Pcdh19 (protocadherin 19) - 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 Behavioral & Substance Use Disorder 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 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
Advanced Search (OLGA)
Gene: Pcdh19 (protocadherin 19) Rattus norvegicus
Analyze
Symbol: Pcdh19
Name: protocadherin 19
RGD ID: 1565392
Description: Predicted to enable cell adhesion molecule binding activity. Predicted to be involved in cell adhesion. Predicted to be located in membrane. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 9. Orthologous to human PCDH19 (protocadherin 19); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: LOC317183; protocadherin-19; RGD1565392; similar to Protocadherin 19 precursor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X101,061,002 - 101,166,777 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX101,065,263 - 101,165,269 (-)EnsemblGRCr8
mRatBN7.2X96,767,686 - 96,873,477 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX96,771,947 - 96,873,524 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX98,446,113 - 98,545,930 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X101,955,888 - 102,055,706 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X99,460,081 - 99,559,883 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X104,387,346 - 104,493,914 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX104,391,607 - 104,493,757 (-)Ensemblrn6Rnor6.0
Rnor_5.0X104,230,786 - 104,335,207 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X121,108,772 - 121,209,099 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX97,823,518 - 97,922,991 (-)NCBICelera
Cytogenetic MapXq32NCBI
JBrowse:




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

Biological Process

Cellular Component
membrane  (IEA)
plasma membrane  (IBA,IEA)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:32880860  


Genomics

Comparative Map Data
Pcdh19
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X101,061,002 - 101,166,777 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX101,065,263 - 101,165,269 (-)EnsemblGRCr8
mRatBN7.2X96,767,686 - 96,873,477 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX96,771,947 - 96,873,524 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX98,446,113 - 98,545,930 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X101,955,888 - 102,055,706 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X99,460,081 - 99,559,883 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X104,387,346 - 104,493,914 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX104,391,607 - 104,493,757 (-)Ensemblrn6Rnor6.0
Rnor_5.0X104,230,786 - 104,335,207 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X121,108,772 - 121,209,099 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX97,823,518 - 97,922,991 (-)NCBICelera
Cytogenetic MapXq32NCBI
PCDH19
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X100,291,644 - 100,410,273 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX100,291,644 - 100,410,296 (-)Ensemblhg38GRCh38
GRCh37X99,546,642 - 99,665,271 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X99,433,298 - 99,551,927 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34X99,352,786 - 99,468,297NCBI
CeleraX100,067,096 - 100,185,714 (-)NCBICelera
Cytogenetic MapXq22.1NCBI
HuRefX89,347,660 - 89,465,802 (-)NCBIHuRef
CHM1_1X99,439,320 - 99,557,952 (-)NCBICHM1_1
T2T-CHM13v2.0X98,734,021 - 98,852,681 (-)NCBIT2T-CHM13v2.0
Pcdh19
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X132,483,609 - 132,589,802 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX132,483,609 - 132,589,736 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X133,582,860 - 133,689,044 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX133,582,860 - 133,688,987 (-)Ensemblmm10GRCm38
MGSCv37X130,117,399 - 130,223,532 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X128,933,367 - 129,035,343 (-)NCBIMGSCv36mm8
CeleraX116,456,789 - 116,562,258 (-)NCBICelera
Cytogenetic MapXE3NCBI
cM MapX55.21NCBI
Pcdh19
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555036,434,047 - 6,567,253 (-)Ensembl
ChiLan1.0NW_0049555036,428,894 - 6,567,253 (-)NCBIChiLan1.0ChiLan1.0
PCDH19
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X99,901,156 - 100,018,434 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X99,904,761 - 100,022,039 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X89,504,404 - 89,622,354 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X99,643,595 - 99,759,631 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX99,643,595 - 99,759,631 (-)EnsemblpanPan2panpan1.1
PCDH19
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X74,179,609 - 74,319,138 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX74,184,772 - 74,317,391 (-)EnsemblcanFam3CanFam3.1
ROS_Cfam_1.0X75,589,131 - 75,726,986 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX75,594,295 - 75,727,552 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X73,151,338 - 73,289,267 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X74,820,721 - 74,958,753 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X74,582,488 - 74,720,481 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pcdh19
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X63,884,867 - 63,984,266 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365845,568,728 - 5,668,116 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365845,568,740 - 5,668,095 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCDH19
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX82,036,199 - 82,151,652 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X82,031,365 - 82,153,159 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X89,912,438 - 89,992,739 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PCDH19
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X88,613,546 - 88,730,740 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX88,616,743 - 88,730,519 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606513,547,408 - 13,659,207 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pcdh19
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249022,354,856 - 2,502,527 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046249022,354,109 - 2,502,478 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Pcdh19
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X85,924,738 - 86,025,377 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pcdh19
329 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:418
Count of miRNA genes:241
Interacting mature miRNAs:300
Transcripts:ENSRNOT00000064458
Prediction methods:Microtar, Miranda, Pita, 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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X97528096142528096Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X80434318125434318Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX92979612117740458Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
2302047Pia34Pristane induced arthritis QTL 345.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1996916163141916163Rat

Markers in Region
DXS7002E  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X96,772,536 - 96,772,652 (+)MAPPERmRatBN7.2
Rnor_6.0X104,392,197 - 104,392,312NCBIRnor6.0
Rnor_5.0X104,235,637 - 104,235,752UniSTSRnor5.0
RGSC_v3.4X121,109,362 - 121,109,477UniSTSRGSC3.4
CeleraX97,824,108 - 97,824,223UniSTS
Cytogenetic MapXq34UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 163 82 81 50 31 50 6 286 131 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000064458   ⟹   ENSRNOP00000062902
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX101,065,263 - 101,165,269 (-)Ensembl
mRatBN7.2 EnsemblX96,771,947 - 96,873,524 (-)Ensembl
Rnor_6.0 EnsemblX104,391,607 - 104,493,714 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000080386   ⟹   ENSRNOP00000074621
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX101,065,263 - 101,165,269 (-)Ensembl
mRatBN7.2 EnsemblX96,771,947 - 96,873,524 (-)Ensembl
Rnor_6.0 EnsemblX104,392,267 - 104,493,757 (-)Ensembl
RefSeq Acc Id: NM_001169129   ⟹   NP_001162600
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,065,263 - 101,165,070 (-)NCBI
mRatBN7.2X96,771,947 - 96,871,768 (-)NCBI
Rnor_6.0X104,391,607 - 104,493,714 (-)NCBI
Rnor_5.0X104,230,786 - 104,335,207 (-)NCBI
RGSC_v3.4X121,108,772 - 121,209,099 (-)RGD
CeleraX97,823,518 - 97,922,991 (-)RGD
Sequence:
RefSeq Acc Id: XM_006257222   ⟹   XP_006257284
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,061,002 - 101,166,777 (-)NCBI
mRatBN7.2X96,767,686 - 96,873,477 (-)NCBI
Rnor_6.0X104,387,346 - 104,493,914 (-)NCBI
Rnor_5.0X104,230,786 - 104,335,207 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257223   ⟹   XP_006257285
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,061,002 - 101,165,812 (-)NCBI
mRatBN7.2X96,767,686 - 96,872,515 (-)NCBI
Rnor_6.0X104,387,346 - 104,493,914 (-)NCBI
Rnor_5.0X104,230,786 - 104,335,207 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257224   ⟹   XP_006257286
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,061,002 - 101,165,812 (-)NCBI
mRatBN7.2X96,767,686 - 96,872,515 (-)NCBI
Rnor_6.0X104,387,346 - 104,493,914 (-)NCBI
Rnor_5.0X104,230,786 - 104,335,207 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773420   ⟹   XP_008771642
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,061,002 - 101,165,812 (-)NCBI
mRatBN7.2X96,767,686 - 96,872,515 (-)NCBI
Rnor_6.0X104,387,346 - 104,493,914 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099722   ⟹   XP_038955650
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,061,002 - 101,165,812 (-)NCBI
mRatBN7.2X96,767,686 - 96,872,515 (-)NCBI
RefSeq Acc Id: NP_001162600   ⟸   NM_001169129
- Peptide Label: precursor
- UniProtKB: D3ZG18 (UniProtKB/TrEMBL),   A6IVD4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257286   ⟸   XM_006257224
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006257285   ⟸   XM_006257223
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006257284   ⟸   XM_006257222
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K8I5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771642   ⟸   XM_008773420
- Peptide Label: isoform X5
- Sequence:
Ensembl Acc Id: ENSRNOP00000074621   ⟸   ENSRNOT00000080386
Ensembl Acc Id: ENSRNOP00000062902   ⟸   ENSRNOT00000064458
RefSeq Acc Id: XP_038955650   ⟸   XM_039099722
- Peptide Label: isoform X4
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K8I5-F1-model_v2 AlphaFold A0A0G2K8I5 1-1145 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:1565392 AgrOrtholog
BioCyc Gene G2FUF-1703 BioCyc
Ensembl Genes ENSRNOG00000003929 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064458 ENTREZGENE
  ENSRNOT00000064458.5 UniProtKB/TrEMBL
  ENSRNOT00000080386 ENTREZGENE
  ENSRNOT00000080386.3 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
  Protocadherin/Cadherin-CA UniProtKB/TrEMBL
KEGG Report rno:317183 UniProtKB/TrEMBL
NCBI Gene 317183 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PTHR24028:SF40 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
PhenoGen Pcdh19 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000003929 RatGTEx
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt A0A0G2K8I5 ENTREZGENE, UniProtKB/TrEMBL
  A6IVD4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZG18 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Pcdh19  protocadherin 19   Pcdh19_predicted  protocadherin 19 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Pcdh19_predicted  protocadherin 19 (predicted)  RGD1565392_predicted  similar to Protocadherin 19 precursor (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1565392_predicted  similar to Protocadherin 19 precursor (predicted)  LOC317183  similar to Protocadherin 19 precursor  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317183  similar to Protocadherin 19 precursor      Symbol and Name status set to provisional 70820 PROVISIONAL