Pcdh20 (protocadherin 20) - 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: Pcdh20 (protocadherin 20) Chinchilla lanigera
Analyze
Symbol: Pcdh20
Name: protocadherin 20
RGD ID: 8949224
Description: ASSOCIATED WITH chromosome 13q14 deletion syndrome (ortholog); genetic disease (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: protocadherin-20
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540443,611,537 - 43,623,286 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540443,615,300 - 43,623,119 (+)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
Additional References at PubMed
PMID:22301074  


Genomics

Comparative Map Data
Pcdh20
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540443,611,537 - 43,623,286 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540443,615,300 - 43,623,119 (+)NCBIChiLan1.0ChiLan1.0
PCDH20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381361,409,685 - 61,415,849 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1361,409,685 - 61,415,849 (-)EnsemblGRCh38hg38GRCh38
GRCh371361,983,818 - 61,989,982 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361360,881,819 - 60,887,282 (-)NCBINCBI36Build 36hg18NCBI36
Build 341360,881,821 - 60,887,282NCBI
Celera1342,943,860 - 42,949,698 (-)NCBICelera
Cytogenetic Map13q21.2NCBI
HuRef1342,676,001 - 42,681,839 (-)NCBIHuRef
CHM1_11361,951,075 - 61,956,914 (-)NCBICHM1_1
T2T-CHM13v2.01360,629,962 - 60,647,554 (-)NCBIT2T-CHM13v2.0
Pcdh20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391488,702,183 - 88,708,832 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1488,702,179 - 88,708,832 (-)EnsemblGRCm39 Ensembl
GRCm381488,464,743 - 88,471,396 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1488,464,743 - 88,471,396 (-)EnsemblGRCm38mm10GRCm38
MGSCv371488,864,554 - 88,871,203 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361487,313,336 - 87,318,675 (-)NCBIMGSCv36mm8
Celera1486,065,796 - 86,072,441 (-)NCBICelera
Cytogenetic Map14E1NCBI
cM Map1444.43NCBI
Pcdh20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81570,834,042 - 70,840,298 (-)NCBIGRCr8
mRatBN7.21564,425,534 - 64,431,790 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1564,425,534 - 64,431,790 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1568,508,598 - 68,514,858 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01569,594,125 - 69,600,385 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01566,500,291 - 66,506,551 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01571,772,777 - 71,779,033 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1571,772,777 - 71,779,033 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01575,353,079 - 75,359,335 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41570,760,564 - 70,766,820 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11570,777,005 - 70,782,599 (-)NCBI
Celera1563,904,183 - 63,910,439 (-)NCBICelera
Cytogenetic Map15q12NCBI
PCDH20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21462,928,019 - 62,946,184 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11361,520,013 - 61,538,276 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01342,582,806 - 42,588,890 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11361,300,554 - 61,306,218 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1361,300,554 - 61,318,534 (-)Ensemblpanpan1.1panPan2
PCDH20
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12217,150,498 - 17,156,091 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2217,151,913 - 17,155,892 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2217,127,397 - 17,132,942 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02217,388,437 - 17,393,997 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12217,080,556 - 17,086,114 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02217,107,275 - 17,112,816 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02217,173,189 - 17,178,743 (-)NCBIUU_Cfam_GSD_1.0
Pcdh20
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945143,033,047 - 143,039,622 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936705326,349 - 332,242 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCDH20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1134,384,511 - 34,389,730 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11134,384,507 - 34,390,265 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PCDH20
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1339,182,981 - 39,190,128 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl339,185,301 - 39,189,206 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660574,466,517 - 4,472,511 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pcdh20
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474822,678,713 - 22,686,742 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474822,680,984 - 22,686,488 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSCLAT00000003492   ⟹   ENSCLAP00000003422
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_00495540443,611,537 - 43,623,286 (+)Ensembl
RefSeq Acc Id: XM_005374200   ⟹   XP_005374257
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495540443,615,300 - 43,621,603 (+)NCBI
Sequence:
RefSeq Acc Id: XR_259336
Type: NON-CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495540443,615,300 - 43,623,119 (+)NCBI
Sequence:
RefSeq Acc Id: XR_259337
Type: NON-CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_00495540443,615,300 - 43,623,119 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005374257 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCLAP00000003422
  ENSCLAP00000003422.1
Reference Protein Sequences
RefSeq Acc Id: XP_005374257   ⟸   XM_005374200
- UniProtKB: A0A8C2UP29 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCLAP00000003422   ⟸   ENSCLAT00000003492
Protein Domains
Cadherin


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000002449 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000003492 ENTREZGENE
  ENSCLAT00000003492.1 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin-like_dom UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
NCBI Gene Pcdh20 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN-20 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP SSF49313 UniProtKB/TrEMBL
UniProt A0A8C2UP29 ENTREZGENE, UniProtKB/TrEMBL