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 calcium ion binding activity. Predicted to be involved in cell adhesion. 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
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease 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. 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 (-)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
(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
(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
(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

Variants

.
Variants in Pcdh20
25 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
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
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
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

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
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 21
Low 2 42 15 6 1 6 7 9 51 14 29 9 7
Below cutoff 1 1 34 27 16 27 1 2 2 11 12 2 1

Sequence


RefSeq Acc Id: ENSRNOT00000017765   ⟹   ENSRNOP00000017765
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
RefSeq 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
  ENSRNOT00000017765.5 UniProtKB/TrEMBL
Gene3D-CATH Cadherins UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CS 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