Pcdh1 (protocadherin 1) - Rat Genome Database

Name: Pcdh1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Pcdh1 (protocadherin 1) Rattus norvegicus

Analyze

Symbol:

Pcdh1

Name:

protocadherin 1

RGD ID:

1308490

Description:

Predicted to have calcium ion binding activity. Predicted to be involved in homophilic cell adhesion via plasma membrane adhesion molecules. Predicted to localize to cell junction; nucleolus; and nucleoplasm. Orthologous to human PCDH1 (protocadherin 1); INTERACTS WITH 17alpha-ethynylestradiol; aflatoxin B1; all-trans-retinoic acid.

Type:

protein-coding

RefSeq Status:

MODEL

Also known as:

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

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

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)	HGNC	NCBI, HomoloGene, Inparanoid, Panther, Ensembl
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 (African 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
Alliance orthologs ³
Homo sapiens (human):	PCDH1 (protocadherin 1)	Alliance	DIOPT (HGNC)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	18	30,011,692 - 30,039,679 (-)	NCBI
Rnor_6.0 Ensembl	18	31,328,919 - 31,343,797 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	18	31,330,081 - 31,343,147 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	18	31,011,244 - 31,023,532 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	31,110,955 - 31,124,786 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	18	31,137,850 - 31,157,777 (-)	NCBI
Celera	18	29,658,359 - 29,671,795 (-)	NCBI		Celera
Cytogenetic Map	18	p11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Hereditary Neoplastic Syndromes (ISO)

Neurodevelopmental Disorders (ISO)

Tracheoesophageal Fistula (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

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)

amiodarone (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

beta-carotene (ISO)

bisphenol A (EXP)

bisphenol F (ISO)

butanal (ISO)

calcitriol (ISO)

cisplatin (ISO)

diazinon (ISO)

dimethylarsinic acid (ISO)

doxorubicin (ISO)

ethanol (ISO)

flutamide (EXP)

isotretinoin (ISO)

leflunomide (ISO)

methamphetamine (ISO)

N-Nitrosopyrrolidine (ISO)

nefazodone (EXP)

omega-6 fatty acid (ISO)

paracetamol (ISO)

pentanal (ISO)

perfluorononanoic acid (ISO)

pirinixic acid (ISO)

propanal (ISO)

rac-lactic acid (ISO)

rotenone (EXP)

silicon dioxide (ISO)

Soman (EXP)

tamibarotene (ISO)

testosterone (ISO)

tremolite asbestos (ISO)

triclosan (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)

homophilic cell adhesion via plasma membrane adhesion molecules (IEA)

Cellular Component

cell junction (IEA,ISO)

integral component of plasma membrane (IBA)

intracellular membrane-bounded organelle (ISO)

nucleolus (IEA,ISO)

nucleoplasm (IEA,ISO)

Molecular Function

calcium ion binding (IEA)

protein binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	RGD automated data pipeline
4.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	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
mRatBN7.2	18	30,011,692 - 30,039,679 (-)	NCBI
Rnor_6.0 Ensembl	18	31,328,919 - 31,343,797 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	18	31,330,081 - 31,343,147 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	18	31,011,244 - 31,023,532 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	31,110,955 - 31,124,786 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	18	31,137,850 - 31,157,777 (-)	NCBI
Celera	18	29,658,359 - 29,671,795 (-)	NCBI		Celera
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.p13 Ensembl	5	141,853,090 - 141,879,246 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	5	141,853,111 - 141,879,246 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	5	141,850,393 - 141,878,410 (-)	NCBI	GRCh38	GRCh38	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	NCBI36		hg18	NCBI36
Build 34	5	141,212,858 - 141,238,128	NCBI
Celera	5	137,309,824 - 137,335,077 (-)	NCBI
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

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 - 38,345,090 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	18	38,318,967 - 38,345,106 (-)	Ensembl
GRCm38	18	38,185,914 - 38,212,048 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	18	38,185,914 - 38,212,053 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	18	38,356,348 - 38,369,416 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	18	38,322,668 - 38,335,736 (-)	NCBI			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
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
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	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	137,209,537 - 137,237,977 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

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	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	2	33,863,495 - 33,889,885 (-)	NCBI
ROS_Cfam_1.0	2	37,265,925 - 37,292,153 (-)	NCBI
UMICH_Zoey_3.1	2	34,340,392 - 34,366,791 (-)	NCBI
UNSW_CanFamBas_1.0	2	35,151,686 - 35,177,896 (-)	NCBI
UU_Cfam_GSD_1.0	2	35,959,180 - 35,985,407 (-)	NCBI

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
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	143,475,933 - 143,501,748 (-)	Ensembl	Sscrofa11.1		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 - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	23	44,483,355 - 44,510,131 (-)	NCBI
ChlSab1.1 Ensembl	23	44,481,056 - 44,500,780 (-)	Ensembl

Pcdh1
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624774	1,071,155 - 1,097,960 (-)	NCBI

Position Markers

RH138467

Rat Assembly	Chr	Position (strand)	Source	JBrowse
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

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
61388	Bp2	Blood pressure QTL 2	3.23		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	1	35097280	Rat
2300180	Bmd67	Bone mineral density QTL 67	4.8	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	18	1	38195967	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	38195967	Rat
9589153	Insul31	Insulin level QTL 31	7.15	0.05	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	18	1	38753381	Rat
2312598	Bp340	Blood pressure QTL 340		0.05	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	3719547	32487870	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	4407513	62570466	Rat
2312568	Glom21	Glomerulus QTL 21	2	0.005	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	18	5430134	41781619	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	14678852	59678852	Rat
631264	Scl22	Serum cholesterol level QTL 22	6.2		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	18	15532963	32704022	Rat
61382	Bp46	Blood pressure QTL 46	18.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	15532963	32704022	Rat
1331766	Bp236	Blood pressure QTL 236	3.022		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	15539427	32670473	Rat
1331753	Bp231	Blood pressure QTL 231	3.643		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	15539427	53861431	Rat
1358358	Sradr6	Stress Responsive Adrenal Weight QTL 6	2.49		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	18	15539427	61499684	Rat
6903359	Bp355	Blood pressure QTL 355	3.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	15539671	61985648	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	15695872	68524999	Rat
1578661	Bss20	Bone structure and strength QTL 20	3.7		femur morphology trait (VT:0000559)	femoral neck cross-sectional area (CMO:0001697)	18	15695872	87080053	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	15695872	87080053	Rat
1358193	Emca2	Estrogen-induced mammary cancer QTL 2	1.6		mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	18	19031030	68436105	Rat
1331775	Bp235	Blood pressure QTL 235	3.201		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	19251717	32670473	Rat
1331735	Rf44	Renal function QTL 44	2.981		total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	18	19251717	32670473	Rat
1600373	Mamtr6	Mammary tumor resistance QTL 6			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	18	20285758	87080053	Rat
7387267	Uae42	Urinary albumin excretion QTL 42		0.61	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	14	21639491	66639491	Rat
1331741	Bp232	Blood pressure QTL 232	3.59112		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	22603736	87074531	Rat
6903353	Bp353	Blood pressure QTL 353	2.8		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	22604764	61985648	Rat
1641923	Colcr8	Colorectal carcinoma resistance QTL 8	3.1	0.0014	intestine integrity trait (VT:0010554)	poorly differentiated malignant colorectal tumor number (CMO:0002076)	18	23184227	53861431	Rat
1331733	Bp233	Blood pressure QTL 233	3.97196		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	25961026	81761656	Rat
2325839	Bp348	Blood pressure QTL 348		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	26743404	43659626	Rat
2301413	Bp318	Blood pressure QTL 318		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	27743024	48499517	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	27743024	48499517	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	27743024	48499517	Rat
12904677	Kidm72	Kidney mass QTL 72		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	18	27743024	48499517	Rat
12904668	Bw188	Body weight QTL 188		0.03	body mass (VT:0001259)	body weight (CMO:0000012)	18	27743024	48499517	Rat
12904669	Cm125	Cardiac mass QTL 125		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	18	27743024	48499517	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	27743024	48499517	Rat
2300157	Bmd66	Bone mineral density QTL 66	13.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	18	30533614	75533614	Rat
2300177	Bmd65	Bone mineral density QTL 65	19.7	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	18	30533614	75533614	Rat
2293704	Bss35	Bone structure and strength QTL 35	4.59	0.0002	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	18	30533614	75533614	Rat

miRNA Target Status

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.

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	2	4	15	15		15			64	27	10	11
Low	1	39	42	26	19	26	8	11	10	8	29		8
Below cutoff											2

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	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_039097354	(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
	JACYVU010000299	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000081850 ⟹ ENSRNOP00000073940

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	18	31,328,919 - 31,343,797 (-)	Ensembl

RefSeq Acc Id:

XM_006222565 ⟹ XP_006222627

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Celera	18	29,658,359 - 29,671,795 (-)	NCBI

Sequence:

show sequence

GCACTGCTGCTCCTATTGGCTCCATCTGCCAGCCATACCACCCAGGTAGTATACAAGGTGCCAG
AGGAACAGCCGCCCAACACACTCATTGGGAGCCTTGCCGCTGACTACGGTTTGCCAGACGTGGG
TCATCTGTACAAACTAGAGGTAGGTGCTCCATATCTTCGAGTGGATGGCAAGACTGGAGACATT
TTCACCACAGAGACCTCCATTGATCGAGAGGGGCTTCGTGAATGCCAGAACCAGATCTCCGGGA
GTCCCTGTATCCTGGAGTTTGAGGTGTCAATCACGGACCTTGTGCAGAACGGCAGCCCCCGACT
GCTAGAGGGCCAGATAGAGGTGCAAGACATCAATGACAACACGCCGAACTTTGCCTCACCAGTC
ATCACCCTGGCTATCCCGGAGAACACCAACATCGGCTCACTCTTCCCCATCCCACTGGCCACAG
ACCGTGACGCTGGCCCCAATGGCGTAGCATCCTATGAGCTGCAGGCTGGGCCTGAGGCCCAGGA
GCTATTTGGACTGCAGGTGGCTGAGGACCAGGAGGAGAAGCAGCCACAGCTCATTGTCATGGGC
AACCTGGACCGCGAACGGTGGGACTCCTACGACCTCACCATCAAGGTACAGGATGGTGGCAGTC
CTCCACGTGCCAGCAGCGCCCTGCTTCGTGTCACTGTGCTTGATACAAATGACAACGCTCCCAA
GTTTGAACGGCCAACCTACGAAGCCGAGCTGTCTGAGAACAGTCCCATTGGCCACTCGGTCATC
CAGGTGAAAGCTAATGACTCGGACCAAGGTGCCAATGCGGAGATTGACTACACGTTCCACCAGG
CACCCGAGGTTGTCAGGCGTCTTTTGCGACTAGACAGAAACACTGGACTTATCACCGTCCAGGG
CCCTGTGGATCGTGAGGATCTAAGCACTCTGCGTTTCTCAGTGCTCGCCAAGGACCGAGGTGCC
AACCCCAAGAGTGCCCGTGCCCAGGTAGTTGTGACTGTGAAAGACATGAATGACAATGCCCCGA
CCATTGAGATCCGAGGCATAGGGCTGGTGACTCATCAAGATGGGATGGCTAACATATCAGAGGA
TGTGGCAGAGGAGACCGCGGTGGCCTTGGTACAGGTGTCTGATCGAGATGAGGGAGAGAATGCA
GCTGTCACCTGTGTAGTAGCAGGTGATGTGCCCTTCCAGCTACGCCAGGCCAGCGAGACAGGCA
GCGACAGCAAGAAAAAGTATTTCCTGCAGACCACCACCCCTCTCGACTATGAGAAAGTCAAAGA
CTACACCATTGAGATCGTGGCGGTGGACTCCGGCAACCCTCCGCTCTCTAGCACCAACTCCCTC
AGGGTGCAGGTGGTAGACGTCAATGACAATGCCCCCGTCTTCACCCAGAGCATCACTGAAGTTG
CCTTCCCAGAAAACAACAAGCCTGGTGAAGTGGTAGCCGAGGTCACGGCCAGCGACGCCGACTC
TGGCTCTAACGCAGAGCTGGTGTATTCTCTGGAACCTGAGCCAGCTGCCCAGGGGCTGTTCACT
ATCTCACCCGAGAACGGAGAGGTCAGGGTAAAGACATCGCTGGATCGGGAACAGAGAGACAGCT
ATGAGCTGAAGGTGGTGGCAGCCGACAGGGGCAGTCCCAGCCTTCAGGGCACAGCCACGGTCCT
TGTCAACGTGCTTGACTGTAATGACAATGACCCCAAATTTATGCTGAGTGGCTACAACTTCTCA
GTGATGGAGAACATGCCAGCGCTGAGTCCAGTGGGTATGGTGACTGTCATCGACGGAGACAAGG
GGGAGAATGCCCGGGTGCAGCTCTCAGTCGAGCAGGACAATGGTGACTTTGTTATCCAGAATGG
CACAGGCACCATCTTATCCAGTTTGAGCTTTGATCGGGAACAACAGAGTACCTACACCTTCCAA
CTGAAGGCCGTGGATGGTGGTGTCCCACCTCGTTCGGCGTACGTCGGTGTCACCATCAATGTGT
TGGATGAGAATGACAATGCGCCCTTTATCACCGCCCCCTCCAACACGTCTCACCGGCTGCTGAC
CCCGCAGACACGTCTCGGCGAGACAGTCAGCCAGGTGACAGCGGAGGACATTGACTCTGGTATC
AATGCCGAGCTGACCTATAGCATCGCTGGCGGCAACCCTTACGGACTCTTCCAGATTGGATCAC
ATTCAGGTGCCATCACGCTGGAGAAGGAGATTGAACGGCGCCACCACGGGTTACACCGCCTTGT
GGTGAAGGTCAGCGACCGTGGCAAGCCCCCTCGCTATGGTACAGCCTTGGTCCACCTTTACGTC
AACGAGACCTTAGCCAACCGCACGCTGCTAGAGGCCGGGGATCCAGAATATGAGCGTTCCAAGC
AACGTGGCAACATTCTCTTTGGTGTTGTAGCCGGCGTGGTGGCCGTCGCCTTACTCATCGCCCT
GGCAGTACTCGTGCGCTACTGCCGGCAGCGGGAGGCCAAGAGTGGCTACCAGGCGGGTAAGAAG
GAGACTAAGGACCTATACGCCCCCAAGCCTAGCGGCAAAGCTGCTAAGGGAAGCAAGAGCAAGG
GGAAGAAAAGCAAGTCGCCGAAACCTGTGAAGCCCGTGGAGGATGAGGATGACACTGGGCTACA
AAAGTCTCTCAAGTTCAACCTTATGAGTGATGCCCCCGGGGACAGTCCCCGAATCCACCTACCC
CTCAACTACCCGCCCGGCAGCCCCGACTTAGGCCGCCATTACCGCTCCAATTCCCCACTGCCTT
CCATCCAGCTGCAACCCCAGTCACCCTCGGCCTCCAAGAAGCACCAGGTGGTGCAGGACCTGCC
GCCCGCAAACACATTTGTGGGCACTGGGGACACCACGTCCACGGGCTCCGAGCAGTACTCCGAC
TACAGCTATCGCACCAACCCCCCCAAATACCCCAGCAAGCAGTTACCTCACCGCCGTGTCACCT
TCTCGGCCACCAGTCAGGCCCAGGAGCTGCAGGATCCATCACAGCACAGTTATTATGACAGTGG
CCTGGAAGAGTCTGAAACGCCATCTAGCAAGTCATCCTCAGGCCCCCGACTTGGTCCCCTGGCC
CTCCCGGAGGACCACTATGAGCGCACCACCCCTGACGGCAGCATAGGTGAAATGGAACACCCTG
AGAACGACCTCCGCCCTTTGCCCGACGTCGCCATGACGGGCACATGTACCCGGGAGTGCAGCGA
GTTTGGTCACTCTGACACATGCTGGATGCCTGGCCAGTCGTCTCCCAGCCGCCGGACCAAGAGC
AGCGCCCTCAAACTCTCCACCTTCGTGCCTTACCAGGACCGAGGAGGGCAGGAGCCTGCGGGCA
CATCCGCCAAGCGTGAGATCTACCTGTGA

hide sequence

RefSeq Acc Id:

XM_017601102 ⟹ XP_017456591

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
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

RefSeq Status:

Type:

CODING

Position:

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

RefSeq Acc Id:

XM_039097354 ⟹ XP_038953282

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	18	30,011,692 - 30,039,295 (-)	NCBI

RefSeq Acc Id:

XM_039097355 ⟹ XP_038953283

RefSeq Status:

Type:

CODING

Position:

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

RefSeq Acc Id:

XM_039097356 ⟹ XP_038953284

RefSeq Status:

Type:

CODING

Position:

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

Protein Sequences


Protein RefSeqs	XP_017456591	(Get FASTA)	NCBI Sequence Viewer
	XP_038953281	(Get FASTA)	NCBI Sequence Viewer
	XP_038953282	(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

Reference Sequences

RefSeq Acc Id:

XP_006222627 ⟸ XM_006222565

- Peptide Label:

isoform X2

- Sequence:

show sequence

ALLLLLAPSASHTTQVVYKVPEEQPPNTLIGSLAADYGLPDVGHLYKLEVGAPYLRVDGKTGDI
FTTETSIDREGLRECQNQISGSPCILEFEVSITDLVQNGSPRLLEGQIEVQDINDNTPNFASPV
ITLAIPENTNIGSLFPIPLATDRDAGPNGVASYELQAGPEAQELFGLQVAEDQEEKQPQLIVMG
NLDRERWDSYDLTIKVQDGGSPPRASSALLRVTVLDTNDNAPKFERPTYEAELSENSPIGHSVI
QVKANDSDQGANAEIDYTFHQAPEVVRRLLRLDRNTGLITVQGPVDREDLSTLRFSVLAKDRGA
NPKSARAQVVVTVKDMNDNAPTIEIRGIGLVTHQDGMANISEDVAEETAVALVQVSDRDEGENA
AVTCVVAGDVPFQLRQASETGSDSKKKYFLQTTTPLDYEKVKDYTIEIVAVDSGNPPLSSTNSL
RVQVVDVNDNAPVFTQSITEVAFPENNKPGEVVAEVTASDADSGSNAELVYSLEPEPAAQGLFT
ISPENGEVRVKTSLDREQRDSYELKVVAADRGSPSLQGTATVLVNVLDCNDNDPKFMLSGYNFS
VMENMPALSPVGMVTVIDGDKGENARVQLSVEQDNGDFVIQNGTGTILSSLSFDREQQSTYTFQ
LKAVDGGVPPRSAYVGVTINVLDENDNAPFITAPSNTSHRLLTPQTRLGETVSQVTAEDIDSGI
NAELTYSIAGGNPYGLFQIGSHSGAITLEKEIERRHHGLHRLVVKVSDRGKPPRYGTALVHLYV
NETLANRTLLEAGDPEYERSKQRGNILFGVVAGVVAVALLIALAVLVRYCRQREAKSGYQAGKK
ETKDLYAPKPSGKAAKGSKSKGKKSKSPKPVKPVEDEDDTGLQKSLKFNLMSDAPGDSPRIHLP
LNYPPGSPDLGRHYRSNSPLPSIQLQPQSPSASKKHQVVQDLPPANTFVGTGDTTSTGSEQYSD
YSYRTNPPKYPSKQLPHRRVTFSATSQAQELQDPSQHSYYDSGLEESETPSSKSSSGPRLGPLA
LPEDHYERTTPDGSIGEMEHPENDLRPLPDVAMTGTCTRECSEFGHSDTCWMPGQSSPSRRTKS
SALKLSTFVPYQDRGGQEPAGTSAKREIYL

hide sequence

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

RefSeq Acc Id:

ENSRNOP00000073940 ⟸ ENSRNOT00000081850

RefSeq Acc Id:	XP_038953283 ⟸ XM_039097355
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038953282 ⟸ XM_039097354
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038953281 ⟸ XM_039097353
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038953284 ⟸ XM_039097356
- Peptide Label:	isoform X2

Protein Domains

Cadherin

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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CSV

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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CSV

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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CSV

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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CSV

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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CSV

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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CSV

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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CSV

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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CSV

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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CSV

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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CSV

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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CSV

TAB

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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CSV

TAB

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Damaging Variants

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
18	31338340	31338341	T	C	snv	WKY/N (MCW)
18	31338494	31338495	C	T	snv	BBDP/Wor (RGD)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308490	AgrOrtholog
Ensembl Genes	ENSRNOG00000060410	Ensembl, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000073940	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000081850	UniProtKB/TrEMBL
InterPro	Cadherin-like_dom	UniProtKB/TrEMBL
	Cadherin-like_sf	UniProtKB/TrEMBL
	Cadherin_CS	UniProtKB/TrEMBL
	Cadherin_N	UniProtKB/TrEMBL
	Protocadherin	UniProtKB/TrEMBL
NCBI Gene	307481	ENTREZGENE
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
SMART	SM00112	UniProtKB/TrEMBL
Superfamily-SCOP	SSF49313	UniProtKB/TrEMBL
UniProt	A0A0G2K6T9_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)

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Imported Disease Annotations - ClinVar