor5.0
RGSC_v3.41576,115,380 - 76,115,762RGDRGSC3.4
RGSC_v3.41576,115,491 - 76,115,661UniSTSRGSC3.4
RGSC_v3.11576,131,160 - 76,131,542RGD
Celera1569,012,625 - 69,012,795UniSTS
SHRSP x BN Map1541.3498RGD
SHRSP x BN Map1541.3498UniSTS
Cytogenetic Map15q21UniSTS
D15Got211  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21569,545,428 - 69,545,505 (+)MAPPERmRatBN7.2
Rnor_6.01576,991,703 - 76,991,779NCBIRnor6.0
Rnor_5.01580,546,433 - 80,546,509UniSTSRnor5.0
RGSC_v3.41576,034,917 - 76,034,993UniSTSRGSC3.4
Celera1568,932,391 - 68,932,467UniSTS
Cytogenetic Map15q21UniSTS
BE102165  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21569,898,848 - 69,898,997 (+)MAPPERmRatBN7.2
Rnor_6.01577,397,613 - 77,397,761NCBIRnor6.0
Rnor_5.01580,949,492 - 80,949,640UniSTSRnor5.0
RGSC_v3.41576,396,481 - 76,396,629UniSTSRGSC3.4
Celera1569,278,271 - 69,278,419UniSTS
Cytogenetic Map15q21UniSTS
RH45841  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21569,340,410 - 69,340,548 (+)MAPPERmRatBN7.2
Rnor_6.01576,787,411 - 76,787,548NCBIRnor6.0
Rnor_5.01580,342,141 - 80,342,278UniSTSRnor5.0
RGSC_v3.41575,827,481 - 75,827,618UniSTSRGSC3.4
Celera1568,728,689 - 68,728,826UniSTS
Cytogenetic Map15q21UniSTS
BE102662  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21569,705,889 - 69,706,061 (+)MAPPERmRatBN7.2
Rnor_6.01577,164,994 - 77,165,165NCBIRnor6.0
Rnor_5.01580,719,657 - 80,719,828UniSTSRnor5.0
RGSC_v3.41576,198,767 - 76,198,938UniSTSRGSC3.4
Celera1569,092,212 - 69,092,383UniSTS
Cytogenetic Map15q21UniSTS
RH137936  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21570,212,748 - 70,212,894 (+)MAPPERmRatBN7.2
Rnor_6.01577,713,859 - 77,714,004NCBIRnor6.0
Rnor_5.01581,263,572 - 81,263,717UniSTSRnor5.0
RGSC_v3.41576,714,386 - 76,714,531UniSTSRGSC3.4
Celera1569,591,251 - 69,591,396UniSTS
Cytogenetic Map15q21UniSTS
BF390670  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21569,913,712 - 69,913,909 (+)MAPPERmRatBN7.2
Rnor_6.01577,411,078 - 77,411,274NCBIRnor6.0
Rnor_5.01580,962,957 - 80,963,153UniSTSRnor5.0
RGSC_v3.41576,411,340 - 76,411,536UniSTSRGSC3.4
Celera1569,293,090 - 69,293,286UniSTS
Cytogenetic Map15q21UniSTS
fb39b03.x1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1568,735,414 - 68,737,035UniSTS
Celera1568,735,432 - 68,737,035UniSTS
Cytogenetic Map15q21UniSTS
UniSTS:546922  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21569,340,247 - 69,341,246 (+)MAPPERmRatBN7.2
Rnor_6.01576,787,248 - 76,788,246NCBIRnor6.0
Rnor_5.01580,341,978 - 80,342,976UniSTSRnor5.0
Celera1568,728,525 - 68,729,524UniSTS
Cytogenetic Map15q21UniSTS


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 60 1
Low 18 20 4 16 4 7 7 14 26 32 10 7
Below cutoff 2 24 11 11 3 11 1 3 9 4 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001191688 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770867 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599711 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093372 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063274318 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063274319 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063274320 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ863132 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000057924   ⟹   ENSRNOP00000054733
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1569,340,645 - 70,237,538 (-)Ensembl
Rnor_6.0 Ensembl1577,733,402 - 77,736,892 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096830   ⟹   ENSRNOP00000077280
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1569,340,645 - 70,237,538 (-)Ensembl
RefSeq Acc Id: NM_001191688   ⟹   NP_001178617
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,748,474 - 76,643,952 (-)NCBI
mRatBN7.21569,340,110 - 70,235,665 (-)NCBI
Rnor_6.01576,787,110 - 77,736,775 (-)NCBI
Rnor_5.01580,341,840 - 80,658,843 (-)NCBI
Rnor_5.01580,956,263 - 81,286,488 (-)NCBI
Celera1568,728,387 - 69,614,167 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770867   ⟹   XP_008769089
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,748,472 - 76,646,644 (-)NCBI
mRatBN7.21569,340,108 - 70,237,531 (-)NCBI
Rnor_6.01576,787,108 - 77,738,666 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599710   ⟹   XP_017455199
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,748,472 - 76,646,644 (-)NCBI
mRatBN7.21569,340,108 - 70,237,531 (-)NCBI
Rnor_6.01576,787,108 - 77,738,668 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599711   ⟹   XP_017455200
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,748,472 - 76,646,644 (-)NCBI
mRatBN7.21569,340,108 - 70,237,531 (-)NCBI
Rnor_6.01576,787,108 - 77,738,667 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599712   ⟹   XP_017455201
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,748,472 - 76,646,644 (-)NCBI
mRatBN7.21569,340,108 - 70,237,531 (-)NCBI
Rnor_6.01576,787,108 - 77,738,667 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599713   ⟹   XP_017455202
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,750,522 - 76,646,644 (-)NCBI
mRatBN7.21569,559,030 - 70,237,531 (-)NCBI
Rnor_6.01577,004,358 - 77,738,668 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039093368   ⟹   XP_038949296
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,748,472 - 76,645,821 (-)NCBI
mRatBN7.21569,340,108 - 70,237,528 (-)NCBI
RefSeq Acc Id: XM_039093371   ⟹   XP_038949299
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,817,746 - 76,646,644 (-)NCBI
mRatBN7.21569,409,392 - 70,237,531 (-)NCBI
RefSeq Acc Id: XM_039093372   ⟹   XP_038949300
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,750,522 - 76,646,644 (-)NCBI
mRatBN7.21569,559,030 - 70,237,531 (-)NCBI
RefSeq Acc Id: XM_039093373   ⟹   XP_038949301
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,750,522 - 76,646,644 (-)NCBI
mRatBN7.21569,559,030 - 70,237,531 (-)NCBI
RefSeq Acc Id: XM_039093374   ⟹   XP_038949302
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,817,748 - 76,646,644 (-)NCBI
mRatBN7.21569,409,395 - 70,237,531 (-)NCBI
RefSeq Acc Id: XM_063274318   ⟹   XP_063130388
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,748,472 - 76,645,820 (-)NCBI
RefSeq Acc Id: XM_063274319   ⟹   XP_063130389
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,748,472 - 76,645,820 (-)NCBI
RefSeq Acc Id: XM_063274320   ⟹   XP_063130390
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81575,817,747 - 76,646,644 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001178617   ⟸   NM_001191688
- Peptide Label: precursor
- UniProtKB: A0A8I5ZK96 (UniProtKB/TrEMBL),   A6HU40 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769089   ⟸   XM_008770867
- Peptide Label: isoform X4
- UniProtKB: A6HU40 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455199   ⟸   XM_017599710
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZK96 (UniProtKB/TrEMBL),   A6HU40 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455200   ⟸   XM_017599711
- Peptide Label: isoform X2
- UniProtKB: F1LS01 (UniProtKB/TrEMBL),   A6HU38 (UniProtKB/TrEMBL),   A6HU40 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455201   ⟸   XM_017599712
- Peptide Label: isoform X3
- UniProtKB: A6HU40 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455202   ⟸   XM_017599713
- Peptide Label: isoform X5
- UniProtKB: A6HU40 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000054733   ⟸   ENSRNOT00000057924
RefSeq Acc Id: XP_038949296   ⟸   XM_039093368
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZK96 (UniProtKB/TrEMBL),   A6HU40 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038949299   ⟸   XM_039093371
- Peptide Label: isoform X6
- UniProtKB: A6HU40 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038949302   ⟸   XM_039093374
- Peptide Label: isoform X10
- UniProtKB: A6HU40 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038949301   ⟸   XM_039093373
- Peptide Label: isoform X9
- UniProtKB: A6HU40 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038949300   ⟸   XM_039093372
- Peptide Label: isoform X7
- UniProtKB: A6HU40 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000077280   ⟸   ENSRNOT00000096830
RefSeq Acc Id: XP_063130389   ⟸   XM_063274319
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063130388   ⟸   XM_063274318
- Peptide Label: isoform X2
- UniProtKB: A6HU38 (UniProtKB/TrEMBL),   F1LS01 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063130390   ⟸   XM_063274320
- Peptide Label: isoform X8
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LS01-F1-model_v2 AlphaFold F1LS01 1-1032 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306348 AgrOrtholog
BioCyc Gene G2FUF-12869 BioCyc
Ensembl Genes ENSRNOG00000038068 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000057924.5 UniProtKB/TrEMBL
  ENSRNOT00000096830.1 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin-like_dom UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
  Protocadherin UniProtKB/TrEMBL
KEGG Report rno:306091 UniProtKB/TrEMBL
NCBI Gene 306091 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN-9 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
  Protocadherin UniProtKB/TrEMBL
PharmGKB PCDH9 RGD
PhenoGen Pcdh9 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000038068 RatGTEx
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP SSF49313 UniProtKB/TrEMBL
UniProt A0A8I5ZK96 ENTREZGENE, UniProtKB/TrEMBL
  A6HU38 ENTREZGENE, UniProtKB/TrEMBL
  A6HU40 ENTREZGENE, UniProtKB/TrEMBL
  F1LS01 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Pcdh9  protocadherin 9   Pcdh9_predicted  protocadherin 9 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pcdh9_predicted  protocadherin 9 (predicted)      Symbol and Name status set to approved 70820 APPROVED