Pcdh19 (protocadherin 19) - Rat Genome Database

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Gene: Pcdh19 (protocadherin 19) Rattus norvegicus
Analyze
Symbol: Pcdh19
Name: protocadherin 19
RGD ID: 1565392
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in cell adhesion. 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
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X101,061,002 - 101,166,777 (-)NCBIGRCr8
mRatBN7.2X96,767,686 - 96,873,477 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX96,771,947 - 96,873,524 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX98,446,113 - 98,545,930 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X101,955,888 - 102,055,706 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X99,460,081 - 99,559,883 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X104,387,346 - 104,493,914 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX104,391,607 - 104,493,757 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X104,230,786 - 104,335,207 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X121,108,772 - 121,209,099 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX97,823,518 - 97,922,991 (-)NCBICelera
Cytogenetic MapXq32NCBI
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

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. 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 (-)NCBIGRCr8
mRatBN7.2X96,767,686 - 96,873,477 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX96,771,947 - 96,873,524 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX98,446,113 - 98,545,930 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X101,955,888 - 102,055,706 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X99,460,081 - 99,559,883 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X104,387,346 - 104,493,914 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX104,391,607 - 104,493,757 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X104,230,786 - 104,335,207 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X121,108,772 - 121,209,099 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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 - 100,410,273 (-)EnsemblGRCh38hg38GRCh38
GRCh37X99,546,642 - 99,665,271 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X99,433,298 - 99,551,927 (-)NCBINCBI36Build 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 Ensembl
GRCm38X133,582,860 - 133,689,044 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX133,582,860 - 133,688,987 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X130,117,399 - 130,223,532 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0X75,589,131 - 75,726,986 (-)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249022,354,109 - 2,502,478 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pcdh19
156 total Variants
miRNA Target Status

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 (mRatBN7.2)
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 time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat

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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 82 81 50 25 50 6 209 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000064458   ⟹   ENSRNOP00000062902
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064458.4 UniProtKB/TrEMBL
  ENSRNOT00000080386.2 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