Cdh10 (cadherin 10) - Rat Genome Database

Name: Cdh10
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Cdh10 (cadherin 10) Rattus norvegicus

Analyze

Symbol:

Cdh10

Name:

cadherin 10

RGD ID:

619741

Description:

Predicted to enable cadherin binding activity and calcium ion binding activity. Predicted to be involved in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules; cell morphogenesis; and cell-cell junction organization. Located in glutamatergic synapse. Is integral component of postsynaptic specialization membrane. Is active in GABA-ergic synapse. Is integral component of presynaptic active zone membrane. Orthologous to human CDH10 (cadherin 10); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

cadherin-10

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):	CDH10 (cadherin 10)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Cdh10 (cadherin 10)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Cdh10 (cadherin 10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LOC100990096 (cadherin-10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CDH10 (cadherin 10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	LOC101962167 (cadherin-10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CDH10 (cadherin 10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LOC103215064 (cadherin-10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cdh10 (cadherin 10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	CDH6 (cadherin 6)	HGNC	OrthoDB
Homo sapiens (human):	CDH12 (cadherin 12)	HGNC	OrthoDB
Homo sapiens (human):	CDH9 (cadherin 9)	HGNC	OrthoDB
Alliance orthologs ³
Mus musculus (house mouse):	Cdh10 (cadherin 10)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Homo sapiens (human):	CDH10 (cadherin 10)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)
Danio rerio (zebrafish):	cdh10a (cadherin 10, type 2a (T2-cadherin))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|TreeFam)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	2	68,628,623 - 68,850,995 (+)	NCBI	mRatBN7.2
Rnor_6.0 Ensembl	2	69,415,057 - 69,637,524 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	2	69,415,174 - 69,636,849 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	2	89,140,727 - 89,362,817 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	69,472,301 - 69,696,553 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	69,616,979 - 69,624,237 (+)	NCBI
Celera	2	64,500,664 - 64,722,818 (+)	NCBI		Celera
Cytogenetic Map	2	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autism spectrum disorder (ISO)

autistic disorder (ISO)

Neurodevelopmental Disorders (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

2,2',4,4'-Tetrabromodiphenyl ether (EXP)

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

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

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

bromobenzene (EXP)

cisplatin (ISO)

cyclosporin A (ISO)

dorsomorphin (ISO)

flavonoids (EXP)

folic acid (ISO)

genistein (ISO)

mercury dibromide (ISO)

methylmercury chloride (ISO)

N-methyl-4-phenylpyridinium (ISO)

panobinostat (ISO)

paracetamol (ISO)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

rotenone (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

Soman (EXP)

succimer (ISO)

sulforaphane (ISO)

sunitinib (ISO)

temozolomide (ISO)

thalidomide (ISO)

trichostatin A (ISO)

triclosan (ISO)

triptonide (ISO)

tunicamycin (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adherens junction organization (IBA)

calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules (IBA)

cell morphogenesis (IBA)

cell-cell adhesion (TAS)

cell-cell adhesion via plasma-membrane adhesion molecules (IBA)

cell-cell junction assembly (IBA)

homophilic cell adhesion via plasma membrane adhesion molecules (IEA)

Cellular Component

adherens junction (IBA)

catenin complex (IBA)

GABA-ergic synapse (IDA)

glutamatergic synapse (IDA)

integral component of postsynaptic specialization membrane (IDA)

integral component of presynaptic active zone membrane (IDA)

Molecular Function

cadherin binding (IBA)

calcium ion binding (IBA)

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.	Johnson KJ, etal., Endocrinology 2000 Feb;141(2):675-83.
4.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	RGD automated data pipeline
6.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	RGD automated import pipeline for gene-chemical interactions
8.	Smith KR, etal., J Neurosci. 2017 Nov 15;37(46):11127-11139. doi: 10.1523/JNEUROSCI.1153-17.2017. Epub 2017 Oct 13.

Genomics

Comparative Map Data

Cdh10
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	2	68,628,623 - 68,850,995 (+)	NCBI	mRatBN7.2
Rnor_6.0 Ensembl	2	69,415,057 - 69,637,524 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	2	69,415,174 - 69,636,849 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	2	89,140,727 - 89,362,817 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	2	69,472,301 - 69,696,553 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	2	69,616,979 - 69,624,237 (+)	NCBI
Celera	2	64,500,664 - 64,722,818 (+)	NCBI		Celera
Cytogenetic Map	2	q21	NCBI

CDH10
(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	24,487,100 - 24,644,978 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	5	24,487,100 - 24,644,978 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	5	24,487,209 - 24,645,087 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	24,522,967 - 24,680,668 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	5	24,522,966 - 24,680,668	NCBI
Celera	5	24,372,049 - 24,530,965 (-)	NCBI
Cytogenetic Map	5	p14.2-p14.1	NCBI
HuRef	5	24,451,668 - 24,610,300 (-)	NCBI		HuRef
CHM1_1	5	24,486,997 - 24,644,932 (-)	NCBI		CHM1_1

Cdh10
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	15	18,818,763 - 19,014,883 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	15	18,819,033 - 19,014,322 (+)	Ensembl
GRCm38	15	18,818,869 - 19,016,206 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	15	18,818,947 - 19,014,236 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	15	18,750,084 - 18,943,989 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	15	18,763,672 - 18,958,961 (+)	NCBI			mm8
Celera	15	19,628,459 - 19,834,495 (+)	NCBI		Celera
Cytogenetic Map	15	A2	NCBI
cM Map	15	8.2	NCBI

Cdh10
(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_004955426	11,801,568 - 11,974,114 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955426	11,803,669 - 11,974,051 (-)	NCBI	ChiLan1.0	ChiLan1.0

LOC100990096
(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	91,278,256 - 91,437,291 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	91,330,244 - 91,437,290 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	5	85,746,559 - 85,905,904 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

CDH10
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	4	80,927,251 - 81,101,053 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	4	80,927,134 - 81,100,876 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	4	80,568,630 - 80,742,379 (+)	NCBI
ROS_Cfam_1.0	4	81,537,321 - 81,711,547 (+)	NCBI
UMICH_Zoey_3.1	4	81,065,083 - 81,239,483 (+)	NCBI
UNSW_CanFamBas_1.0	4	81,324,433 - 81,498,510 (+)	NCBI
UU_Cfam_GSD_1.0	4	82,014,016 - 82,188,194 (+)	NCBI

LOC101962167
(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	216,458,212 - 216,618,620 (-)	NCBI
SpeTri2.0	NW_004936811	386,933 - 547,222 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CDH10
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	16	12,094,707 - 12,277,315 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	16	12,094,687 - 12,277,672 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	16	12,626,221 - 12,737,897 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LOC103215064
(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	4	23,828,202 - 23,994,019 (-)	NCBI
ChlSab1.1 Ensembl	4	23,828,262 - 23,994,076 (-)	Ensembl
Vero_WHO_p1.0	NW_023666064	4,445,931 - 4,557,354 (+)	NCBI

Cdh10
(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 1.0	NW_004624873	4,278,264 - 4,480,609 (-)	NCBI

Position Markers

D2Rat206

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	2	68,642,568 - 68,642,799 (+)	MAPPER	mRatBN7.2
Rnor_6.0	2	69,429,183 - 69,429,411	NCBI	Rnor6.0
Rnor_5.0	2	89,154,547 - 89,154,775	UniSTS	Rnor5.0
RGSC_v3.4	2	69,486,089 - 69,486,318	RGD	RGSC3.4
RGSC_v3.4	2	69,486,090 - 69,486,318	UniSTS	RGSC3.4
RGSC_v3.1	2	69,414,127 - 69,414,594	RGD
Celera	2	64,514,314 - 64,514,542	UniSTS
SHRSP x BN Map	2	29.7798	RGD
SHRSP x BN Map	2	29.7798	UniSTS
Cytogenetic Map	2	q21	UniSTS

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
61355	Bp36	Blood pressure QTL 36	2.9		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	2	5873687	102844969	Rat
10402051	Gdil2	Gastrointestinal dilation QTL 2			enteric ganglion morphology trait (VT:0001045)	length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)	2	24903853	74786777	Rat
1302794	Stl27	Serum triglyceride level QTL 27	4.4	0.0001	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	2	25413423	143657569	Rat
1358894	Kidm24	Kidney mass QTL 24	4.03		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358899	Kidm23	Kidney mass QTL 23	3.88		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358901	Cm38	Cardiac mass QTL 38	2		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	157142209	Rat
1358904	Cm39	Cardiac mass QTL 39	2.26		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	157142209	Rat
1358910	Kidm27	Kidney mass QTL 27	5.77		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358911	Kidm28	Kidney mass QTL 28	5.42		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	2	25413423	157142209	Rat
1358913	Cm41	Cardiac mass QTL 41	2.73		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	203928301	Rat
1358917	Cm42	Cardiac mass QTL 42	2.82		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	25413423	203928301	Rat
1358887	Bw50	Body weight QTL 50	2.39		body mass (VT:0001259)	body weight (CMO:0000012)	2	25413652	157142078	Rat
1358908	Bw49	Body weight QTL 49	3.36		body mass (VT:0001259)	body weight (CMO:0000012)	2	25413652	157142078	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	26917817	81754745	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	26917817	81754745	Rat
1354617	Bp240	Blood pressure QTL 240	4		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	26917817	81754745	Rat
1354603	Bp243	Blood pressure QTL 243	3.9		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	26917817	127469484	Rat
2290453	Scl55	Serum cholesterol level QTL 55	2.83		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	2	26917817	136917119	Rat
9590095	Sffal3	Serum free fatty acids level QTL 3	6.78	0.001	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	2	27157160	72157160	Rat
10755434	Coatc7	Coat color QTL 7		0.04794	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	2	30648065	75648065	Rat
10755436	Coatc8	Coat color QTL 8		0.02431	coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	2	35023117	80023117	Rat
61371	Edpm1	Estrogen-dependent pituitary mass QTL 1	4	0.05	pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	2	35134841	88029593	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	40067944	102785628	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	40067944	102785628	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	40067944	102785628	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	2	40067944	102785628	Rat
70174	BpQTLCluster2	Blood pressure QTL cluster 2	4.24		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	2	40067944	102785628	Rat
2293835	Kiddil5	Kidney dilation QTL 5	3.8		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42804607	157142209	Rat
2293843	Kiddil6	Kidney dilation QTL 6	3.1		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	2	42804607	182042367	Rat
1298074	Bp164	Blood pressure QTL 164		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42804607	202447032	Rat
1298085	Bp165	Blood pressure QTL 165		0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	42804607	202447032	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	2	43154682	202446871	Rat
61467	Bp14	Blood pressure QTL 14	2.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	43154682	202446871	Rat
2293676	Bmd19	Bone mineral density QTL 19	10.7	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	2	43162366	111362592	Rat
2293682	Bmd24	Bone mineral density QTL 24	8.9	0.0001	femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	2	43162366	111362592	Rat
2293671	Bss44	Bone structure and strength QTL 44	10.97	0.0001	lumbar vertebra morphology trait (VT:0010494)	lumbar vertebra cortical cross-sectional area (CMO:0001690)	2	43162366	148478373	Rat
631208	Bw1	Body weight QTL1	5.09		mesenteric fat pad mass (VT:0010427)	mesenteric fat pad weight to body weight ratio (CMO:0000654)	2	43171017	83575226	Rat
1354601	Slep1	Serum leptin concentration QTL 1	5.39		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	2	43171017	184114403	Rat
631266	Bp132	Blood pressure QTL 132		0.0005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	46123260	202447032	Rat
1354592	Rf50	Renal function QTL 50	3.5		urine output (VT:0003620)	timed urine volume (CMO:0000260)	2	53822747	74786777	Rat
1331760	Bp206	Blood pressure QTL 206	3.62454		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	2	56043031	202447032	Rat
6480225	Gdil1	Gastrointestinal dilation QTL 1			enteric ganglion morphology trait (VT:0001045)	length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)	2	56660879	74786777	Rat
1582246	Cm60	Cardiac mass QTL 60	5.8		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	2	57605612	76539510	Rat
1558648	Smcn1	Smooth muscle cell number QTL 1		0.039	blood vessel smooth muscle cell quantity (VT:0010525)	aorta smooth muscle cell count per unit vessel length (CMO:0001646)	2	59134147	127460910	Rat
5684990	Bmd82	Bone mineral density QTL 82	2.8		tibia mineral mass (VT:1000283)	bone mineral content (CMO:0001554)	2	59324377	103795077	Rat
5684996	Bmd85	Bone mineral density QTL 85	4.7	0.024	tibia mineral mass (VT:1000283)	bone mineral density (CMO:0001226)	2	59324377	103795077	Rat
61438	Cia7	Collagen induced arthritis QTL 7	4.6	0.0001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	2	59324377	141596857	Rat
631500	Bp99	Blood pressure QTL 99	2.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	59324719	102755241	Rat
1578777	Stresp15	Stress response QTL 15	2	0.05	blood aldosterone amount (VT:0005346)	plasma aldosterone level (CMO:0000551)	2	59846005	104846005	Rat
2306903	Bp336	Blood pressure QTL 336		0.01	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	64366971	109366971	Rat
1298080	Bp163	Blood pressure QTL 163		0.02	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66118275	202447032	Rat
1354648	Bp239	Blood pressure QTL 239		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	2	66118463	226797303	Rat
7411551	Bw131	Body weight QTL 131	29.6	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	2	67942638	112942638	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	65
Count of miRNA genes:	46
Interacting mature miRNAs:	63
Transcripts:	ENSRNOT00000013152
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									50
Low		10							22	16	21	1
Below cutoff	2	13	30	14	18	14	7	8	2	11	18	8	7

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001168631	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006232079	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006232080	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF177676	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF468011	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473992	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000066	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000013152 ⟹ ENSRNOP00000013152

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	2	69,415,057 - 69,637,524 (+)	Ensembl

RefSeq Acc Id:

NM_001168631 ⟹ NP_001162102

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	68,628,780 - 68,850,995 (+)	NCBI
Rnor_6.0	2	69,415,394 - 69,636,849 (+)	NCBI
Rnor_5.0	2	89,140,727 - 89,362,817 (+)	NCBI
RGSC_v3.4	2	69,472,301 - 69,696,553 (+)	RGD
Celera	2	64,500,664 - 64,722,818 (+)	RGD

Sequence:

show sequence

GAAAGCTTGAGTTAGACCGAAGTAGAATCAGTGAGAGAAAATAACAGCAGAAAACAAACAAAAA
GGGGACAGGGTGACAGTCTCTTCAGGGTTATTTGGCTGGAACCAACTTCCGTTTTCCAGAAGCT
GATGAAACAAGCTCTTGGAAATATGTACATAGCACTAATGAAGTCTTGGAAACCAGTCGAGATC
TGATACCATAAACTGGACTACTTTTTCATCATCTGCACTGGAATTTTTCAAGAAGTAAACTATG
TCAATCTATTCGTTCTTGAGACTGTTTGTTCTCTGGGCATGCCTGCCCCAATTCTGCTGTCCAG
AATTAACGTTCAGAAGGACTCCTGGGCTTCAGCAAATGACTGCAGAATCCCATGTCCCTAGGGG
TGATGGTAAAATCCTTCACCGTCAAAAACGTGGCTGGATGTGGAACCAGTTTTTCTTACTGGAA
GAATATACTGGATCTGATTATCAATATGTCGGCAAGCTTCATTCAGACCAAGATAAAGGAGACG
GATCGCTCAAATATATTTTGTCTGGAGATGGAGCTGGTACTCTTTTTATTATTGATGAAAAAAC
AGGTGATATTCACGCCACAAGAAGAATTGATAGGGAAGAAAAGGCCTTTTATACTCTGCGTGCA
CAAGCTATTAACAGAAGAACTCTGAGGCCAGTTGAGCCAGAGTCAGAATTTGTGATCAAAATTC
ACGATATCAACGACAATGAGCCTACATTCCCAGAAGAAATTTATACAGCCAGCGTTCCTGAAAT
GTCTGTTGTAGGTACTTCTGTGGTGCAAGTCACAGCTACAGATGCCGATGACCCTTCATATGGA
AACAGCGCCAGAGTCATTTACAGCATACTTCAAGGGCAGCCTTATTTCTCTGTGGAACCAGAAA
CAGGTATCATAAGGACAGCTCTACCAAACATGAACAGAGAGAACAAGGAACAGTACCAGGTGGT
TATTCAAGCCAAGGACATGGGCGGTCAGATGGGGGGTCTGTCTGGAACCACCACAGTGAACATC
ACTCTCACAGATGTCAACGACAATCCTCCTCGCTTCCCCCAAAACACCATCCATCTGCGAGTTC
TTGAATCCTCTCCAGTTGGCACAGCTGTGGGAAGTGTAAAAGCCACCGATGCTGACACGGGGAA
AAATGCCGAAGTGGATTACCGCATTATTGATGGAGATGGCACAGATATGTTTGACATTATAACT
GAGAAGGACACACAGGAAGGCATCATCACTGTGAAAAAGCCACTTGACTATGAGAACCGAAGAC
TATATACTCTGAAGGTGGAGGCAGAAAATACCCATGTGGATCCACGTTTTTACTATTTAGGGCC
ATTCAAAGATACAACAATTGTAAAAATCTCCATAGAAGACGTGGATGAGCCTCCAGTTTTCAGT
CGATCCTCCTATCTGTTTGAGGTTCATGAGGATATTGAAGTGGGCACAATCATCGGTACTGTAA
TGGCAAGAGACCCAGATTCTACTTCCAGTCCCATCAGATTTACTTTAGATCGCCATACTGATCT
TGACAGGATCTTTAACATTCATTCTGGAAACGGATCACTTTATACATCAAAGCCACTTGATCGT
GAACTATCTCAATGGCACAACCTTACCGTCATAGCTGCCGAGATCAATAATCCTAAAGAAACAA
CTCGTGTGTCTGTTTTTGTGAGGATTTTGGATGTTAATGACAACGCTCCACAATTTGCTGTGTT
TTATGACACATTTGTATGTGAAAATGCCAGACCAGGACAGCTGATACAGACAATAAGTGCAGTT
GACAAAGATGACCCCTTAGGTGGACAGAAGTTCTTCTTCAGTTTGGCTGCTGTGAATCCTAACT
TCACAGTGCAAGACAATGAAGACAACACTGCCAGAATTTTAACCAGAAAGAATGGCTTCAACCG
TCATGAAATAAGCACCTACCTACTGCCGGTAGTGATATCTGATAATGACTACCCCATTCAGAGC
AGCACTGGCACCCTGACGATCCGTGTTTGCGCCTGTGACAGCCAGGGCAACATGCAGTCCTGCA
GTGCCGAAGCCCTGCTCCTTCCTGCTGGCCTCAGCACTGGCGCCTTGATCGCCATTCTTCTCTG
CATCATCATTCTGCTGGTTATAGTAGTCCTCTTTGCAGCCCTGAAAAGGCAACGGAAGAAAGAG
CCTCTGATTTTATCCAAAGAAGACATCAGAGACAACATTGTGAGCTATAACGACGAAGGTGGCG
GAGAGGAGGACACCCAAGCCTTTGATATTGGAACCCTGAGGAATCCTGCAGCTATCGAGGAGAA
AAAGCTGCGGCGAGATATCATTCCTGAAACGTTATTTATACCGCGGCGGACTCCTACGGCCCCG
GATAACACGGATGTCCGGGATTTCATTAATGAGCGCCTCAAAGAGCACGACTTGGACCCCACTG
CGCCTCCCTACGACTCGCTGGCTACCTATGCCTATGAAGGAAACGACTCCGTTGCTGAATCTCT
GAGCTCCTTAGAATCAGGTACCACTGAAGGAGACCAAAACTACGATTACCTTCGAGAATGGGGG
CCTCGGTTTAATAAACTAGCAGAAATGTACGGTGGTGGTGAGAGCGACAAAGACGCTTAGCCTG
GCCCCTGAGCTCTGTTCAACGAGATACGTAACTTTGCAGACATTGTCTCCACTTCACAATATTT
GATATTCAGGAGAAAAAATTCCTGCCACTCAGCACAAGTTTCCCACCTATTTCTTAATTTGTTC
ATTAATTATATTAATTCCTTCCTGTAGAATGTCTCATGGGATATATACGACATTTTATTTAATC
ACTTCCAAGAGCCAAAGCTATGGAAATTCAATGTTGCCCATCTTAGTAAATAAAAGAAACCCGA
GCAGGATAGTTCTCCCTTAAGCAACCTCACGAACAAGTCGCTTCTGTTAGATACACGTCTTGCC
CTTGCAAATGAAGCTTTGAAAAGACGAAGAAAACATTTAAGATGTATCCTGTTCTGTACATTAA
GTTTAAAAAAAAAAGTCCATGTGGTGTTAGTAGGTGTGATATGCAGCCTGGTATACGAACATTC
GTGCAATTTCATTTCATCAAATTCTATCTGCTAATGTTTTATATTTATATTTTTGTATTTATTT
TTTAAAAAAAATAAACCAGTTTTTACAACTACT

hide sequence

RefSeq Acc Id:

XM_006232079 ⟹ XP_006232141

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	68,628,933 - 68,850,993 (+)	NCBI
Rnor_6.0	2	69,415,539 - 69,636,847 (+)	NCBI
Rnor_5.0	2	89,140,727 - 89,362,817 (+)	NCBI

Sequence:

show sequence

AGAATTCACCTCTTGTCTTTTAACTCCTTTAAGGTCTTGCCTTTTCTTCCCTTGCTGGTGGGAG
ATATCGGGGTAAATATGTTTCTGCTTTTTTTTTTTTTAAGTTATACGAGCAATTATGCCAAAAA
TCTTTACCTTTTAATAAACAAATGAGCATGCAACTCTTCTTGATGAGTTTCCAGGAACAACTGC
TTTCAATGTAGGTAATAGGAAGCCGGATAAATAATATATTATGTTCAACAGTACGGGGGTCTTC
AGAGTGGAGTTTCCGAATTCATTCATTCAGAGCAATTGCTGAAAATGTTTTCGGAGTGTAATTA
GTCATGCTCATTCCTGTTTACCTCTGTTTCAAATGTCAGCTTAGCAGGTAAACACTGTTGGCTG
TGAACTCTAACATCAGCTAACATTACTTTGCATTCCATATGAACGGATTCACTCCTCACTTACC
CCTGGTCACAGTTCGTTATCCCTTCAGTCTAGAGAGAAATGACAGTCAGAGGACAGATGCCTTG
AAGCTGTCAGTGGTCACTAAGCATCTCCACGAAGACAGTCGATTGACATTCATCAGAAACAGGA
TGGGTACAATTCCTATGTTCACCTTTTATATGAGTCCGAAGTGTCAGGGGGTACAATTAAATTA
AAGGGGGTAGGGGGAGTAAATGCACGCAGTCAGCAGTTGCAGCATTTATTGTCTCTGCTGCATT
AAAATCCATATTTTATGTGGTGTTAAATTAATGCAGCATGCTGGCAAGTCTAAATGAATGTCCT
CAACAAGTAACTATTATAGCACTGTACGCATGGGCCAGAGTCTGCAAGTGTTTTCATGCCACCA
CAATAAAAACCAAGTATCTCTTTACTATGGAAAGGGGAGAGGCTATAGGTATAATCAAAGACAA
ACATCATTTTAAAACTGACCTATCATCTCTTGCTTTCAAAAAAGCAGATCTCTTTCCTACAATT
TTTGGTCCTTCATTCCAGTAAAAGCTTCTATTATCCAAAGCGGCACATGCCTTACTTCTCAGCT
TTTCTTTGGAGATGCCTCTTTCTTCCTCTAATTTTTTTCTCTTGAAAAAAAATCTATTTTAAAA
ATAATCTGTCCCTGTGATGCTGCTGACAACTGTTATACTTCAATGCATATGTTAGGAGTCTCTC
TCTCTCTCTCTCCCTCTCCCTCTCTCCACCATCCCCCTCTCTGCCTTTCTTTTAAAACGTAGTT
ACAAGAGCTTCACTGTGGTGAATAGCACTTGGCAAGAGTGTGCTCATTTTTTTTTAGGTCTGGT
ATGGTGAGGATTTTTAATTAGTGGAACTTTCATGAAAACATTATGTCATTGTCAGAGCTGTATG
TTCATTTTTAGTTACAGTGAGGAAGGAAAAGAGAGCCTGTGCTCTAGAGAAATGGGAAATGATA
AGTTGCATGGGTAATCTGCACCCTGGGGTGGTAAGTGGGGCACATATGTATTCCATGTGCAGTG
CAAGAGGAAATGCTGGTTTATTTGGCCAGAGAGGAGCGAATGGATTGAAAAGTGAGCCAATGTG
AACAGCCTGTGCATGTGGCTGAGGGGCACGTCAATTGCAAAGCATCCCAAGGGTAAAAAGCTCT
TGGAAATATGTACATAGCACTAATGAAGTCTTGGAAACCAGTCGAGATCTGATACCATAAACTG
GACTACTTTTTCATCATCTGCACTGGAATTTTTCAAGAAGTAAACTATGTCAATCTATTCGTTC
TTGAGACTGTTTGTTCTCTGGGCATGCCTGCCCCAATTCTGCTGTCCAGAATTAACGTTCAGAA
GGACTCCTGGGCTTCAGCAAATGACTGCAGAATCCCATGTCCCTAGGGGTGATGGTAAAATCCT
TCACCGTCAAAAACGTGGCTGGATGTGGAACCAGTTTTTCTTACTGGAAGAATATACTGGATCT
GATTATCAATATGTCGGCAAGCTTCATTCAGACCAAGATAAAGGAGACGGATCGCTCAAATATA
TTTTGTCTGGAGATGGAGCTGGTACTCTTTTTATTATTGATGAAAAAACAGGTGATATTCACGC
CACAAGAAGAATTGATAGGGAAGAAAAGGCCTTTTATACTCTGCGTGCACAAGCTATTAACAGA
AGAACTCTGAGGCCAGTTGAGCCAGAGTCAGAATTTGTGATCAAAATTCACGATATCAACGACA
ATGAGCCTACATTCCCAGAAGAAATTTATACAGCCAGCGTTCCTGAAATGTCTGTTGTAGGTAC
TTCTGTGGTGCAAGTCACAGCTACAGATGCCGATGACCCTTCATATGGAAACAGCGCCAGAGTC
ATTTACAGCATACTTCAAGGGCAGCCTTATTTCTCTGTGGAACCAGAAACAGGTATCATAAGGA
CAGCTCTACCAAACATGAACAGAGAGAACAAGGAACAGTACCAGGTGGTTATTCAAGCCAAGGA
CATGGGCGGTCAGATGGGGGGTCTGTCTGGAACCACCACAGTGAACATCACTCTCACAGATGTC
AACGACAATCCTCCTCGCTTCCCCCAAAACACCATCCATCTGCGAGTTCTTGAATCCTCTCCAG
TTGGCACAGCTGTGGGAAGTGTAAAAGCCACCGATGCTGACACGGGGAAAAATGCCGAAGTGGA
TTACCGCATTATTGATGGAGATGGCACAGATATGTTTGACATTATAACTGAGAAGGACACACAG
GAAGGCATCATCACTGTGAAAAAGCCACTTGACTATGAGAACCGAAGACTATATACTCTGAAGG
TGGAGGCAGAAAATACCCATGTGGATCCACGTTTTTACTATTTAGGGCCATTCAAAGATACAAC
AATTGTAAAAATCTCCATAGAAGACGTGGATGAGCCTCCAGTTTTCAGTCGATCCTCCTATCTG
TTTGAGGTTCATGAGGATATTGAAGTGGGCACAATCATCGGTACTGTAATGGCAAGAGACCCAG
ATTCTACTTCCAGTCCCATCAGATTTACTTTAGATCGCCATACTGATCTTGACAGGATCTTTAA
CATTCATTCTGGAAACGGATCACTTTATACATCAAAGCCACTTGATCGTGAACTATCTCAATGG
CACAACCTTACCGTCATAGCTGCCGAGATCAATAATCCTAAAGAAACAACTCGTGTGTCTGTTT
TTGTGAGGATTTTGGATGTTAATGACAACGCTCCACAATTTGCTGTGTTTTATGACACATTTGT
ATGTGAAAATGCCAGACCAGGACAGCTGATACAGACAATAAGTGCAGTTGACAAAGATGACCCC
TTAGGTGGACAGAAGTTCTTCTTCAGTTTGGCTGCTGTGAATCCTAACTTCACAGTGCAAGACA
ATGAAGACAACACTGCCAGAATTTTAACCAGAAAGAATGGCTTCAACCGTCATGAAATAAGCAC
CTACCTACTGCCGGTAGTGATATCTGATAATGACTACCCCATTCAGAGCAGCACTGGCACCCTG
ACGATCCGTGTTTGCGCCTGTGACAGCCAGGGCAACATGCAGTCCTGCAGTGCCGAAGCCCTGC
TCCTTCCTGCTGGCCTCAGCACTGGCGCCTTGATCGCCATTCTTCTCTGCATCATCATTCTGCT
GGTTATAGTAGTCCTCTTTGCAGCCCTGAAAAGGCAACGGAAGAAAGAGCCTCTGATTTTATCC
AAAGAAGACATCAGAGACAACATTGTGAGCTATAACGACGAAGGTGGCGGAGAGGAGGACACCC
AAGCCTTTGATATTGGAACCCTGAGGAATCCTGCAGCTATCGAGGAGAAAAAGCTGCGGCGAGA
TATCATTCCTGAAACGTTATTTATACCGCGGCGGACTCCTACGGCCCCGGATAACACGGATGTC
CGGGATTTCATTAATGAGCGCCTCAAAGAGCACGACTTGGACCCCACTGCGCCTCCCTACGACT
CGCTGGCTACCTATGCCTATGAAGGAAACGACTCCGTTGCTGAATCTCTGAGCTCCTTAGAATC
AGGTACCACTGAAGGAGACCAAAACTACGATTACCTTCGAGAATGGGGGCCTCGGTTTAATAAA
CTAGCAGAAATGTACGGTGGTGGTGAGAGCGACAAAGACGCTTAGCCTGGCCCCTGAGCTCTGT
TCAACGAGATACGTAACTTTGCAGACATTGTCTCCACTTCACAATATTTGATATTCAGGAGAAA
AAATTCCTGCCACTCAGCACAAGTTTCCCACCTATTTCTTAATTTGTTCATTAATTATATTAAT
TCCTTCCTGTAGAATGTCTCATGGGATATATACGACATTTTATTTAATCACTTCCAAGAGCCAA
AGCTATGGAAATTCAATGTTGCCCATCTTAGTAAATAAAAGAAACCCGAGCAGGATAGTTCTCC
CTTAAGCAACCTCACGAACAAGTCGCTTCTGTTAGATACACGTCTTGCCCTTGCAAATGAAGCT
TTGAAAAGACGAAGAAAACATTTAAGATGTATCCTGTTCTGTACATTAAGTTTAAAAAAAAAAG
TCCATGTGGTGTTAGTAGGTGTGATATGCAGCCTGGTATACGAACATTCGTGCAATTTCATTTC
ATCAAATTCTATCTGCTAATGTTTTATATTTATATTTTTGTATTTATTTTTTAAAAAAAATAAA
CCAGTTTTTACAACTA

hide sequence

RefSeq Acc Id:

XM_006232080 ⟹ XP_006232142

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	2	68,628,623 - 68,850,993 (+)	NCBI
Rnor_6.0	2	69,415,174 - 69,636,847 (+)	NCBI
Rnor_5.0	2	89,140,727 - 89,362,817 (+)	NCBI

Sequence:

show sequence

GCCGGCACTTCCAGTCTCTAACCTTCTCATGGCGAGTGCTGCAGCTCCATCAGCAGAACCTTTC
TCTCCTTGTGAGGAACGGCTTTCCCCCCCACCCTCTCCTTTTCCCCCCTCCCTTAATCAGAACC
ACTGAATGAAAGCCAATCAGAGAGAGACTTCGCCCCCCCAACCCCCGTTTTCTTTGGTTCCCTG
CGGTCCAGAGTTAAAAGTGACGCTGAGAGAAAGCTTGAGTTAGACCGAAGTAGAATCAGTGAGA
GAAAATAACAGCAGAAAACAAACAAAAAGGGGACAGGGTGACAGTCTCTTCAGGGTTATTTGGC
TGGAACCAACTTCCGTTTTCCAGAAGCTGATGAAACAAGCTCTTGGAAATATGTACATAGCACT
AATGAAGTCTTGGAAACCAGTCGAGATCTGATACCATAAACTGGACTACTTTTTCATCATCTGC
ACTGGAATTTTTCAAGAAGTAAACTATGTCAATCTATTCGTTCTTGAGACTGTTTGTTCTCTGG
GCATGCCTGCCCCAATTCTGCTGTCCAGAATTAACGTTCAGAAGGACTCCTGGGCTTCAGCAAA
TGACTGCAGAATCCCATGTCCCTAGGGGTGATGGTAAAATCCTTCACCGTCAAAAACGTGGCTG
GATGTGGAACCAGTTTTTCTTACTGGAAGAATATACTGGATCTGATTATCAATATGTCGGCAAG
CTTCATTCAGACCAAGATAAAGGAGACGGATCGCTCAAATATATTTTGTCTGGAGATGGAGCTG
GTACTCTTTTTATTATTGATGAAAAAACAGGTGATATTCACGCCACAAGAAGAATTGATAGGGA
AGAAAAGGCCTTTTATACTCTGCGTGCACAAGCTATTAACAGAAGAACTCTGAGGCCAGTTGAG
CCAGAGTCAGAATTTGTGATCAAAATTCACGATATCAACGACAATGAGCCTACATTCCCAGAAG
AAATTTATACAGCCAGCGTTCCTGAAATGTCTGTTGTAGGTACTTCTGTGGTGCAAGTCACAGC
TACAGATGCCGATGACCCTTCATATGGAAACAGCGCCAGAGTCATTTACAGCATACTTCAAGGG
CAGCCTTATTTCTCTGTGGAACCAGAAACAGGTATCATAAGGACAGCTCTACCAAACATGAACA
GAGAGAACAAGGAACAGTACCAGGTGGTTATTCAAGCCAAGGACATGGGCGGTCAGATGGGGGG
TCTGTCTGGAACCACCACAGTGAACATCACTCTCACAGATGTCAACGACAATCCTCCTCGCTTC
CCCCAAAACACCATCCATCTGCGAGTTCTTGAATCCTCTCCAGTTGGCACAGCTGTGGGAAGTG
TAAAAGCCACCGATGCTGACACGGGGAAAAATGCCGAAGTGGATTACCGCATTATTGATGGAGA
TGGCACAGATATGTTTGACATTATAACTGAGAAGGACACACAGGAAGGCATCATCACTGTGAAA
AAGCCACTTGACTATGAGAACCGAAGACTATATACTCTGAAGGTGGAGGCAGAAAATACCCATG
TGGATCCACGTTTTTACTATTTAGGGCCATTCAAAGATACAACAATTGTAAAAATCTCCATAGA
AGACGTGGATGAGCCTCCAGTTTTCAGTCGATCCTCCTATCTGTTTGAGGTTCATGAGGATATT
GAAGTGGGCACAATCATCGGTACTGTAATGGCAAGAGACCCAGATTCTACTTCCAGTCCCATCA
GATTTACTTTAGATCGCCATACTGATCTTGACAGGATCTTTAACATTCATTCTGGAAACGGATC
ACTTTATACATCAAAGCCACTTGATCGTGAACTATCTCAATGGCACAACCTTACCGTCATAGCT
GCCGAGATCAATAATCCTAAAGAAACAACTCGTGTGTCTGTTTTTGTGAGGATTTTGGATGTTA
ATGACAACGCTCCACAATTTGCTGTGTTTTATGACACATTTGTATGTGAAAATGCCAGACCAGG
ACAGCTGATACAGACAATAAGTGCAGTTGACAAAGATGACCCCTTAGGTGGACAGAAGTTCTTC
TTCAGTTTGGCTGCTGTGAATCCTAACTTCACAGTGCAAGACAATGAAGACAACACTGCCAGAA
TTTTAACCAGAAAGAATGGCTTCAACCGTCATGAAATAAGCACCTACCTACTGCCGGTAGTGAT
ATCTGATAATGACTACCCCATTCAGAGCAGCACTGGCACCCTGACGATCCGTGTTTGCGCCTGT
GACAGCCAGGGCAACATGCAGTCCTGCAGTGCCGAAGCCCTGCTCCTTCCTGCTGGCCTCAGCA
CTGGCGCCTTGATCGCCATTCTTCTCTGCATCATCATTCTGCTGGTAGTCCTCTTTGCAGCCCT
GAAAAGGCAACGGAAGAAAGAGCCTCTGATTTTATCCAAAGAAGACATCAGAGACAACATTGTG
AGCTATAACGACGAAGGTGGCGGAGAGGAGGACACCCAAGCCTTTGATATTGGAACCCTGAGGA
ATCCTGCAGCTATCGAGGAGAAAAAGCTGCGGCGAGATATCATTCCTGAAACGTTATTTATACC
GCGGCGGACTCCTACGGCCCCGGATAACACGGATGTCCGGGATTTCATTAATGAGCGCCTCAAA
GAGCACGACTTGGACCCCACTGCGCCTCCCTACGACTCGCTGGCTACCTATGCCTATGAAGGAA
ACGACTCCGTTGCTGAATCTCTGAGCTCCTTAGAATCAGGTACCACTGAAGGAGACCAAAACTA
CGATTACCTTCGAGAATGGGGGCCTCGGTTTAATAAACTAGCAGAAATGTACGGTGGTGGTGAG
AGCGACAAAGACGCTTAGCCTGGCCCCTGAGCTCTGTTCAACGAGATACGTAACTTTGCAGACA
TTGTCTCCACTTCACAATATTTGATATTCAGGAGAAAAAATTCCTGCCACTCAGCACAAGTTTC
CCACCTATTTCTTAATTTGTTCATTAATTATATTAATTCCTTCCTGTAGAATGTCTCATGGGAT
ATATACGACATTTTATTTAATCACTTCCAAGAGCCAAAGCTATGGAAATTCAATGTTGCCCATC
TTAGTAAATAAAAGAAACCCGAGCAGGATAGTTCTCCCTTAAGCAACCTCACGAACAAGTCGCT
TCTGTTAGATACACGTCTTGCCCTTGCAAATGAAGCTTTGAAAAGACGAAGAAAACATTTAAGA
TGTATCCTGTTCTGTACATTAAGTTTAAAAAAAAAAGTCCATGTGGTGTTAGTAGGTGTGATAT
GCAGCCTGGTATACGAACATTCGTGCAATTTCATTTCATCAAATTCTATCTGCTAATGTTTTAT
ATTTATATTTTTGTATTTATTTTTTAAAAAAAATAAACCAGTTTTTACAACTA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001162102	(Get FASTA)	NCBI Sequence Viewer
	XP_006232141	(Get FASTA)	NCBI Sequence Viewer
	XP_006232142	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAF87051	(Get FASTA)	NCBI Sequence Viewer
	AAL78007	(Get FASTA)	NCBI Sequence Viewer
	EDL82596	(Get FASTA)	NCBI Sequence Viewer
	EDL82597	(Get FASTA)	NCBI Sequence Viewer
	EDL82598	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001162102 ⟸ NM_001168631
- Peptide Label:	precursor
- UniProtKB:	F1LR98 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSIYSFLRLFVLWACLPQFCCPELTFRRTPGLQQMTAESHVPRGDGKILHRQKRGWMWNQFFLL EEYTGSDYQYVGKLHSDQDKGDGSLKYILSGDGAGTLFIIDEKTGDIHATRRIDREEKAFYTLR AQAINRRTLRPVEPESEFVIKIHDINDNEPTFPEEIYTASVPEMSVVGTSVVQVTATDADDPSY GNSARVIYSILQGQPYFSVEPETGIIRTALPNMNRENKEQYQVVIQAKDMGGQMGGLSGTTTVN ITLTDVNDNPPRFPQNTIHLRVLESSPVGTAVGSVKATDADTGKNAEVDYRIIDGDGTDMFDII TEKDTQEGIITVKKPLDYENRRLYTLKVEAENTHVDPRFYYLGPFKDTTIVKISIEDVDEPPVF SRSSYLFEVHEDIEVGTIIGTVMARDPDSTSSPIRFTLDRHTDLDRIFNIHSGNGSLYTSKPLD RELSQWHNLTVIAAEINNPKETTRVSVFVRILDVNDNAPQFAVFYDTFVCENARPGQLIQTISA VDKDDPLGGQKFFFSLAAVNPNFTVQDNEDNTARILTRKNGFNRHEISTYLLPVVISDNDYPIQ SSTGTLTIRVCACDSQGNMQSCSAEALLLPAGLSTGALIAILLCIIILLVIVVLFAALKRQRKK EPLILSKEDIRDNIVSYNDEGGGEEDTQAFDIGTLRNPAAIEEKKLRRDIIPETLFIPRRTPTA PDNTDVRDFINERLKEHDLDPTAPPYDSLATYAYEGNDSVAESLSSLESGTTEGDQNYDYLREW GPRFNKLAEMYGGGESDKDA hide sequence

RefSeq Acc Id:

XP_006232142 ⟸ XM_006232080

- Peptide Label:

isoform X2

- Sequence:

show sequence

MSIYSFLRLFVLWACLPQFCCPELTFRRTPGLQQMTAESHVPRGDGKILHRQKRGWMWNQFFLL
EEYTGSDYQYVGKLHSDQDKGDGSLKYILSGDGAGTLFIIDEKTGDIHATRRIDREEKAFYTLR
AQAINRRTLRPVEPESEFVIKIHDINDNEPTFPEEIYTASVPEMSVVGTSVVQVTATDADDPSY
GNSARVIYSILQGQPYFSVEPETGIIRTALPNMNRENKEQYQVVIQAKDMGGQMGGLSGTTTVN
ITLTDVNDNPPRFPQNTIHLRVLESSPVGTAVGSVKATDADTGKNAEVDYRIIDGDGTDMFDII
TEKDTQEGIITVKKPLDYENRRLYTLKVEAENTHVDPRFYYLGPFKDTTIVKISIEDVDEPPVF
SRSSYLFEVHEDIEVGTIIGTVMARDPDSTSSPIRFTLDRHTDLDRIFNIHSGNGSLYTSKPLD
RELSQWHNLTVIAAEINNPKETTRVSVFVRILDVNDNAPQFAVFYDTFVCENARPGQLIQTISA
VDKDDPLGGQKFFFSLAAVNPNFTVQDNEDNTARILTRKNGFNRHEISTYLLPVVISDNDYPIQ
SSTGTLTIRVCACDSQGNMQSCSAEALLLPAGLSTGALIAILLCIIILLVVLFAALKRQRKKEP
LILSKEDIRDNIVSYNDEGGGEEDTQAFDIGTLRNPAAIEEKKLRRDIIPETLFIPRRTPTAPD
NTDVRDFINERLKEHDLDPTAPPYDSLATYAYEGNDSVAESLSSLESGTTEGDQNYDYLREWGP
RFNKLAEMYGGGESDKDA

hide sequence

RefSeq Acc Id:	XP_006232141 ⟸ XM_006232079
- Peptide Label:	isoform X1
- UniProtKB:	F1LR98 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSIYSFLRLFVLWACLPQFCCPELTFRRTPGLQQMTAESHVPRGDGKILHRQKRGWMWNQFFLL EEYTGSDYQYVGKLHSDQDKGDGSLKYILSGDGAGTLFIIDEKTGDIHATRRIDREEKAFYTLR AQAINRRTLRPVEPESEFVIKIHDINDNEPTFPEEIYTASVPEMSVVGTSVVQVTATDADDPSY GNSARVIYSILQGQPYFSVEPETGIIRTALPNMNRENKEQYQVVIQAKDMGGQMGGLSGTTTVN ITLTDVNDNPPRFPQNTIHLRVLESSPVGTAVGSVKATDADTGKNAEVDYRIIDGDGTDMFDII TEKDTQEGIITVKKPLDYENRRLYTLKVEAENTHVDPRFYYLGPFKDTTIVKISIEDVDEPPVF SRSSYLFEVHEDIEVGTIIGTVMARDPDSTSSPIRFTLDRHTDLDRIFNIHSGNGSLYTSKPLD RELSQWHNLTVIAAEINNPKETTRVSVFVRILDVNDNAPQFAVFYDTFVCENARPGQLIQTISA VDKDDPLGGQKFFFSLAAVNPNFTVQDNEDNTARILTRKNGFNRHEISTYLLPVVISDNDYPIQ SSTGTLTIRVCACDSQGNMQSCSAEALLLPAGLSTGALIAILLCIIILLVIVVLFAALKRQRKK EPLILSKEDIRDNIVSYNDEGGGEEDTQAFDIGTLRNPAAIEEKKLRRDIIPETLFIPRRTPTA PDNTDVRDFINERLKEHDLDPTAPPYDSLATYAYEGNDSVAESLSSLESGTTEGDQNYDYLREW GPRFNKLAEMYGGGESDKDA hide sequence

RefSeq Acc Id:

ENSRNOP00000013152 ⟸ ENSRNOT00000013152

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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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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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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-Lx/CubMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/NHsdMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BN/SsN (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH2/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

BXH3/CubMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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)

DA/OlaHsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/DuCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

F344/NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

F344/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/EurMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FHH/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)

FHH/EurMcwi (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

FHL/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)

FHL/EurMcwi (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

FXLE16/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

FXLE18/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

GH/OmrMcwi (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)

GK/FarMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

HXB10/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB2/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB20/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB31/IpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

HXB4/IpcvMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LE/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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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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

LEXF10A/StmMcwi (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF11/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1A/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF1C/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF2B/Stm (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF3/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LEXF4/Stm (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LH/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

LL/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

LN/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/MavRrrcAek (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Kwitek
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

M520/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

M520/NRrrcMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MHS/Gib (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

MNS/Gib (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

MR/N (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

MR/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

MWF/Hsd (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

PVG/Seac (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Japan
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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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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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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

SHR/OlalpcvMcwi (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

SHRSP/A3NCrl (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Envigo
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	MCW
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

WAG/RijCrl (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2019)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	Charles River
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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 (2020)

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Sequenced By:	MCW
Platform:	GSPMC-Illumina-NovaSeq6000
Secondary Analysis:	BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder:	NIH
Description:	Dr. Mindy Dwinell - Hybrid rat diversity program

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:619741	AgrOrtholog
Ensembl Genes	ENSRNOG00000009771	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000013152	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000013152	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	4.10.900.10	UniProtKB/TrEMBL
InterPro	Cadherin	UniProtKB/TrEMBL
	Cadherin	UniProtKB/TrEMBL
	Cadherin-like	UniProtKB/TrEMBL
	Cadherin_CS	UniProtKB/TrEMBL
	Cadherin_cytoplasmic-dom	UniProtKB/TrEMBL
	Catenin_binding_dom	UniProtKB/TrEMBL
KEGG Report	rno:29181	UniProtKB/TrEMBL
NCBI Gene	29181	ENTREZGENE
PANTHER	PTHR24027	UniProtKB/TrEMBL
Pfam	Cadherin	UniProtKB/TrEMBL
	Cadherin_C	UniProtKB/TrEMBL
PhenoGen	Cdh10	PhenoGen
PRINTS	CADHERIN	UniProtKB/TrEMBL
PROSITE	CADHERIN_1	UniProtKB/TrEMBL
	CADHERIN_2	UniProtKB/TrEMBL
SMART	SM00112	UniProtKB/TrEMBL
Superfamily-SCOP	Cadherin	UniProtKB/TrEMBL
UniProt	F1LR98	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-01-20	Cdh10	cadherin 10			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Cdh10	cadherin 10			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in testis	68759

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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD