Pcdh20 (protocadherin 20) - Rat Genome Database

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Gene: Pcdh20 (protocadherin 20) Rattus norvegicus
Analyze
Symbol: Pcdh20
Name: protocadherin 20
RGD ID: 1306297
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. Orthologous to human PCDH20 (protocadherin 20); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; alpha-Zearalanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC306081; protocadherin-20
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
GRCr81570,834,042 - 70,840,298 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1570,834,042 - 70,840,298 (-)EnsemblGRCr8
mRatBN7.21564,425,534 - 64,431,790 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1564,425,534 - 64,431,790 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1568,508,598 - 68,514,858 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01569,594,125 - 69,600,385 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01566,500,291 - 66,506,551 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01571,772,777 - 71,779,033 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1571,772,777 - 71,779,033 (-)Ensemblrn6Rnor6.0
Rnor_5.01575,353,079 - 75,359,335 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41570,760,564 - 70,766,820 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1563,904,183 - 63,910,439 (-)NCBICelera
RGSC_v3.11570,777,005 - 70,782,599 (-)NCBI
Cytogenetic Map15q12NCBI
JBrowse:




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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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:22681889  


Genomics

Comparative Map Data
Pcdh20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81570,834,042 - 70,840,298 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1570,834,042 - 70,840,298 (-)EnsemblGRCr8
mRatBN7.21564,425,534 - 64,431,790 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1564,425,534 - 64,431,790 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1568,508,598 - 68,514,858 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01569,594,125 - 69,600,385 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01566,500,291 - 66,506,551 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01571,772,777 - 71,779,033 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1571,772,777 - 71,779,033 (-)Ensemblrn6Rnor6.0
Rnor_5.01575,353,079 - 75,359,335 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41570,760,564 - 70,766,820 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1563,904,183 - 63,910,439 (-)NCBICelera
RGSC_v3.11570,777,005 - 70,782,599 (-)NCBI
Cytogenetic Map15q12NCBI
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 (-)Ensemblhg38GRCh38
GRCh371361,983,818 - 61,989,982 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361360,881,819 - 60,887,282 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm381488,464,743 - 88,471,396 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1488,464,743 - 88,471,396 (-)Ensemblmm10GRCm38
MGSCv371488,864,554 - 88,871,203 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361487,313,336 - 87,318,675 (-)NCBIMGSCv36mm8
Celera1486,065,796 - 86,072,441 (-)NCBICelera
Cytogenetic Map14E1NCBI
cM Map1444.43NCBI
Pcdh20
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540443,611,537 - 43,623,286 (+)Ensembl
ChiLan1.0NW_00495540443,615,300 - 43,623,119 (+)NCBIChiLan1.0ChiLan1.0
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 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2217,127,397 - 17,132,942 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02217,388,437 - 17,393,997 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2217,388,441 - 17,393,853 (-)EnsemblROS_Cfam_1.0 Ensembl
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_1.0UU_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
SpeTri2.0 EnsemblNW_004936705326,482 - 332,242 (+)EnsemblSpeTri2.0 Ensembl
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 (-)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474822,680,984 - 22,686,488 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Pcdh20
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11236,282,508 - 36,288,910 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pcdh20
56 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:356
Count of miRNA genes:189
Interacting mature miRNAs:258
Transcripts:ENSRNOT00000017765
Prediction methods:Miranda, 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
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1544806773104695021Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)1560213984105213984Rat
61477Aia4Adjuvant induced arthritis QTL 43joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)156244089297773284Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)153185580392671517Rat
724545Niddm54Non-insulin dependent diabetes mellitus QTL 540.02blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)155720389580107161Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152852773273527732Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)154367724488677244Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)154367724488677244Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1525285835104695021Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1564571127108192169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1525285835104695021Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151915576287086765Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)154046315285463152Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151492659471614418Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)1561710951106710951Rat
2317050Aia24Adjuvant induced arthritis QTL 242.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1559257087104257087Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)154367724488677244Rat
2313080Bss65Bone structure and strength QTL 653.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)1567399137108192169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1525285835104695021Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)154367724488677244Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)154367724488677244Rat

Markers in Region
RH144562  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21564,426,413 - 64,426,569 (+)MAPPERmRatBN7.2
Rnor_6.01571,773,657 - 71,773,812NCBIRnor6.0
Rnor_5.01575,353,959 - 75,354,114UniSTSRnor5.0
RGSC_v3.41570,761,444 - 70,761,599UniSTSRGSC3.4
Celera1563,905,063 - 63,905,218UniSTS
Cytogenetic Map15q12UniSTS
BE108656  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21564,425,518 - 64,425,668 (+)MAPPERmRatBN7.2
Rnor_6.01571,772,762 - 71,772,911NCBIRnor6.0
Rnor_5.01575,353,064 - 75,353,213UniSTSRnor5.0
RGSC_v3.41570,760,549 - 70,760,698UniSTSRGSC3.4
Celera1563,904,168 - 63,904,317UniSTS
RH 3.4 Map15577.29UniSTS
Cytogenetic Map15q12UniSTS


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 66 143 81 80 49 26 49 6 234 125 11 122 36 92 31 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000017765   ⟹   ENSRNOP00000017765
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1570,834,042 - 70,840,298 (-)Ensembl
mRatBN7.2 Ensembl1564,425,534 - 64,431,790 (-)Ensembl
Rnor_6.0 Ensembl1571,772,777 - 71,779,033 (-)Ensembl
RefSeq Acc Id: NM_001107280   ⟹   NP_001100750
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81570,834,042 - 70,840,298 (-)NCBI
mRatBN7.21564,425,534 - 64,431,790 (-)NCBI
Rnor_6.01571,772,777 - 71,779,033 (-)NCBI
Rnor_5.01575,353,079 - 75,359,335 (-)NCBI
RGSC_v3.41570,760,564 - 70,766,820 (-)RGD
Celera1563,904,183 - 63,910,439 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100750 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02399 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000017765
  ENSRNOP00000017765.4
RefSeq Acc Id: NP_001100750   ⟸   NM_001107280
- UniProtKB: D4ADD1 (UniProtKB/TrEMBL),   A6HU36 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000017765   ⟸   ENSRNOT00000017765
Protein Domains
Cadherin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ADD1-F1-model_v2 AlphaFold D4ADD1 1-952 view protein structure

Transcriptome

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

Promoters
RGD ID:13699857
Promoter ID:EPDNEW_R10379
Type:initiation region
Name:Pcdh20_1
Description:protocadherin 20
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01571,778,933 - 71,778,993EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306297 AgrOrtholog
BioCyc Gene G2FUF-12918 BioCyc
Ensembl Genes ENSRNOG00000013306 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017765 ENTREZGENE
  ENSRNOT00000017765.6 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Protocadherin/Cadherin-CA UniProtKB/TrEMBL
KEGG Report rno:306081 UniProtKB/TrEMBL
NCBI Gene 306081 ENTREZGENE
PANTHER CADHERIN-87A UniProtKB/TrEMBL
  PROTOCADHERIN-20 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
PhenoGen Pcdh20 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013306 RatGTEx
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt A6HU36 ENTREZGENE, UniProtKB/TrEMBL
  D4ADD1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Pcdh20  protocadherin 20   Pcdh20_predicted  protocadherin 20 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pcdh20_predicted  protocadherin 20 (predicted)      Symbol and Name status set to approved 70820 APPROVED