Advanced Search (OLGA)

Gene: Pcdh1 (protocadherin 1) Rattus norvegicus

Analyze

Symbol:

Pcdh1

Name:

protocadherin 1

RGD ID:

1308490

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 PCDH1 (protocadherin 1); INTERACTS WITH 17alpha-ethynylestradiol; aflatoxin B1; all-trans-retinoic acid.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC307481; protocadherin 1 (cadherin-like 1); protocadherin-1

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):	PCDH1 (protocadherin 1)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, Panther
Mus musculus (house mouse):	Pcdh1 (protocadherin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Pcdh1 (protocadherin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PCDH1 (protocadherin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PCDH1 (protocadherin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pcdh1 (protocadherin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PCDH1 (protocadherin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PCDH1 (protocadherin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pcdh1 (protocadherin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Pcdh1 (protocadherin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	PCDH1 (protocadherin 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Pcdh1 (protocadherin 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	pcdh1a (protocadherin 1a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	pcdh1a (protocadherin 1a)	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	pcdh1b (protocadherin 1b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	pcdh1b (protocadherin 1b)	Alliance	DIOPT (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):	pcdh1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	pcdh1	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)
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	18	30,258,154 - 30,290,828 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	18	30,258,154 - 30,290,436 (-)	Ensembl				GRCr8
mRatBN7.2	18	30,011,692 - 30,039,679 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	18	30,013,185 - 30,039,318 (-)	Ensembl				mRatBN7.2
Rnor_6.0	18	31,330,081 - 31,343,147 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	18	31,328,919 - 31,343,797 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	18	31,011,244 - 31,023,532 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	18	31,110,955 - 31,124,786 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	18	29,658,359 - 29,671,795 (-)	NCBI		Celera
RGSC_v3.1	18	31,137,850 - 31,157,777 (-)	NCBI
Cytogenetic Map	18	p11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

esophageal atresia/tracheoesophageal fistula (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(1->4)-beta-D-glucan (ISO)

17alpha-ethynylestradiol (EXP)

17beta-estradiol (ISO)

17beta-hydroxy-5alpha-androstan-3-one (ISO)

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

2-hydroxypropanoic acid (ISO)

3,4-methylenedioxymethamphetamine (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

aflatoxin B1 (EXP,ISO)

all-trans-retinoic acid (EXP,ISO)

alpha-Zearalanol (EXP)

amiodarone (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

beta-carotene (ISO)

beta-lapachone (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

butanal (ISO)

calcitriol (ISO)

cisplatin (ISO)

DDE (ISO)

diazinon (ISO)

Dibutyl phosphate (ISO)

dimethylarsinic acid (ISO)

doxorubicin (ISO)

epoxiconazole (ISO)

ethanol (ISO)

flutamide (EXP)

FR900359 (ISO)

inulin (ISO)

isotretinoin (ISO)

leflunomide (ISO)

lipopolysaccharide (ISO)

methamphetamine (ISO)

methidathion (ISO)

N-Nitrosopyrrolidine (ISO)

nefazodone (EXP)

okadaic acid (ISO)

omega-6 fatty acid (ISO)

ozone (ISO)

paracetamol (ISO)

pentanal (ISO)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (EXP)

pirinixic acid (ISO)

propanal (ISO)

rac-lactic acid (ISO)

rotenone (EXP)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

Soman (EXP)

tamibarotene (ISO)

testosterone (ISO)

thiram (ISO)

titanium dioxide (ISO)

tremolite asbestos (ISO)

triclosan (ISO)

triphenyl phosphate (ISO)

triptonide (ISO)

troglitazone (ISO)

urethane (ISO)

valproic acid (EXP)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell adhesion (IBA,IEA)

homophilic cell-cell adhesion (IEA)

Cellular Component

cell junction (IEA,ISO)

membrane (IEA)

plasma membrane (IBA,IEA)

Molecular Function

calcium ion binding (IEA)

cell adhesion molecule binding (IBA)

protein binding (ISO)

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 GOA human gene data--August 2006	GOA data from the GO Consortium
3.	GOA pipeline	RGD automated data pipeline
4.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data

Pcdh1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	18	30,258,154 - 30,290,828 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	18	30,258,154 - 30,290,436 (-)	Ensembl				GRCr8
mRatBN7.2	18	30,011,692 - 30,039,679 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	18	30,013,185 - 30,039,318 (-)	Ensembl				mRatBN7.2
Rnor_6.0	18	31,330,081 - 31,343,147 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	18	31,328,919 - 31,343,797 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	18	31,011,244 - 31,023,532 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	18	31,110,955 - 31,124,786 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	18	29,658,359 - 29,671,795 (-)	NCBI		Celera
RGSC_v3.1	18	31,137,850 - 31,157,777 (-)	NCBI
Cytogenetic Map	18	p11	NCBI

PCDH1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	5	141,853,090 - 141,878,410 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	5	141,853,090 - 141,879,246 (-)	Ensembl			hg38	GRCh38
GRCh37	5	141,232,655 - 141,257,975 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	141,212,856 - 141,238,128 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	5	141,212,858 - 141,238,128	NCBI
Celera	5	137,309,824 - 137,335,077 (-)	NCBI		Celera
Cytogenetic Map	5	q31.3	NCBI
HuRef	5	136,376,728 - 136,401,983 (-)	NCBI		HuRef
CHM1_1	5	140,666,027 - 140,691,306 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	5	142,379,045 - 142,404,656 (-)	NCBI		T2T-CHM13v2.0

Pcdh1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	18	38,318,967 - 38,345,023 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	18	38,318,967 - 38,345,106 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	18	38,185,914 - 38,212,048 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	18	38,185,914 - 38,212,053 (-)	Ensembl			mm10	GRCm38
MGSCv37	18	38,356,348 - 38,369,416 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	18	38,322,668 - 38,335,736 (-)	NCBI		MGSCv36	mm8
Celera	18	39,540,949 - 39,554,018 (-)	NCBI		Celera
Cytogenetic Map	18	B3	NCBI
cM Map	18	20.08	NCBI

Pcdh1
(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_004955415	11,916,092 - 11,934,658 (+)	Ensembl
ChiLan1.0	NW_004955415	11,916,095 - 11,934,658 (+)	NCBI	ChiLan1.0	ChiLan1.0

PCDH1
(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	4	137,097,517 - 137,125,958 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	5	135,237,073 - 135,265,510 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	5	137,209,537 - 137,237,977 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	5	143,323,710 - 143,349,575 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	143,324,641 - 143,345,042 (-)	Ensembl			panPan2	panpan1.1

PCDH1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	2	36,813,663 - 36,836,941 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	2	36,813,657 - 36,836,497 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	2	33,863,495 - 33,889,885 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	2	37,265,925 - 37,292,153 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	2	37,265,589 - 37,291,537 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	2	34,340,392 - 34,366,791 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	2	35,151,686 - 35,177,896 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	2	35,959,180 - 35,985,407 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Pcdh1
(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_024407213	150,723,092 - 150,746,625 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936504	12,296,324 - 12,320,611 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936504	12,293,889 - 12,320,598 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PCDH1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	143,475,935 - 143,501,487 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	2	143,475,931 - 143,501,204 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	149,679,040 - 149,699,032 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PCDH1
(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	23	44,483,355 - 44,510,131 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	23	44,481,056 - 44,500,780 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666034	33,341,659 - 33,368,634 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Pcdh1
(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_004624774	1,071,155 - 1,097,854 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624774	1,071,155 - 1,097,960 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Pcdh1
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	15	6,719,737 - 6,733,596 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Pcdh1
197 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	44
Count of miRNA genes:	41
Interacting mature miRNAs:	44
Transcripts:	ENSRNOT00000026324
Prediction methods:	Miranda, 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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1331733	Bp233	Blood pressure QTL 233	3.97196		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	25071126	83910656	Rat
2301409	Cm70	Cardiac mass QTL 70		0.001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	18	7065728	52065728	Rat
1358358	Sradr6	Stress Responsive Adrenal Weight QTL 6	2.49		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	18	22015562	61600538	Rat
1331735	Rf44	Renal function QTL 44	2.981		urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	18	15642280	31610627	Rat
61382	Bp46	Blood pressure QTL 46	18.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	12216684	31644508	Rat
2301413	Bp318	Blood pressure QTL 318		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	26822186	71822186	Rat
12904716	Am21	Aortic mass QTL 21		0.005	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	18	7065728	52065728	Rat
1331741	Bp232	Blood pressure QTL 232	3.59112		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	23494057	85487725	Rat
12904714	Cm131	Cardiac mass QTL 131		0.002	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	18	7065728	52065728	Rat
12904715	Cm132	Cardiac mass QTL 132		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	18	7065728	52065728	Rat
6903345	Bp349	Blood pressure QTL 349	3.9		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	3917226	48917226	Rat
12904668	Bw188	Body weight QTL 188		0.03	body mass (VT:0001259)	body weight (CMO:0000012)	18	26822186	71822186	Rat
2313082	Bss85	Bone structure and strength QTL 85	0.8	0.0001	long bone metaphysis morphology trait (VT:0000133)	tibia midshaft total cross-sectional area (CMO:0001715)	18	15226101	42690662	Rat
12904669	Cm125	Cardiac mass QTL 125		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	18	26822186	71822186	Rat
6903347	Bp350	Blood pressure QTL 350	4.4		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	1	31610627	Rat
12904670	Cm126	Cardiac mass QTL 126		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	18	26822186	71822186	Rat
2312568	Glom21	Glomerulus QTL 21	2	0.005	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	18	5460455	42690191	Rat
6903349	Bp351	Blood pressure QTL 351	3.5		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	3917226	48917226	Rat
631509	Sald2	Serum aldosterone level QTL 2	2.9		blood aldosterone amount (VT:0005346)	serum aldosterone level (CMO:0000487)	18	26415821	71415821	Rat
6903351	Bp352	Blood pressure QTL 352	3.3		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	3917226	48917226	Rat
12904677	Kidm72	Kidney mass QTL 72		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	18	26822186	71822186	Rat
1331766	Bp236	Blood pressure QTL 236	3.022		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	1	31610627	Rat
12904673	Cm127	Cardiac mass QTL 127		0.005	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	18	26822186	71822186	Rat
12904675	Am19	Aortic mass QTL 19		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	18	26822186	71822186	Rat
631264	Scl22	Serum cholesterol level QTL 22	6.2		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	18	12216684	31644508	Rat
1331775	Bp235	Blood pressure QTL 235	3.201		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	15642280	31610627	Rat
2325839	Bp348	Blood pressure QTL 348		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	1	44930869	Rat
1600373	Mamtr6	Mammary tumor resistance QTL 6			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	18	19553532	85493247	Rat
2293708	Bss46	Bone structure and strength QTL 46	8.8	0.0001	lumbar vertebra morphology trait (VT:0010494)	lumbar vertebra cortical cross-sectional area (CMO:0001690)	18	12066482	57066482	Rat
1578667	Bss21	Bone structure and strength QTL 21	3.5		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	18	12066482	85493247	Rat
2312598	Bp340	Blood pressure QTL 340		0.05	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	3811902	30809809	Rat
2300180	Bmd67	Bone mineral density QTL 67	4.8	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	18	1	34566578	Rat
2299160	Iddm35	Insulin dependent diabetes mellitus QTL 35	2.79		blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	18	4482648	49482648	Rat
1331753	Bp231	Blood pressure QTL 231	3.643		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	1	54490981	Rat
1578661	Bss20	Bone structure and strength QTL 20	3.7		femur morphology trait (VT:0000559)	femoral neck cross-sectional area (CMO:0001697)	18	12066482	85493247	Rat
11565454	Kidm59	Kidney mass QTL 59		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	18	7065728	52065728	Rat
1331754	Bp230	Blood pressure QTL 230	4.61609		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	15642280	86134022	Rat
2293661	Bss50	Bone structure and strength QTL 50	4.64	0.0003	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	18	1	34566578	Rat
61375	Bp41	Blood pressure QTL 41	2.4		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	18	4307354	49307354	Rat

Markers in Region

RH138467

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	18	30,010,899 - 30,011,063 (+)	MAPPER	mRatBN7.2
Rnor_6.0	18	31,322,916 - 31,323,079	NCBI	Rnor6.0
Rnor_5.0	18	31,004,208 - 31,004,371	UniSTS	Rnor5.0
RGSC_v3.4	18	31,105,164 - 31,105,327	UniSTS	RGSC3.4
Celera	18	29,652,436 - 29,652,599	UniSTS
RH 3.4 Map	18	435.7	UniSTS
Cytogenetic Map	18	p11	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	67	162	91	90	59	49	59	6	313	149	11	141	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001100689	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006222565	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601102	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039097353	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039097355	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039097356	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473974	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DQ863133	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000018	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000081850 ⟹ ENSRNOP00000073940

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	18	30,269,501 - 30,290,436 (-)	Ensembl
mRatBN7.2 Ensembl	18	30,015,778 - 30,038,005 (-)	Ensembl
Rnor_6.0 Ensembl	18	31,328,919 - 31,343,797 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000101935 ⟹ ENSRNOP00000077172

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	18	30,258,154 - 30,288,987 (-)	Ensembl
mRatBN7.2 Ensembl	18	30,013,185 - 30,030,688 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000113171 ⟹ ENSRNOP00000086663

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	18	30,258,154 - 30,290,436 (-)	Ensembl
mRatBN7.2 Ensembl	18	30,013,185 - 30,039,318 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000121742 ⟹ ENSRNOP00000109324

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	18	30,269,501 - 30,281,870 (-)	Ensembl

RefSeq Acc Id:

NM_001100689 ⟹ NP_001094159

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	18	30,258,154 - 30,290,436 (-)	NCBI

RefSeq Acc Id:

XM_017601102 ⟹ XP_017456591

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	18	30,268,221 - 30,290,051 (-)	NCBI
mRatBN7.2	18	30,017,040 - 30,038,929 (-)	NCBI
Rnor_6.0	18	31,330,081 - 31,343,147 (-)	NCBI

Sequence:

show sequence

GTAGCATCCTATGAGCTGCAGGCTGGGCCTGAGGCCCAGGAGCTATTTGGACTGCAGGTGGCTG
AGGACCAGGAGGAGAAGCAGCCACAGCTCATTGTCATGGGCAACCTGGACCGCGAACGGTGGGA
CTCCTACGACCTCACCATCAAGGTACAGGATGGTGGCAGTCCTCCACGTGCCAGCAGCGCCCTG
CTTCGTGTCACTGTGCTTGATACAAATGACAACGCTCCCAAGTTTGAACGGCCAACCTACGAAG
CCGAGCTGTCTGAGAACAGTCCCATTGGCCACTCGGTCATCCAGGTGAAAGCTAATGACTCGGA
CCAAGGTGCCAATGCGGAGATTGACTACACGTTCCACCAGGCACCCGAGGTTGTCAGGCGTCTT
TTGCGACTAGACAGAAACACTGGACTTATCACCGTCCAGGGCCCTGTGGATCGTGAGGATCTAA
GCACTCTGCGTTTCTCAGTGCTCGCCAAGGACCGAGGTGCCAACCCCAAGAGTGCCCGTGCCCA
GGTAGTTGTGACTGTGAAAGACATGAATGACAATGCCCCGACCATTGAGATCCGAGGCATAGGG
CTGGTGACTCATCAAGATGGGATGGCTAACATATCAGAGGATGTGGCAGAGGAGACCGCGGTGG
CCTTGGTACAGGTGTCTGATCGAGATGAGGGAGAGAATGCAGCTGTCACCTGTGTAGTAGCAGG
TGATGTGCCCTTCCAGCTACGCCAGGCCAGCGAGACAGGCAGCGACAGCAAGAAAAAGTATTTC
CTGCAGACCACCACCCCTCTCGACTATGAGAAAGTCAAAGACTACACCATTGAGATCGTGGCGG
TGGACTCCGGCAACCCTCCGCTCTCTAGCACCAACTCCCTCAGGGTGCAGGTGGTAGACGTCAA
TGACAATGCCCCCGTCTTCACCCAGAGCATCACTGAAGTTGCCTTCCCAGAAAACAACAAGCCT
GGTGAAGTGGTAGCCGAGGTCACGGCCAGCGACGCCGACTCTGGCTCTAACGCAGAGCTGGTGT
ATTCTCTGGAACCTGAGCCAGCTGCCCAGGGGCTGTTCACTATCTCACCCGAGAACGGAGAGGT
CAGGGTAAAGACATCGCTGGATCGGGAACAGAGAGACAGCTATGAGCTGAAGGTGGTGGCAGCC
GACAGGGGCAGTCCCAGCCTTCAGGGCACAGCCACGGTCCTTGTCAACGTGCTTGACTGTAATG
ACAATGACCCCAAATTTATGCTGAGTGGCTACAACTTCTCAGTGATGGAGAACATGCCAGCGCT
GAGTCCAGTGGGTATGGTGACTGTCATCGACGGAGACAAGGGGGAGAATGCCCGGGTGCAGCTC
TCAGTCGAGCAGGACAATGGTGACTTTGTTATCCAGAATGGCACAGGCACCATCTTATCCAGTT
TGAGCTTTGATCGGGAACAACAGAGTACCTACACCTTCCAACTGAAGGCCGTGGATGGTGGTGT
CCCACCTCGTTCGGCGTACGTCGGTGTCACCATCAATGTGTTGGATGAGAATGACAATGCGCCC
TTTATCACCGCCCCCTCCAACACGTCTCACCGGCTGCTGACCCCGCAGACACGTCTCGGCGAGA
CAGTCAGCCAGGTGACAGCGGAGGACATTGACTCTGGTATCAATGCCGAGCTGACCTATAGCAT
CGCTGGCGGCAACCCTTACGGACTCTTCCAGATTGGATCACATTCAGGTGCCATCACGCTGGAG
AAGGAGATTGAACGGCGCCACCACGGGTTACACCGCCTTGTGGTGAAGGTCAGCGACCGTGGCA
AGCCCCCTCGCTATGGTACAGCCTTGGTCCACCTTTACGTCAACGAGACCTTAGCCAACCGCAC
GCTGCTAGAGACCCTCCTTGTCCATAGCCTGGACACGCCCCTGGATATTGACATTGCCGGGGAT
CCAGAATATGAGCGTTCCAAGCAACGTGGCAACATTCTCTTTGGTGTTGTAGCCGGCGTGGTGG
CCGTCGCCTTACTCATCGCCCTGGCAGTACTCGTGCGCTACTGCCGGCAGCGGGAGGCCAAGAG
TGGCTACCAGGCGGGTAAGAAGGAGACTAAGGACCTATACGCCCCCAAGCCTAGCGGCAAAGCT
GCTAAGGGAAGCAAGAGCAAGGGGAAGAAAAGCAAGTCGCCGAAACCTGTGAAGCCCGTGGAGG
ATGAGGATGACACTGGGCTACAAAAGTCTCTCAAGTTCAACCTTATGAGTGATGCCCCCGGGGA
CAGTCCCCGAATCCACCTACCCCTCAACTACCCGCCCGGCAGCCCCGACTTAGGCCGCCATTAC
CGCTCCAATTCCCCACTGCCTTCCATCCAGCTGCAACCCCAGTCACCCTCGGCCTCCAAGAAGC
ACCAGGTGGTGCAGGACCTGCCGCCCGCAAACACATTTGTGGGCACTGGGGACACCACGTCCAC
GGGCTCCGAGCAGTACTCCGACTACAGCTATCGCACCAACCCCCCCAAATACCCCAGCAAGCAG
TTACCTCACCGCCGTGTCACCTTCTCGGCCACCAGTCAGGCCCAGGAGCTGCAGGATCCATCAC
AGCACAGTTATTATGACAGTGGCCTGGAAGAGTCTGAAACGCCATCTAGCAAGTCATCCTCAGG
CCCCCGACTTGGTCCCCTGGCCCTCCCGGAGGACCACTATGAGCGCACCACCCCTGACGGCAGC
ATAGGTGAAATGGAACACCCTGAGAACGAGCCGGCTGGCCGGAGCAGGCCCTGAGGCAGAGTGC
CAGACCTCCGCCCTTTGCCCGACGTCGCCATGACGGGCACATGTACCCGGGAGTGCAGCGAGTT
TGGTCACTCTGACACATGCTGGATGC

hide sequence

RefSeq Acc Id:

XM_039097353 ⟹ XP_038953281

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	18	30,264,372 - 30,290,050 (-)	NCBI
mRatBN7.2	18	30,011,692 - 30,038,928 (-)	NCBI

RefSeq Acc Id:

XM_039097355 ⟹ XP_038953283

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	18	30,264,372 - 30,290,828 (-)	NCBI
mRatBN7.2	18	30,011,692 - 30,039,679 (-)	NCBI

RefSeq Acc Id:

XM_039097356 ⟹ XP_038953284

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	18	30,264,372 - 30,288,395 (-)	NCBI
mRatBN7.2	18	30,011,692 - 30,037,189 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001094159	(Get FASTA)	NCBI Sequence Viewer
	XP_017456591	(Get FASTA)	NCBI Sequence Viewer
	XP_038953281	(Get FASTA)	NCBI Sequence Viewer
	XP_038953283	(Get FASTA)	NCBI Sequence Viewer
	XP_038953284	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	ABJ52184	(Get FASTA)	NCBI Sequence Viewer
	EDL76431	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000073940
	ENSRNOP00000073940.3
	ENSRNOP00000077172
	ENSRNOP00000077172.2
	ENSRNOP00000086663
	ENSRNOP00000086663.1
	ENSRNOP00000109324.1

RefSeq Acc Id:

XP_017456591 ⟸ XM_017601102

- Peptide Label:

isoform X3

- Sequence:

show sequence

MGNLDRERWDSYDLTIKVQDGGSPPRASSALLRVTVLDTNDNAPKFERPTYEAELSENSPIGHS
VIQVKANDSDQGANAEIDYTFHQAPEVVRRLLRLDRNTGLITVQGPVDREDLSTLRFSVLAKDR
GANPKSARAQVVVTVKDMNDNAPTIEIRGIGLVTHQDGMANISEDVAEETAVALVQVSDRDEGE
NAAVTCVVAGDVPFQLRQASETGSDSKKKYFLQTTTPLDYEKVKDYTIEIVAVDSGNPPLSSTN
SLRVQVVDVNDNAPVFTQSITEVAFPENNKPGEVVAEVTASDADSGSNAELVYSLEPEPAAQGL
FTISPENGEVRVKTSLDREQRDSYELKVVAADRGSPSLQGTATVLVNVLDCNDNDPKFMLSGYN
FSVMENMPALSPVGMVTVIDGDKGENARVQLSVEQDNGDFVIQNGTGTILSSLSFDREQQSTYT
FQLKAVDGGVPPRSAYVGVTINVLDENDNAPFITAPSNTSHRLLTPQTRLGETVSQVTAEDIDS
GINAELTYSIAGGNPYGLFQIGSHSGAITLEKEIERRHHGLHRLVVKVSDRGKPPRYGTALVHL
YVNETLANRTLLETLLVHSLDTPLDIDIAGDPEYERSKQRGNILFGVVAGVVAVALLIALAVLV
RYCRQREAKSGYQAGKKETKDLYAPKPSGKAAKGSKSKGKKSKSPKPVKPVEDEDDTGLQKSLK
FNLMSDAPGDSPRIHLPLNYPPGSPDLGRHYRSNSPLPSIQLQPQSPSASKKHQVVQDLPPANT
FVGTGDTTSTGSEQYSDYSYRTNPPKYPSKQLPHRRVTFSATSQAQELQDPSQHSYYDSGLEES
ETPSSKSSSGPRLGPLALPEDHYERTTPDGSIGEMEHPENEPAGRSRP

hide sequence

Ensembl Acc Id:

ENSRNOP00000073940 ⟸ ENSRNOT00000081850

RefSeq Acc Id:	XP_038953283 ⟸ XM_039097355
- Peptide Label:	isoform X2
- UniProtKB:	A0A8I6AAW9 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_038953281 ⟸ XM_039097353
- Peptide Label:	isoform X1
- UniProtKB:	A0A0G2K6T9 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_038953284 ⟸ XM_039097356
- Peptide Label:	isoform X2
- UniProtKB:	A0A8I6AAW9 (UniProtKB/TrEMBL)

Ensembl Acc Id:

ENSRNOP00000077172 ⟸ ENSRNOT00000101935

Ensembl Acc Id:

ENSRNOP00000086663 ⟸ ENSRNOT00000113171

RefSeq Acc Id:	NP_001094159 ⟸ NM_001100689
- Peptide Label:	precursor
- UniProtKB:	A0A8I6AAW9 (UniProtKB/TrEMBL)

Ensembl Acc Id:

ENSRNOP00000109324 ⟸ ENSRNOT00000121742

Protein Domains

Cadherin

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-A0A0G2K6T9-F1-model_v2	AlphaFold	A0A0G2K6T9	1-1191	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308490	AgrOrtholog
BioCyc Gene	G2FUF-7780	BioCyc
Ensembl Genes	ENSRNOG00000060410	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000081850	ENTREZGENE
	ENSRNOT00000081850.3	UniProtKB/TrEMBL
	ENSRNOT00000101935	ENTREZGENE
	ENSRNOT00000101935.2	UniProtKB/TrEMBL
	ENSRNOT00000113171	ENTREZGENE
	ENSRNOT00000113171.2	UniProtKB/TrEMBL
	ENSRNOT00000121742.1	UniProtKB/TrEMBL
Gene3D-CATH	Cadherins	UniProtKB/TrEMBL
InterPro	Cadherin-like_dom	UniProtKB/TrEMBL
	Cadherin-like_sf	UniProtKB/TrEMBL
	Cadherin_CS	UniProtKB/TrEMBL
	Cadherin_N	UniProtKB/TrEMBL
	Protocadherin	UniProtKB/TrEMBL
	Protocadherin/Cadherin-CA	UniProtKB/TrEMBL
NCBI Gene	307481	ENTREZGENE
PANTHER	CADHERIN-87A	UniProtKB/TrEMBL
	PROTOCADHERIN-1	UniProtKB/TrEMBL
Pfam	Cadherin	UniProtKB/TrEMBL
	Cadherin_2	UniProtKB/TrEMBL
	Protocadherin	UniProtKB/TrEMBL
PhenoGen	Pcdh1	PhenoGen
PRINTS	CADHERIN	UniProtKB/TrEMBL
PROSITE	CADHERIN_1	UniProtKB/TrEMBL
	CADHERIN_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000060410	RatGTEx
SMART	SM00112	UniProtKB/TrEMBL
Superfamily-SCOP	SSF49313	UniProtKB/TrEMBL
UniProt	A0A0G2K6T9	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I5XVV3_RAT	UniProtKB/TrEMBL
	A0A8I6AAW9	ENTREZGENE, UniProtKB/TrEMBL
	A0ABK0LEW1_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-06	Pcdh1	protocadherin 1	Pcdh1_predicted	protocadherin 1 (cadherin-like 1) (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-12	Pcdh1_predicted	protocadherin 1 (cadherin-like 1) (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)

Send us a Message

Imported Disease Annotations - ClinVar