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Gene: Pcdh20 (protocadherin 20) Rattus norvegicus

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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

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	PCDH20 (protocadherin 20)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, Panther, Treefam
Mus musculus (house mouse):	Pcdh20 (protocadherin 20)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Pcdh20 (protocadherin 20)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PCDH20 (protocadherin 20)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PCDH20 (protocadherin 20)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pcdh20 (protocadherin 20)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PCDH20 (protocadherin 20)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PCDH20 (protocadherin 20)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pcdh20 (protocadherin 20)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	CNGA1 (cyclic nucleotide gated channel subunit alpha 1)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	PCDH20 (protocadherin 20)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Pcdh20 (protocadherin 20)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	cdh-9	Alliance	DIOPT (Ensembl Compara\|InParanoid)
Drosophila melanogaster (fruit fly):	Cad96Cb	Alliance	DIOPT (Ensembl Compara\|InParanoid)
Xenopus tropicalis (tropical clawed frog):	pcdh20	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	shg	Alliance	DIOPT (Ensembl Compara\|Hieranoid)
Drosophila melanogaster (fruit fly):	shg	Alliance	DIOPT (Ensembl Compara\|Hieranoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	15	70,834,042 - 70,840,298 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	15	70,834,042 - 70,840,298 (-)	Ensembl				GRCr8
mRatBN7.2	15	64,425,534 - 64,431,790 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	64,425,534 - 64,431,790 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	15	68,508,598 - 68,514,858 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	15	69,594,125 - 69,600,385 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	15	66,500,291 - 66,506,551 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	15	71,772,777 - 71,779,033 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	15	71,772,777 - 71,779,033 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	15	75,353,079 - 75,359,335 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	15	70,760,564 - 70,766,820 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	15	63,904,183 - 63,910,439 (-)	NCBI		Celera
RGSC_v3.1	15	70,777,005 - 70,782,599 (-)	NCBI
Cytogenetic Map	15	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

chromosome 13q14 deletion syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

2,3,7,8-tetrachlorodibenzodioxine (EXP)

2,4-dibromophenyl 2,4,5-tribromophenyl ether (ISO)

3,3',5,5'-tetrabromobisphenol A (ISO)

4,4'-sulfonyldiphenol (ISO)

6-propyl-2-thiouracil (EXP)

8-Br-cAMP (ISO)

all-trans-retinoic acid (ISO)

alpha-Zearalanol (EXP)

antirheumatic drug (ISO)

arsenous acid (ISO)

atrazine (EXP)

benzo[a]pyrene (ISO)

beta-lapachone (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

bisphenol F (ISO)

buta-1,3-diene (ISO)

cadmium dichloride (EXP)

CGP 52608 (ISO)

Cuprizon (EXP)

cyclosporin A (ISO)

cytarabine (ISO)

DDT (EXP)

diarsenic trioxide (ISO)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

entinostat (ISO)

fenvalerate (EXP)

folic acid (ISO)

glycidol (EXP)

medroxyprogesterone acetate (ISO)

mercury dibromide (ISO)

methylmercury chloride (ISO)

N-methyl-4-phenylpyridinium (ISO)

nickel atom (ISO)

niclosamide (ISO)

nitrofen (EXP)

okadaic acid (ISO)

ozone (EXP,ISO)

panobinostat (ISO)

paracetamol (EXP)

perfluorooctanoic acid (EXP)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

rotenone (ISO)

SB 431542 (ISO)

temozolomide (ISO)

testosterone (EXP)

trichostatin A (ISO)

triclosan (ISO)

valproic acid (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell adhesion (IBA,IEA)

homophilic cell adhesion via plasma membrane adhesion molecules (IEA)

Cellular Component

membrane (IEA)

plasma membrane (IBA,IEA)

Molecular Function

calcium ion binding (IEA)

cell adhesion molecule binding (IBA)

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	15	70,834,042 - 70,840,298 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	15	70,834,042 - 70,840,298 (-)	Ensembl				GRCr8
mRatBN7.2	15	64,425,534 - 64,431,790 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	64,425,534 - 64,431,790 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	15	68,508,598 - 68,514,858 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	15	69,594,125 - 69,600,385 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	15	66,500,291 - 66,506,551 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	15	71,772,777 - 71,779,033 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	15	71,772,777 - 71,779,033 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	15	75,353,079 - 75,359,335 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	15	70,760,564 - 70,766,820 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	15	63,904,183 - 63,910,439 (-)	NCBI		Celera
RGSC_v3.1	15	70,777,005 - 70,782,599 (-)	NCBI
Cytogenetic Map	15	q12	NCBI

PCDH20
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	13	61,409,685 - 61,415,849 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	13	61,409,685 - 61,415,849 (-)	Ensembl			hg38	GRCh38
GRCh37	13	61,983,818 - 61,989,982 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	13	60,881,819 - 60,887,282 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	13	60,881,821 - 60,887,282	NCBI
Celera	13	42,943,860 - 42,949,698 (-)	NCBI		Celera
Cytogenetic Map	13	q21.2	NCBI
HuRef	13	42,676,001 - 42,681,839 (-)	NCBI		HuRef
CHM1_1	13	61,951,075 - 61,956,914 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	13	60,629,962 - 60,647,554 (-)	NCBI		T2T-CHM13v2.0

Pcdh20
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	14	88,702,183 - 88,708,832 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	14	88,702,179 - 88,708,832 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	14	88,464,743 - 88,471,396 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	14	88,464,743 - 88,471,396 (-)	Ensembl			mm10	GRCm38
MGSCv37	14	88,864,554 - 88,871,203 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	14	87,313,336 - 87,318,675 (-)	NCBI		MGSCv36	mm8
Celera	14	86,065,796 - 86,072,441 (-)	NCBI		Celera
Cytogenetic Map	14	E1	NCBI
cM Map	14	44.43	NCBI

Pcdh20
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955404	43,611,537 - 43,623,286 (+)	Ensembl
ChiLan1.0	NW_004955404	43,615,300 - 43,623,119 (+)	NCBI	ChiLan1.0	ChiLan1.0

PCDH20
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	14	62,928,019 - 62,946,184 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	13	61,520,013 - 61,538,276 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	13	42,582,806 - 42,588,890 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	13	61,300,554 - 61,306,218 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	13	61,300,554 - 61,318,534 (-)	Ensembl			panPan2	panpan1.1

PCDH20
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	22	17,150,498 - 17,156,091 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	22	17,151,913 - 17,155,892 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	22	17,127,397 - 17,132,942 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	22	17,388,437 - 17,393,997 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	22	17,388,441 - 17,393,853 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	22	17,080,556 - 17,086,114 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	22	17,107,275 - 17,112,816 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	22	17,173,189 - 17,178,743 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Pcdh20
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	143,033,047 - 143,039,622 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936705	326,482 - 332,242 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936705	326,349 - 332,242 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PCDH20
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	11	34,384,511 - 34,389,730 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	11	34,384,507 - 34,390,265 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

PCDH20
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	3	39,182,981 - 39,190,128 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	3	39,185,301 - 39,189,206 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666057	4,466,517 - 4,472,511 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Pcdh20
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624748	22,678,713 - 22,686,742 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624748	22,680,984 - 22,686,488 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Variants

Variants in Pcdh20
25 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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1300144	Rf23	Renal function QTL 23	3.61		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	15	40631268	98288169	Rat
1576315	Schws6	Schwannoma susceptibility QTL 6		0.0069	nervous system integrity trait (VT:0010566)	post-insult time of death (CMO:0002005)	15	53806152	98806152	Rat
1331729	Rf42	Renal function QTL 42	3.071		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal blood flow rate (CMO:0001168)	15	17362897	73690657	Rat
61477	Aia4	Adjuvant induced arthritis QTL 4	3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	15	55596089	91365858	Rat
152025253	Hrtrt24	Heart rate QTL 24	3.82		heart pumping trait (VT:2000009)		15	27885774	86257085	Rat
724545	Niddm54	Non-insulin dependent diabetes mellitus QTL 54		0.02	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	15	50794494	73699215	Rat
10054130	Srcrt8	Stress Responsive Cort QTL 8	2.18	0.0085	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	15	22117933	67117933	Rat
1582227	Gluco30	Glucose level QTL 30	3.6	0.0003	blood glucose amount (VT:0000188)	absolute change in blood glucose level area under curve (CMO:0002034)	15	28030665	82262678	Rat
1582228	Epfw3	Epididymal fat weight QTL 3	4.1	0.0002	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	15	28030665	82262678	Rat
1578646	Bmd18	Bone mineral density QTL 18	5.2		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	15	22806240	98288169	Rat
631655	Bp126	Blood pressure QTL 126	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	15	58156477	101769107	Rat
1578647	Bmd17	Bone mineral density QTL 17	4		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	15	22806240	98288169	Rat
61424	Scl1	Serum cholesterol level QTL 1	7.7	0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	15	16725528	80672115	Rat
2293686	Bmd36	Bone mineral density QTL 36	7.4	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	15	33611058	71477291	Rat
1598828	Glom14	Glomerulus QTL 14	2.5		kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	15	34054139	79054139	Rat
2317750	Glom26	Glomerulus QTL 26	4.3		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	15	12496141	65205939	Rat
631516	Gluco31	Glucose level QTL 31	7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	15	55596089	95018120	Rat
2293691	Bmd37	Bone mineral density QTL 37	6.6	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	15	33611058	71477291	Rat
2317050	Aia24	Adjuvant induced arthritis QTL 24	2.06		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	15	52847908	73690657	Rat
1582242	Gluco28	Glucose level QTL 28	3.3	0.0008	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	15	28030665	82262678	Rat
2313080	Bss65	Bone structure and strength QTL 65	3.9	0.0001	long bone metaphysis morphology trait (VT:0000133)	tibia midshaft total cross-sectional area (CMO:0001715)	15	60990468	73690657	Rat
1578660	Bss19	Bone structure and strength QTL 19	4.3		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	15	22806240	98288169	Rat
1582244	Bw79	Body weight QTL 79	4	0.0002	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	15	28030665	82262678	Rat
1582214	Stl21	Serum triglyceride level QTL 21	3.1	0.022	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	15	28030665	82262678	Rat

Markers in Region

RH144562

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	64,426,413 - 64,426,569 (+)	MAPPER	mRatBN7.2
Rnor_6.0	15	71,773,657 - 71,773,812	NCBI	Rnor6.0
Rnor_5.0	15	75,353,959 - 75,354,114	UniSTS	Rnor5.0
RGSC_v3.4	15	70,761,444 - 70,761,599	UniSTS	RGSC3.4
Celera	15	63,905,063 - 63,905,218	UniSTS
Cytogenetic Map	15	q12	UniSTS

BE108656

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	64,425,518 - 64,425,668 (+)	MAPPER	mRatBN7.2
Rnor_6.0	15	71,772,762 - 71,772,911	NCBI	Rnor6.0
Rnor_5.0	15	75,353,064 - 75,353,213	UniSTS	Rnor5.0
RGSC_v3.4	15	70,760,549 - 70,760,698	UniSTS	RGSC3.4
Celera	15	63,904,168 - 63,904,317	UniSTS
RH 3.4 Map	15	577.29	UniSTS
Cytogenetic Map	15	q12	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

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

Nucleotide Sequences


RefSeq Transcripts	NM_001107280	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473951	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000015	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000017765 ⟹ ENSRNOP00000017765

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	15	70,834,042 - 70,840,298 (-)	Ensembl
mRatBN7.2 Ensembl	15	64,425,534 - 64,431,790 (-)	Ensembl
Rnor_6.0 Ensembl	15	71,772,777 - 71,779,033 (-)	Ensembl

RefSeq Acc Id:

NM_001107280 ⟹ NP_001100750

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	15	70,834,042 - 70,840,298 (-)	NCBI
mRatBN7.2	15	64,425,534 - 64,431,790 (-)	NCBI
Rnor_6.0	15	71,772,777 - 71,779,033 (-)	NCBI
Rnor_5.0	15	75,353,079 - 75,359,335 (-)	NCBI
RGSC_v3.4	15	70,760,564 - 70,766,820 (-)	RGD
Celera	15	63,904,183 - 63,910,439 (-)	RGD

Sequence:

show sequence

ACCAGTGACTATTGGCTGAAGTTCCCCAGCGATTTGCATGAACAGAGAGGGAGTGTCCTCTGCC
ACCCTCCCTTCTGGAGCGCTCTGACTGCAGCCTCCCAGGGAATGCGCGGCCAAGGGAACGCGCG
CAGCTCGCTGGTCCAGGCAGTGAGCTTGCGCCCAGCGACCTGGCACCCGTGCCTGGATATGGGG
CATCTACATCGTCCCAGCAGCAGGACCAGCCACAGGAACCTGCCGCATGTTGTTCTGCTTTTCC
TCTTCGTGGGACCCTTCAACTGCCTCGCGAGTTACAGTCGTGCTACCGAGCTTCTGTACAGCCT
AAACGAAGGACTGCCCGCGGGAGTGCTCATAGGCAGCTTGGCGGAGGACCTGAGGTTGCTGCCT
CGGGCCTCTGGGAGACAGAGCCAGCAGTTGCTGCATCCAGAGCGCACTGCTGCTGAGGGGAACC
CCCCTCTCTCTTTCAGCTTGGCCTCCGGGGGACTGAGTGGCCAGTATGTGACCCTAGACAACCG
CTCCGGGGAGCTGCACACTTCTGCACAGGAGATCGACAGAGAAGCATTGTGCTTGGATGGTGGT
GGAGGGGCTGCCTGGGGCGGCAGTACCTCCATTGCCTCCTCTCCTTCTTCTGATTCTTGCCTTT
TGCTTCTGGATGTGCTGGTCCTGCCTCAGGAATATTTTAGGTTTGTGAAGGTGAAAATTGCCAT
CAGGGATATCAATGACAATGCTCCGCAGTTCCCCATTTCTGAAATCTCTGTTTGGGTCCCGGAA
AATTCACCTGTAAATACCCGATTGGCGATAGAGCATCCTGCTGTGGACCCGGATGTAGGCATTA
ATGGTGTGCAAACCTATCGCTTACTGGACTACCATGGTATGTTTACCCTAGACGTGGAGGAGAA
TGAGAATGGGGAACGCACACCCTACTTGATTGTCATGGGCGCTTTGGACAGAGAAACCCAGGAC
CAGTATGTGAGCATCATCATAGCTGAGGATGGTGGGTCTCCGCCATTGCTGGGCAGCGCCACCC
TCACCATTGGCATAAGTGACATTAATGACAATTGTCCTCTCTTCATAGACTCACAAATTAATGT
CACCGTTTATGGAAATGCTACAGTGGGCACCCCTGTCACAACAGTCCAGGCTGTGGATAGAGAC
TTGGGGACAAACGCACAGATCACTTACAGTTACAGTCAGAAAGTTCCACAAGAATCCAAGGAAT
TATTCCACCTGGATGAAGTTACTGGAGTCGTTAAGCTTTCCAGTAAGATCGGTGGGAATGTTCT
ACAGACACATAAGCTCACCATCCTCGCTAACGGACCTGGCTGTATTCCCGCAGTGATCACTGCT
CTCGTGTCGATCATCAAAGTCGTTTTCAGACCCCCAGAAATTGTCCCACGTTATATCGCAAATG
AGATGGATGGTGTCGTGTATCTGAAAGAATTGGAGCCTGTTAATACTCCAATCGCGTTTTTTAC
CATCAGAGATCCGGAAGGCAAATACAAAATTAACTGCTACTTGGAGGGTGAAGGGCCATTCAGG
CTAGCACCCTACAAGCCATACAACAATGAATACTTGTTGGAGACCACAAAACCTATGGACTATG
AGCTGCAGCCGTTCTATGAAATAGCTGTAGTGGCCTGGAACTCAGAGGGGTTTCATGACAAGAG
AATCATTAAAGTACAACTTCTAGATGACAATGACAATGCCCCTGTTTTCCTTCAGCCCTTGATA
GAACTGACCATTGAAGAAAACAATGCACCCAATGCCTTTCTGACGAAGCTCTATGCTACAGATG
CCGACAGTGGAGAGATGGGCCGAGTTTCCTACTTCTTGGGACCCGATGCTCCGTCCTATTTTTC
CTTAGACAGCGTCACAGGGATTCTGACCGTTTCCACTCAGCTGGACAGAGAAGAGAAAGAAAAG
TACAGGTACACTGTCCGAGCAGTGGACTGTGGGAAGCCACCCAGAGAATCAGTGGCTACAGTGG
CTCTCACCGTGTTGGATAAAAATGACAACAGTCCGAGGTTCATCAACAAAGACTTCAGCTTTTT
TGTGCCAGAAAACTTTCCGGGATATGGTGAAATTGGAGTCATTAGTGTAACAGATGCTGATGCT
GGGAGGAATGGATGGGTAGCCCTCTCGGTAATGAACCAGAGTGATATTTTCGTCATAGATACAG
GTAAAGGCATGTTGAGAGCTAAAGTCTCTTTAGACAGAGAACAGCAAAGCTCATACACTCTGTG
GGTGGAAGCTGTTGATGGGGGTGAGCCCGCCCTTTCTTCTACCACAAAAATCACAATTCTCCTT
CTGGACATCAATGATAACCCTCCCCTTGTTTTGTTTCCTCAATCTAATATGTCTTACTTGCTGG
TCCTACCTTCTACTCTCCCTGGCTCACCAGTGACAGAGGTCTATGCAGTTGACAAAGATACAGG
CATGAATGCAGTCATAGCTTATAGTATCATAGGGAGAAGAGGTCCCAGGCCTGAGTCCTTCAGA
ATTGACCCCAAGACTGGCAACATCACTCTGGAGGAAGCCTTGCTGCAGACAGATTATGGTTTGC
ATCGCTTACTCGTGAAAGTGAGTGATCACGGATACCCCGAACCTCTCCATTCCACGGTCATGGT
GAACTTATTTGTCAATGACACTGTCAGTAACGAGAGCTACATTGAGAGCCTTTTAAGGAAGGAA
CCAGAAATTAATATAGAAGAGAAAGAACCACAAATCTCAATAAAGCCAACTCATAGGAAGGTAG
AGTCTATGTCCTGTATGCCCACATTGGTGGCTCTGTCTGTCATAAGCTTGGCTTCCATCACACT
AGTTACAGGGATGGGGATATACATTTGCTTACGGAAAGGTAAAAAACATCACAGGGAAGACGAC
AATTTGGAAGTACAGATTCCATTGAAAGGAAGAATTGACTTGTGTATGAGAGAGAGAAAACCAA
TGGACATTTCTAACATTTGATATGCCATCGTGGAGTCACACGGAGGGACGTTTTAACTGCCACA
GGGAGTCTTTGTCACACGAACAACAGTGTGCTGATGCAGTTCCACTAAAGGACAATTAATTTAT
AATTTGTATCATATTGTAAATAGCTGTTTACAGGTTTTTAATTCAAATTCAGAAGTTATAAAAT
GTGTACAGAATTTTTAAATGAAAATTAGTACTAACAGCTCTATCATTGTTATTTATATATATAA
ATACATATATATATATAAAATGTTGGATATAACTGGCAGCTCTAATACACCAAGCAGATGACTG
GAAAAGCTCAAGACTAAGGTAAGAAAAGAACATTTTTGTTGTTTCTAAAATGTCTTTTCACCAC
AAGAGGGCACCAGCTTCCCCTTAGCAGGGAACTGTGGTATTGTACATGATAGTTGTACATGAAA
TTAAGGAGAGAGTATATTTTAAATATATTGTTTTTAACATTAAATATAAAATTAGGGTAAATTG
ACTTCTCTACTTAAATGTATGACGAGAAAGAAAAAAAATCCACTTGTAAACCGAAAATGTATTA
CCTCGTAGGTACATGGATTATAGTTTGAAAGAGACGTCATTTAAAAAGAAGTGCAATTCATTTT
GGGCACGCATCAAAACATTGCCATGTGTTACAAAATTTGACCTGCTGAAGAGTGCGATGTTTTG
TGTAACCCCACCTGCTTTCTGTTTGTTTCCCGCTGCACTTGCTAGAATTACAGGGGGTGGGCAT
CATCTATGTATTCTTCCTTACATAAAAAGTATCTAGTCGATGCACTCAGTAAAAGAGCAAGACA
CTCGTCAGTGTCTCAATCTCTACTTGCTTGCTTGGTGTTTATTATATCTTAGTGCATTCTCAAC
TTGTCAGCAGCAACTTTCCCCCCGTGGGTTTAATGTTAGCCTGAGTACACTTCTGTTCACCTAC
ACTATGAGAAAAATAAAAGTTGTATTCAAATTCCTCAAAAGGCTACTGTACACCATTGGTTGTT
TGAGGTAGGCATTTTTATATGAAAGTGATACCTTTTGTGGTTGTTTTGGACCATCGGCTAATGT
TCTGACTTCTTTATTTGGTTCTGGAATACATCCAAAGTTTTATTTGTAAGCCCATCTGCACATT
CCTTTGATAATTTAGTTTTTACCAGCTCTTGTGCAATGAAGAAAACTGGCTTGTCAGTGATTTC
TAACGCTTCCTTCTTTGCATGAGATGGAAATTTTACTTTATGTACGAACTGTAGCGAAGCTGTC
TGTATAAACAAGAAATGTGTTAGCTTCAAAATGGGTCACTTTACTTATCATCATCATGTGTCTG
TACCATACCAAAATTGTTTATATGTTTGCAAATTAAAAGTATATATTTTCATATTTTCTTGATT
ATATTTACCATTTTATATTTGAATATGGGATTGTTCTTTCACTGAAGTGCCTGCTATTGGTGTC
TGTGTGTTTTTAGGATTAGTGAGAAATGGTAGTATTCTGCTATGCTAAAGTTTATATTAAACTA
ATCCATGACCTAATTAAGTATTTGGGTAAATTATTAAGGGTTTGTAAATGGTAGACATATGTAG
AAGAGAATTCACTTCTATGTTTAAGTTCCTATGAAAACTTACACTCATGCATGTCTATTTTCAC
ACTAACTAATTATAGATTTTATATCACCATAACTTCCCTCATACTCTAGCAACCTCCATGCTTA
TTGTGTTTCACTAACTTGCAATATTTTAAGGTAATCACACACCATAAAGAAAAGGCTTAAACAT
AAACACAGGATTTCTTAGGTTTATATTGATTGCTTGTTCTTGCTTTCTTCACTTTGATACTCTG
GATAAATAAGTATATAAGGTAGCAGGATCTTAGACAAAAAATTCAATATATTTTGAGGAAAGTT
CCTTTTGTATGACAGGCGCTTGAACTAAGAGACTGATGAGACCATTTAAGTCCATAAGCTGTTC
TTTCACAACTCTTACGTAACAAAGAAGAAACACAATTTATTTGCAGTCCTGTTTGGCTTAGTTT
CTTTTTAAAATAGAGAAGCTACATAAAAGACATGTAGCAGCATTAATAAAAAACGTGTGCTCCA
CAGGCTTCATGACTTTCAGCGCGATTCTAAACAGAAAAAAAAAAACATTCTATTCACTTCACAG
TTTGAACATGGCTCATGTGTTTGGGGGGATGGTTATTGAAATTCATTTCTTGCATGAGA

hide 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:

show sequence

MRGQGNARSSLVQAVSLRPATWHPCLDMGHLHRPSSRTSHRNLPHVVLLFLFVGPFNCLASYSR
ATELLYSLNEGLPAGVLIGSLAEDLRLLPRASGRQSQQLLHPERTAAEGNPPLSFSLASGGLSG
QYVTLDNRSGELHTSAQEIDREALCLDGGGGAAWGGSTSIASSPSSDSCLLLLDVLVLPQEYFR
FVKVKIAIRDINDNAPQFPISEISVWVPENSPVNTRLAIEHPAVDPDVGINGVQTYRLLDYHGM
FTLDVEENENGERTPYLIVMGALDRETQDQYVSIIIAEDGGSPPLLGSATLTIGISDINDNCPL
FIDSQINVTVYGNATVGTPVTTVQAVDRDLGTNAQITYSYSQKVPQESKELFHLDEVTGVVKLS
SKIGGNVLQTHKLTILANGPGCIPAVITALVSIIKVVFRPPEIVPRYIANEMDGVVYLKELEPV
NTPIAFFTIRDPEGKYKINCYLEGEGPFRLAPYKPYNNEYLLETTKPMDYELQPFYEIAVVAWN
SEGFHDKRIIKVQLLDDNDNAPVFLQPLIELTIEENNAPNAFLTKLYATDADSGEMGRVSYFLG
PDAPSYFSLDSVTGILTVSTQLDREEKEKYRYTVRAVDCGKPPRESVATVALTVLDKNDNSPRF
INKDFSFFVPENFPGYGEIGVISVTDADAGRNGWVALSVMNQSDIFVIDTGKGMLRAKVSLDRE
QQSSYTLWVEAVDGGEPALSSTTKITILLLDINDNPPLVLFPQSNMSYLLVLPSTLPGSPVTEV
YAVDKDTGMNAVIAYSIIGRRGPRPESFRIDPKTGNITLEEALLQTDYGLHRLLVKVSDHGYPE
PLHSTVMVNLFVNDTVSNESYIESLLRKEPEINIEEKEPQISIKPTHRKVESMSCMPTLVALSV
ISLASITLVTGMGIYICLRKGKKHHREDDNLEVQIPLKGRIDLCMRERKPMDISNI

hide 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	15	71,778,933 - 71,778,993	EPDNEW

Additional Information

External Database Links

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
	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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - ClinVar