Epha10 (EPH receptor A10) - Rat Genome Database

Name: Epha10
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

	Submit Data \| Help \| Video Tutorials \| News \| Publications \| Download \| REST API \| Citing RGD \| Contact
	Search RGD Grant Resources Citing RGD About Us Contact Us Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper VCMap Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease Find Models new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive Pathways Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
	Advanced Search (OLGA)

Gene: Epha10 (EPH receptor A10) Rattus norvegicus

Analyze

Symbol:

Epha10

Name:

EPH receptor A10

RGD ID:

1562679

Description:

Predicted to enable transmembrane-ephrin receptor activity. Predicted to be involved in axon guidance; positive regulation of kinase activity; and transmembrane receptor protein tyrosine kinase signaling pathway. Predicted to be part of receptor complex. Predicted to be active in neuron projection. Predicted to be integral component of plasma membrane. Orthologous to human EPHA10 (EPH receptor A10); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acetamide.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

ephrin type-A receptor 10; LOC298528; RGD1562679; similar to Ephrin type-A receptor 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):	EPHA10 (EPH receptor A10)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Epha10 (Eph receptor A10)	HGNC	EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB
Chinchilla lanigera (long-tailed chinchilla):	Epha10 (EPH receptor A10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	EPHA10 (EPH receptor A10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	EPHA10 (EPH receptor A10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Epha10 (EPH receptor A10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	EPHA10 (EPH receptor A10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	EPHA10 (EPH receptor A10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Epha10 (EPH receptor A10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	EPHA7 (EPH receptor A7)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	EPHA10 (EPH receptor A10)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Epha10 (Eph receptor A10)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Eph	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	vab-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

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	5	137,139,588 - 137,175,637 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	5	137,140,735 - 137,174,157 (+)	Ensembl
Rnor_6.0	5	142,875,171 - 142,910,537 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	142,875,773 - 142,908,395 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	146,645,808 - 146,680,199 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	144,228,301 - 144,248,902 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	5	135,661,767 - 135,694,928 (+)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Charcot-Marie-Tooth disease dominant intermediate C (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

2,3',4,4',5-Pentachlorobiphenyl (ISO)

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

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

4,4'-sulfonyldiphenol (ISO)

acetamide (EXP)

acrylamide (ISO)

aflatoxin B1 (ISO)

amphetamine (EXP)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

butanal (ISO)

cadmium dichloride (ISO)

cyclosporin A (ISO)

diazinon (ISO)

ethanol (ISO)

gentamycin (EXP)

kojic acid (ISO)

methapyrilene (ISO)

methylphenidate (ISO)

paracetamol (EXP)

pentanal (ISO)

potassium dichromate (ISO)

propanal (ISO)

sodium arsenite (ISO)

triclosan (ISO)

triptonide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

axon guidance (IBA)

ephrin receptor signaling pathway (IEA)

peptidyl-tyrosine phosphorylation (IEA)

positive regulation of kinase activity (IBA)

transmembrane receptor protein tyrosine kinase signaling pathway (IBA)

Cellular Component

integral component of plasma membrane (IBA)

neuron projection (IBA)

receptor complex (IBA)

Molecular Function

ATP binding (IEA)

protein binding (ISO)

transmembrane receptor protein tyrosine kinase activity (IBA)

transmembrane-ephrin receptor activity (IBA,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.	RGD automated data pipeline
3.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:15777695	PMID:23376485

Genomics

Comparative Map Data

Epha10
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	137,139,588 - 137,175,637 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	5	137,140,735 - 137,174,157 (+)	Ensembl
Rnor_6.0	5	142,875,171 - 142,910,537 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	142,875,773 - 142,908,395 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	146,645,808 - 146,680,199 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	144,228,301 - 144,248,902 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	5	135,661,767 - 135,694,928 (+)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

EPHA10
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	1	37,713,880 - 37,765,133 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	37,713,888 - 37,765,120 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	38,181,648 - 38,230,792 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	37,954,233 - 38,003,411 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	37,895,050 - 37,899,882	NCBI
Celera	1	36,459,675 - 36,508,664 (-)	NCBI
Cytogenetic Map	1	p34.3	NCBI
HuRef	1	36,298,901 - 36,347,866 (-)	NCBI		HuRef
CHM1_1	1	38,297,768 - 38,346,680 (-)	NCBI		CHM1_1

Epha10
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	124,775,408 - 124,811,594 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	4	124,774,692 - 124,811,593 (+)	Ensembl
GRCm38	4	124,881,530 - 124,917,801 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	124,880,899 - 124,917,800 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	124,559,029 - 124,563,752 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	4	124,384,128 - 124,388,812 (+)	NCBI			mm8
Celera	4	123,204,101 - 123,208,828 (+)	NCBI		Celera
Cytogenetic Map	4	D2.2	NCBI

Epha10
(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	NW_004955452	15,510,054 - 15,547,769 (-)	NCBI	ChiLan1.0	ChiLan1.0

EPHA10
(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	1	38,335,783 - 38,375,186 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	38,337,871 - 38,386,946 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	1	36,987,683 - 37,038,611 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

EPHA10
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	15	4,756,136 - 4,789,494 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	15	4,998,036 - 5,039,458 (+)	NCBI
ROS_Cfam_1.0	15	4,884,835 - 4,926,444 (+)	NCBI
UMICH_Zoey_3.1	15	4,744,492 - 4,785,852 (+)	NCBI
UNSW_CanFamBas_1.0	15	4,810,975 - 4,852,222 (+)	NCBI
UU_Cfam_GSD_1.0	15	4,827,371 - 4,868,788 (+)	NCBI

Epha10
(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_024405058	54,091,884 - 54,128,201 (-)	NCBI
SpeTri2.0	NW_004936474	19,916,666 - 19,935,958 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

EPHA10
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	93,765,128 - 93,803,894 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	93,764,732 - 93,804,069 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

EPHA10
(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	20	95,094,971 - 95,145,264 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	20	95,098,283 - 95,142,863 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666033	21,664,826 - 21,712,734 (-)	NCBI	Vero_WHO_p1.0

Epha10
(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_004624764	20,441,465 - 20,480,421 (-)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

34.MMHAP10FRD10.seq

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	137,140,800 - 137,140,908 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	142,875,827 - 142,875,934	NCBI	Rnor6.0
Rnor_5.0	5	146,646,447 - 146,646,554	UniSTS	Rnor5.0
Celera	5	135,661,911 - 135,662,018	UniSTS
Cytogenetic Map	5	q36	UniSTS

RH137663

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	137,144,350 - 137,144,512 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	142,879,376 - 142,879,537	NCBI	Rnor6.0
Rnor_5.0	5	146,649,996 - 146,650,157	UniSTS	Rnor5.0
Celera	5	135,665,448 - 135,665,609	UniSTS
RH 3.4 Map	5	890.7	UniSTS
Cytogenetic Map	5	q36	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
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	2138965	166875058	Rat
1641912	Alcrsp18	Alcohol response QTL 18			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	35189153	141643988	Rat
1549845	Scl44	Serum cholesterol level QTL 44	6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	40128307	148607290	Rat
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	46711509	161317411	Rat
1576312	Emca8	Estrogen-induced mammary cancer QTL 8	4.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	50328551	141643988	Rat
61426	Scl2	Serum cholesterol level QTL 2	7.3	0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	59793399	143070159	Rat
61393	Bp7	Blood pressure QTL 7	4.5	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	60293434	161481680	Rat
1354598	Srn6	Serum renin concentration QTL 6	3.8		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	5	69540295	151018848	Rat
1302790	Scl20	Serum cholesterol level QTL 20	6.4	0.0001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	82394392	166664054	Rat
61452	Ciaa5	CIA Autoantibody QTL 5	3.5		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	5	94858972	143070159	Rat
1331796	Thshl2	Thyroid stimulating hormone level QTL 2	2.3		blood thyroid-stimulating hormone amount (VT:0005119)	serum thyroid stimulating hormone level (CMO:0001248)	5	97059760	147465714	Rat
1358187	Emca1	Estrogen-induced mammary cancer QTL 1	4.4		mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	5	99216724	148607142	Rat
1578673	Bmd13	Bone mineral density QTL 13	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	5	103689353	148689353	Rat
2317056	Wbc3	White blood cell count QTL 3	2.51	0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	5	105999803	150999803	Rat
7207488	Bss110	Bone structure and strength QTL 1	8.4		femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	5	106906205	151906205	Rat
7207491	Bss112	Bone structure and strength QTL 112	7		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	5	106906205	151906205	Rat
7207481	Bss106	Bone structure and strength QTL 106	7.9		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	106906205	151906205	Rat
7207486	Bss109	Bone structure and strength QTL 109			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	5	106906205	151906205	Rat
1549838	Bss4	Bone structure and strength QTL 4	9.2		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	5	106906205	151906205	Rat
1298089	Scl14	Serum cholesterol level QTL 14	5.8	0.0004	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	108845856	153845856	Rat
1598847	Cm62	Cardiac mass QTL 62	3.4		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	108845856	153845856	Rat
8657050	Bw146	Body weight QTL 146	19.84	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	108938288	153938288	Rat
8694441	Bw169	Body weight QTL 169	17.61	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	5	111416838	156416838	Rat
8694198	Abfw3	Abdominal fat weight QTL 3	16.13	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	5	111416838	156416838	Rat
8694389	Bw160	Body weight QTL 160	6.17	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	5	111416838	156416838	Rat
8552960	Pigfal15	Plasma insulin-like growth factor 1 level QTL 15			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	111416838	156416838	Rat
1581510	Cm54	Cardiac mass QTL 54	3.4	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	5	120740824	143608494	Rat
2293642	Bss37	Bone structure and strength QTL 37	4.64	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	120740824	151018848	Rat
1641920	Colcs1	Colorectal carcinoma susceptibility QTL 1	2.99	0.0055	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	5	121846814	166846814	Rat
10053720	Scort26	Serum corticosterone level QTL 26	2.06	0.0147	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	124965598	166875058	Rat
1300122	Wbc1	White blood cell count QTL 1	2.75		leukocyte quantity (VT:0000217)	total white blood cell count (CMO:0000365)	5	125392826	139989768	Rat
724525	Bp147	Blood pressure QTL 147	4.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	126424772	166875058	Rat
1598819	Bp292	Blood pressure QTL 292	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	127798274	166875058	Rat
1598861	Cm64	Cardiac mass QTL 64	2.9		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	127798274	166875058	Rat
8552908	Pigfal4	Plasma insulin-like growth factor 1 level QTL 4	6.6		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	128506074	166875058	Rat
8694169	Bw148	Body weight QTL 148	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	128506074	166875058	Rat
634349	Bp139	Blood pressure QTL 139		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	128924607	166875058	Rat
1331803	Rf32	Renal function QTL 32	2.798		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	5	129132428	143070159	Rat
70156	Niddm30	Non-insulin dependent diabetes mellitus QTL 30	3.98		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	5	129132447	151006154	Rat
738018	Anxrr4	Anxiety related response QTL 4	5.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	5	130130159	166875058	Rat
7794791	Mcs33	Mammary carcinoma susceptibility QTL 33	1.93		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	5	131345754	166875058	Rat
631505	Bp103	Blood pressure QTL 103	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	132717196	165560427	Rat
7411722	Strs6	Sensitivity to stroke QTL 6	3.9		cerebrum integrity trait (VT:0010549)	percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)	5	134972980	138113556	Rat
631562	Apr2	Acute phase response QTL 2	3.7		blood murinoglobulin 1 amount (VT:0010597)	plasma murinoglobulin 1 level (CMO:0001931)	5	135927956	166875058	Rat
61444	Strs2	Sensitivity to stroke QTL 2	4.7		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	5	135929696	166875058	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	117
Count of miRNA genes:	86
Interacting mature miRNAs:	102
Transcripts:	ENSRNOT00000056496, ENSRNOT00000075431
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

	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	reproductive system	respiratory system	appendage
High
Medium								21	1
Low								49	8
Below cutoff	2	7	1	10	1	3	3	4	20	1	3

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001135709	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_001395095	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006238858	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017593293	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109629	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039109630	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005504407	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005504408	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC113890	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000162	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000056496 ⟹ ENSRNOP00000053334

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	137,140,735 - 137,174,157 (+)	Ensembl
Rnor_6.0 Ensembl	5	142,875,773 - 142,908,395 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000082120 ⟹ ENSRNOP00000068718

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	5	142,875,773 - 142,880,212 (+)	Ensembl

RefSeq Acc Id:

NM_001135709 ⟹ NP_001129181

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	137,140,657 - 137,174,157 (+)	NCBI
Rnor_6.0	5	142,875,683 - 142,909,057 (+)	NCBI
Rnor_5.0	5	146,645,808 - 146,680,199 (+)	NCBI
RGSC_v3.4	5	144,228,301 - 144,248,902 (+)	RGD
Celera	5	135,661,767 - 135,694,928 (+)	RGD

Sequence:

show sequence

AGCCGGCGCTGGGGTCTGGGGGCACTGCTCAGCGGTGCTGGGCTGGCGAGGCTGGAGCCGCCGC
CGCACTGACAGCTCCGTCTGTGGACCATGGAGACTGGCGCCGGTCCACACCCGCTGCGCCTGTT
CGTCTGCCTGATGCCACTCTGTCTTGCTCTGCTTCTGGGACCCGGGCGGCCTGGGACCGCCGAG
GAAGTTACCCTCCTGGACTCCAAAGCCTCTCAGGCTGAGCTGGGCTGGACTGCACTGCCAAGCA
CTGGGTGGGAGGAGATTAGTGGCGTGGATGAACATGATCGTCCCATCCGCACGTACCAAGTGTG
CAACGTGTTGGAGCCCAACCAGGACAACTGGCTTCAGACTGGCTGGATCAGCCGTGGCCGTGGG
CAGCGCATCTTCGTGGAGCTGCAGTTCACGCTGCGTGACTGCAGCAGCATACCTGGAGCCACTG
GCACCTGCAAAGAGACCTTCAACGCATACTACCTGGAAACCGAGGCCGACTTAGGCCGAGGACA
TCCCCACCTAGGAGGCAACCGACCCCGCAAGATTGACACCATCGCAGCTGATGAGAGCTTCACG
CAGGGCGACTTGGGGGAGCGAAAGATGAAGCTGAACACAGAGGTGCGTGAGATTGGCCCCCTCA
GCCGTCAAGGCTTCCACCTGGCCTTCCAGGACGTGGGTGCATGCGTGGCGTTGGTCTCAGTGCG
TGTCTACTACAAGCAGTGCCGTGCCACAGTGCGAGGCTTGGCAGCCTTCCCCGCCACCGCAGCT
GAGAGCGCCTTCTCCACGCTGGTGGAAGTGGCTGGAACGTGCGTGGCCCACTCGGAAGGGGAGC
CCAGCAGCCCTCCACGCATGCACTGTGGCGCGGATGGCGAGTGGCTGGTGCCTGTGGGCCGTTG
CAGCTGCAGTGCAGGATTCCAGGAACGTGGTGACATCTGCGAAGCCTGTCCCCCAGGTTTTTAC
AAGGTGTCCCCAAGGCGGCCCCTCTGCTCACCCTGCCCGGAGCACAGCTTGGCCCTGGAGAATG
CCTCTACATTCTGTGTGTGCCAGGACACCTATGCTCGCTCGCCCACCGACCCGCCCTCAGCTTC
CTGCACTCGGCCGCCGTCCGCGCCGCGGGACCTGCAGTACAGCCTGAGCCGTTCCCCGCTGGCG
CTGCGGCTGCGCTGGCTGCCGCCTGAGGACTCCGGTGGCCGCTCCGACGTCACCTACTCGCTGC
TGTGCCTGCGCTGCGGGCGCGACGGTCCGGCGGGCGCGTGCCAACCCTGCGGGCCGCGCGTGGC
CTTCGTCCCGCGCCAGGCTGGGCTACGGGAACGCGCCGCCACGCTACTGCACCTGCGGCCGGGC
GCGCGCTACACCGTGCGCGTGGCCGCGCTCAACGGCGTCTCGGGCCCGGCGGCTGCCGCGGGAG
CCACTTATGCGCAGGTCACCGTGTCCACCGGACCCGGGGCACCCTGGGAGGAGGATGAAATCCG
TAGGGACCGCGTGGAGCCCCAGAGCGTGTCGCTGTCGTGGAGAGAGCCTGTCCCTGCTGGAGCT
TCCGGAACCAACAGGACTGAGTATGAGATCCGCTACTACGAGAAGGGTTTGGGGGACAGGTTCC
AGTCTTGGGTTCACCTGGGTTCACCCTTGGCTACACAAGTCGGAGGTCAGCCCAGGCTACGTGA
TTCTCCATTTCAAAACCGAAACCAAAACCTCACAAAATCCTGGGAAACCAACCCCAGCTACCTG
GACTCTTGCCTCCTCCCAGAGCTGGGCTGCATTGCCCCTGGGTCCAGAGACCAGAGCCCAGCAG
TGGTTGTCACTGTGGTGACCATCTCAGCCCTCTTGGTCCTGGGCTCCGTGATGAGTGTACTGGC
CATCTGGAGGAGGCCCTGTGATGGCAAAGGAAGTGGCAACGCCCATGATGAAGAGGAACTGTAT
TTCCACTTCAAAGTTCCGACACGCCGCACGTTTCTGGACCCCCAAAGCTGCGGGGACCCGTTGC
AGGCTGTGCATTTGTTTGCCAAAGAGCTAGATGCCAAAAGCGTCACCCTGGAGAAGAGCTTGGG
AGCAGGCCGATTTGGGGACCTGTGCTGCGGCTGCCTGCAGCTGCCGGGTCGCCAGGAACTACCC
GTGGCCGTGCACACTCTGAGGGAGGGTTGCTCAGACTCCCAGAAGCTCAGCTTCCTGGCTGAGG
CCCTCACCCTGGGACAGTTTGACCACAGCCACATCGTGCGGCTGGAAGGCGTGGTCACCCGAGG
GAACCCCTTGATGATTGTCACCGAGTACATGAACCTCGGGGCCCTAGATGACTTCCTCAGGCAT
CACGAGGCAGAGCTGGTGACTGCGCAGCTGATGGGTCTGCTGCCCGGGCTGGCATCGGCCATGA
AGTATCTGTCGGAAATGGGCTATGTCCACCGGGGCCTCGCGGCCCGCCGAGTGCTCCTCAGCAG
TGGCCTCATCTGTAAGATCTCTGGCTTTGGGCGGGGTCCCCGGGACCGAGCGGAAGCTGTCTAC
ACCACCATGAGTGGCAGGAGCCCAGCGCTCTGGGCAGCTCCTGAGACTCTACAGTTTGGCCACT
TCAGCTCTGCCAGTGACGTGTGGAGCTTTGGCATTGTCATGTGGGAAGTGATGGCCTTTGGGGA
GCGGCCCTACTGGGACATGTCTGGACAAGATGTAATCAAGGCCGTGGAGGATGGTTTCCGGCTG
CCACCCCCCAGAAACTGTCCCTCCCAGCTGCACCGATTGATGCTTGAGTGCTGGCAGAAAGACC
CAGGTGAGCGGCCCAGGTTCTCCCAGATCCACAGCATCCTGAGCAAGATGGGGCAGGAGCCAGA
ACCCTCCAAGTGTGCCTCGACCACCTGTCTCAGGCCTCCCACCCCACTGGCAGACCGTGCCTTT
TCTGCCTTCCCCTCCTTTGGCTCCGTGGGTGCCTGGCTGGAGGCCCTAGACTTGTGTCGCTACA
AGGACAACTTCTCTGCAGCCGGCTATGGGAGCCTGGAGGCCGTGACAGAGATGACTGCCCAGGA
CCTGGGGAGCCTTGGGATCTCTTCTGCGGAGCATCGAGAGGCCCTCCTTAGTGGGATCAGTGCC
CTGCAGACTCGAGTGCTACAACTACAGGGTCAGGGGGTGCAAGTGTGAGCCGCTCAGCCCTGCC
CCAGGACCTACAAGCGACACTCCCCTAGGGTGGGAGGAGTGCTTATTCTCAGTGGCCTCTGAGC
TGGTTGGTACCACGTTGTCCCCCCATTTCATTTTTCCTCTCAACACCTTGCTGACCTAGTGGTC
CTAAAACGAGGTTCAGATCCCTGGAGAGGGCCCCAGACATAACAGTAGGAAGAGGGCTAGGGTG
TCAAGGGAAGGTTGGGGTGTCAAGGGTGTTGGTTGGGGAAGACAGTTTCAGTTGTCCTGGCTCA
GGCCCCTTAGACTCCCACACTCAGTGGGGGTTGGGCCTAATCAGTGGGCATCTCATTTCTCCAG
AGAGCTTTTGACTTGGGCAATATGGGTCCCTGTGAGAGACCCATTGTTTCTGACAGGGACCATA
GCTGCGTAGGCACCAGAGTATGGGAGCCTGAGCCAGTGGGTGGTGCCCCTTACATCCTGTGCCT
TGGCTAGGTCTATCTGCACACTGGTGACAAGGCCCTAGCAGGCAAGTGGTGCTGAGCTCAGGGA
CTGGGCCTCCAGGTGGAGACTCCAGAGCTGATGGCTTCCTGCCTTGGGGTTGGCAGTTCAGGAT
GAGGGCCAGGCTCCTAGTAGGTCATGCAAAGTCCTGGTGCTCGCCCTGGGCCGATGTCTGATTT
GATTGG

hide sequence

RefSeq Acc Id:

XM_006238858 ⟹ XP_006238920

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	137,139,629 - 137,175,637 (+)	NCBI
Rnor_6.0	5	142,875,188 - 142,910,537 (+)	NCBI
Rnor_5.0	5	146,645,808 - 146,680,199 (+)	NCBI

Sequence:

show sequence

GGAGGGATCGAACCATGCAACACTGGGAGCCGCAGACACAGGAAGAGGCCAAGGGCTGGGAGAC
ACCAGAACTCCCTAGAGCTTGAGGTCAGGATATCAAGCTCGGAAACCCCCTGCAAGTAATGGGA
ACAAGGGTGCTCCCAAGGCTAGCTAAGAGGCTGCAAGTGTCACCGCTTCCCCGCGGACCGCCCC
CCCGTAAGCCACGCCCACAGCGCCTACTTCTCAGGATTCAGAGAGCTAAGGTTTAAGGGTCTCT
AGTCCACCGACGCCAGCTTGTCTCGCTCTCCGGCAACCCTGCTAACGCTCAGAGCCGCCCTACC
CCCACGGTTTGGAGATCTGCGGGACCCCTTGGTTTCCCCCTCCAGCTCGGCGTTCCGCCCCTGG
CCTATGAAACTCCACCTTCTCATCCTCTGCTGACCCGGATTGGTGGACCTCCCGCGGCGATGCG
TAGCGATTGGTCCCCATGGATGATGGTGACCAGCGAGACTCCGCCCCAGCCGGCGCTGGGGTCT
GGGGGCACTGCTCAGCGGTGCTGGGCTGGCGAGGCTGGAGCCGCCGCCGCACTGACAGCTCCGT
CTGTGGACCATGGAGACTGGCGCCGGTCCACACCCGCTGCGCCTGTTCGTCTGCCTGATGCCAC
TCTGTCTTGCTCTGCTTCTGGGACCCGGGCGGCCTGGGACCGCCGAGGAAGTTACCCTCCTGGA
CTCCAAAGCCTCTCAGGCTGAGCTGGGCTGGACTGCACTGCCAAGCACTGGGTGGGAGGAGATT
AGTGGCGTGGATGAACATGATCGTCCCATCCGCACGTACCAAGTGTGCAACGTGTTGGAGCCCA
ACCAGGACAACTGGCTTCAGACTGGCTGGATCAGCCGTGGCCGTGGGCAGCGCATCTTCGTGGA
GCTGCAGTTCACGCTGCGTGACTGCAGCAGCATACCTGGCGCCACTGGCACCTGCAAAGAGACC
TTCAACGCATACTACCTGGAAACCGAGGCCGACTTAGGCCGAGGACATCCCCACCTAGGAGGCA
ACCGACCCCGCAAGATTGACACCATCGCAGCTGATGAGAGCTTCACGCAGGGCGACTTGGGGGA
GCGAAAGATGAAGCTGAACACAGAGGTGCGTGAGATTGGCCCCCTCAGCCGTCAAGGCTTCCAC
CTGGCCTTCCAGGACGTGGGTGCATGCGTGGCGTTGGTCTCAGTGCGTGTCTACTACAAGCAGT
GCCGTGCCACAGTGCGAGGCTTGGCAGCCTTCCCCGCCACCGCAGCTGAGAGCGCCTTCTCCAC
GCTGGTGGAAGTGGCTGGAACGTGCGTGGCCCACTCGGAAGGGGAGCCCAGCAGCCCTCCACGC
ATGCACTGTGGCGCGGATGGCGAGTGGCTGGTGCCTGTGGGCCGTTGCAGCTGCAGTGCAGGAT
TCCAGGAACGTGGTGACATCTGCGAAGCCTGTCCCCCAGGTTTTTACAAGGTGTCCCCAAGGCG
GCCCCTCTGCTCACCCTGCCCGGAGCACAGCTTGGCCCTGGAGAATGCCTCTACATTCTGTGTG
TGCCAGGACACCTATGCTCGCTCGCCCACCGACCCGCCCTCAGCTTCCTGCACTCGGCCGCCGT
CCGCGCCGCGGGACCTGCAGTACAGCCTGAGCCGTTCCCCGCTGGCGCTGCGGCTGCGCTGGCT
GCCGCCTGAGGACTCCGGTGGCCGCTCCGACGTCACCTACTCGCTGCTGTGCCTGCGCTGCGGG
CGCGACGGTCCGGCGGGCGCGTGCCAACCCTGCGGGCCGCGCGTGGCCTTCGTCCCGCGCCAGG
CTGGGCTACGGGAACGCGCCGCCACGCTACTGCACCTGCGGCCGGGCGCGCGCTACACCGTGCG
CGTGGCCGCGCTCAACGGCGTCTCGGGCCCGGCGGCTGCCGCGGGAGCCACTTATGCGCAGGTC
ACCGTGTCCACCGGACCCGGGGCACCCTGGGAGGAGGATGAAATCCGTAGGGACCGCGTGGAGC
CCCAGAGCGTGTCGCTGTCGTGGAGAGAGCCTGTCCCTGCTGGAGCTTCCGGAACCAACAGGAC
TGAGTATGAGATCCGCTACTACGAGAAGGGTCAGAGTGAGCAGACTTACTCCACAGTGAAGACT
GGGGCACCGGCTGTCACTGTCACCAACCTGAAGCCAGCTACCAGATACGTTTTTCAGATCCGGG
CAGCCTCCCCAGGGCCTTCCTGGGAGGCCCAGAGCTTCAGTCCAAGCATCGAAGTGCAGACCCC
AGGGGAAGTTGCCCCTGGGTCCAGAGACCAGAGCCCAGCAGTGGTTGTCACTGTGGTGACCATC
TCAGCCCTCTTGGTCCTGGGCTCCGTGATGAGTGTACTGGCCATCTGGAGGAGGCCCTGTGATG
GCAAAGGAAGTGGCAACGCCCATGATGAAGAGGAACTGTATTTCCACTTCAAAGTTCCGACACG
CCGCACGTTTCTGGACCCCCAAAGCTGCGGGGACCCGTTGCAGGCTGTGCATTTGTTTGCCAAA
GAGCTAGATGCCAAAAGCGTCACCCTGGAGAAGAGCTTGGGAGCAGGCCGATTTGGGGACCTGT
GCTGCGGCTGCCTGCAGCTGCCGGGTCGCCAGGAACTACCCGTGGCCGTGCACACTCTGAGGGA
GGGTTGCTCAGACTCCCAGAAGCTCAGCTTCCTGGCTGAGGCCCTCACCCTGGGACAGTTTGAC
CACAGCCACATCGTGCGGCTGGAAGGCGTGGTCACCCGAGGGAACCCCTTGATGATTGTCACCG
AGTACATGAACCTCGGGGCCCTAGATGACTTCCTCAGGCATCACGAGGCAGAGCTGGTGACTGC
GCAGCTGATGGGTCTGCTGCCCGGGCTGGCATCGGCCATGAAGTATCTGTCGGAAATGGGCTAT
GTCCACCGGGGCCTCGCGGCCCGCCGAGTGCTCCTCAGCAGTGGCCTCATCTGTAAGATCTCTG
GCTTTGGGCGGGGTCCCCGGGACCGAGCGGAAGCTGTCTACACCACCATGAGTGGCAGGAGCCC
AGCGCTCTGGGCAGCTCCTGAGACTCTACAGTTTGGCCACTTCAGCTCTGCCAGTGACGTGTGG
AGCTTTGGCATTGTCATGTGGGAAGTGATGGCCTTTGGGGAGCGGCCCTACTGGGACATGTCTG
GACAAGATGTAATCAAGGCCGTGGAGGATGGTTTCCGGCTGCCACCCCCCAGAAACTGTCCCTC
CCAGCTGCACCGATTGATGCTTGAGTGCTGGCAGAAAGACCCAGGTGAGCGGCCCAGGTTCTCC
CAGATCCACAGCATCCTGAGCAAGATGGGGCAGGAGCCAGAACCCTCCAAGTGTGCCTCGACCA
CCTGTCTCAGGCCTCCCACCCCACTGGCAGACCGTGCCTTTTCTGCCTTCCCCTCCTTTGGCTC
CGTGGGTGCCTGGCTGGAGGCCCTAGACTTGTGTCGCTACAAGGACAACTTCTCTGCAGCCGGC
TATGGGAGCCTGGAGGCCGTGACAGAGATGACTGCCCAGGACCTGGGGAGCCTTGGGATCTCTT
CTGCGGAGCATCGAGAGGCCCTCCTTAGTGGGATCAGTGCCCTGCAGACTCGAGTGCTACAACT
ACAGGGTCAGGGGGTGCAAGTGTGAGCCGCTCAGCCCTGCCCCAGGACCTACAAGCGACACTCC
CCTAGGGTGGGAGGAGTGCTTATTCTCAGTGGCCTCTGAGCTGGTTGGTACCACGTTGTCCCCC
CATTTCATTTTTCCTCTCAACACCTTGCTGACCTAGTGGTCCTAAAACGAGGTTCAGATCCCTG
GAGAGGGCCCCAGACATAACAGTAGGAAGAGGGCTAGGGTGTCAAGGGAAGGTTGGGGTGTCAA
GGGTGTTGGTTGGGGAAGACAGTTTCAGTTGTCCTGGCTCAGGCCCCTTAGACTCCCACACTCA
GTGGGGGTTGGGCCTAATCAGTGGGCATCTCATTTCTCCAGAGAGCTTTTGACTTGGGCAATAT
GGGTCCCTGTGAGAGACCCATTGTTTCTGACAGGGACCATAGCTGCGTAGGCACCAGAGTATGG
GAGCCTGAGCCAGTGGGTGGTGCCCCTTACATCCTGTGCCTTGGCTAGGTCTATCTGCACACTG
GTGACAAGGCCCTAGCAGGCAAGTGGTGCTGAGCTCAGGGACTGGGCCTCCAGGTGGAGACTCC
AGAGCTGATGGCTTCCTGCCTTGGGGTTGGCAGTTCAGGATGAGGGCCAGGCTCCTAGTAGGTC
ATGCAAAGTCCTGGTGCTCGCCCTGGGCCGATGTCTGATTTGATTGGAAGTGATTTCAGAAGAG
CACAGCGGGCTTACTCTGCATTCTGGAGGGTGGAAAGGAGAATGAGACTGAGGGAGTGGATAGG
CTGGTCCAATCACACTATATACTTGGGGAAGTCAGAGCCCGTATAGTCTCAGAGCCAGGGTTAA
TGCCAGACCGAAATCCAGGGAGAAGTCTGGCCCTCAAGAGAGCTTGCCCTGCCCCATGGCACCA
GCATTCCTCCCTGGGCGGCACAGTGAATGGTCCCTGGGTTGAACCCCTTCAGGCCGCTCTGTCC
CTCAACACTAGAGTACAGTTCCCCTCCAGAGTGCCTCCCTGTGTGCTGTTCAGAGCTCTTGAAG
GTGCTAAGCAAGGACCCTGGCAGCTGTTGAGACCTTGAGACCAAAGCCATCCCAGAGGGCAGAA
AGGCATGGATGTGTACAGGACCTGGGGCTGTTTGTCTACATGACCCCTGATGGATGCCTGTTTG
CTATGGTAGGGAGGAAGGGTGGCATAGGCTTGAGACAGAGTAGGTGGGAGTGGAGAGGAGTAGG
CAGGATACAGAGAGTACCTCTGGAGGGAGCACACTAGGAGGGGATCCCCTGGGGCACAGGGGAA
ATGGGCAGGTGGACTGTGGATTATGTTTGTGTAGTGGGGGGTGTCCAAAAAGGCTTCTTAAATG
AAGTCAAAATTGAGTAAGGCCTTGATGGGCAGGGTATTGTCTCCTTGGGGTGAATGGAGTCATC
AGCAGGCTTGGAATCCAAGTAAGGATGACTAACAGAAAGCCTGAGGGAGGGGGCTGGAAACCAC
GATTCGACTTTGGGGACTCCCAGCAGTGCCTTTGGCCTTGACCTGCCAGCAGCAGCTCTTTCTT
CCTCAGACCCTACCCCATTTCCAACTCTACTCCCTGGGCACTTGACTGAGCTCAGTGACTGCAG
GAATACTGGGGTAGACTGGGATACTGCTCCCTTTGACAGAACTGGGGGAATTGAAACATCCCCA
CACGATCTCCCTTCATCCTCCCTCCAGGGAAAACTGGCTCAACGTCCAAGGCTCTTGGGCACCA
GTAGTGCCCTGTTTTGGGTTATCAGAACCTCATCCCCATCTCCAGCTACATCAGTCATTAAGGT
CAAACTCCTCCCCTCCCCAGCTGTTTGCAGAGGGGTCCCTGGCTGTGCTGGCAGGACTTCGGTG
TCCAGGGTAGACCTCCCCTCTGATGAGGAGGTCCTAGAATCCCGAGGGGTCCCAGGCCTCAGCC
CTGCACAGGCACCAGCATGATACAGGGTGCTGGGCCACTGGGGACCCTCCACAGATTTATTTTT
ATATACAGAGCTTGTTCATTGGACAGAGGGAGGTCACCTGCAACCCATATTGCTGTCACCCACC
CAGGGAGGGAGGGAGGGACTGGTTGTGGGTAGAGGCTCCTTTGCGAAACTCTGGAGATGTGTTT
ATATTTCTGGGTTCTATATGCAGTACCAAGTAATAAACACTTGTGTGTTATGGTC

hide sequence

RefSeq Acc Id:

XM_017593293 ⟹ XP_017448782

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	137,139,588 - 137,159,303 (+)	NCBI
Rnor_6.0	5	142,875,171 - 142,894,220 (+)	NCBI

Sequence:

show sequence

GGGCGGGAGGAAAAGGAGGAGGGATCGAACCATGCAACACTGGGAGCCGCAGACACAGGAAGAG
GCCAAGGGCTGGGAGACACCAGAACTCCCTAGAGCTTGAGGTCAGGATATCAAGCTCGGAAACC
CCCTGCAAGTAATGGGAACAAGGGTGCTCCCAAGGCTAGCTAAGAGGCTGCAAGTGTCACCGCT
TCCCCGCGGACCGCCCCCCCGTAAGCCACGCCCACAGCGCCTACTTCTCAGGATTCAGAGAGCT
AAGGTTTAAGGGTCTCTAGTCCACCGACGCCAGCTTGTCTCGCTCTCCGGCAACCCTGCTAACG
CTCAGAGCCGCCCTACCCCCACGGTTTGGAGATCTGCGGGACCCCTTGGTTTCCCCCTCCAGCT
CGGCGTTCCGCCCCTGGCCTATGAAACTCCACCTTCTCATCCTCTGCTGACCCGGATTGGTGGA
CCTCCCGCGGCGATGCGTAGCGATTGGTCCCCATGGATGATGGTGACCAGCGAGACTCCGCCCC
AGCCGGCGCTGGGGTCTGGGGGCACTGCTCAGCGGTGCTGGGCTGGCGAGGCTGGAGCCGCCGC
CGCACTGACAGCTCCGTCTGTGGACCATGGAGACTGGCGCCGGTCCACACCCGCTGCGCCTGTT
CGTCTGCCTGATGCCACTCTGTCTTGCTCTGCTTCTGGGACCCGGGCGGCCTGGGACCGCCGAG
GAAGTTACCCTCCTGGACTCCAAAGCCTCTCAGGCTGAGCTGGGCTGGACTGCACTGCCAAGCA
CTGGGTGGGAGGAGATTAGTGGCGTGGATGAACATGATCGTCCCATCCGCACGTACCAAGTGTG
CAACGTGTTGGAGCCCAACCAGGACAACTGGCTTCAGACTGGCTGGATCAGCCGTGGCCGTGGG
CAGCGCATCTTCGTGGAGCTGCAGTTCACGCTGCGTGACTGCAGCAGCATACCTGGCGCCACTG
GCACCTGCAAAGAGACCTTCAACGCATACTACCTGGAAACCGAGGCCGACTTAGGCCGAGGACA
TCCCCACCTAGGAGGCAACCGACCCCGCAAGATTGACACCATCGCAGCTGATGAGAGCTTCACG
CAGGGCGACTTGGGGGAGCGAAAGATGAAGCTGAACACAGAGGTGCGTGAGATTGGCCCCCTCA
GCCGTCAAGGCTTCCACCTGGCCTTCCAGGACGTGGGTGCATGCGTGGCGTTGGTCTCAGTGCG
TGTCTACTACAAGCAGTGCCGTGCCACAGTGCGAGGCTTGGCAGCCTTCCCCGCCACCGCAGCT
GAGAGCGCCTTCTCCACGCTGGTGGAAGTGGCTGGAACGTGCGTGGCCCACTCGGAAGGGGAGC
CCAGCAGCCCTCCACGCATGCACTGTGGCGCGGATGGCGAGTGGCTGGTGCCTGTGGGCCGTTG
CAGCTGCAGTGCAGGATTCCAGGAACGTGGTGACATCTGCGAAGCCTGTCCCCCAGGTTTTTAC
AAGGTGTCCCCAAGGCGGCCCCTCTGCTCACCCTGCCCGGAGCACAGCTTGGCCCTGGAGAATG
CCTCTACATTCTGTGTGTGCCAGGACACCTATGCTCGCTCGCCCACCGACCCGCCCTCAGCTTC
CTGCACTCGGCCGCCGTCCGCGCCGCGGGACCTGCAGTACAGCCTGAGCCGTTCCCCGCTGGCG
CTGCGGCTGCGCTGGCTGCCGCCTGAGGACTCCGGTGGCCGCTCCGACGTCACCTACTCGCTGC
TGTGCCTGCGCTGCGGGCGCGACGGTCCGGCGGGCGCGTGCCAACCCTGCGGGCCGCGCGTGGC
CTTCGTCCCGCGCCAGGCTGGGCTACGGGAACGCGCCGCCACGCTACTGCACCTGCGGCCGGGC
GCGCGCTACACCGTGCGCGTGGCCGCGCTCAACGGCGTCTCGGGCCCGGCGGCTGCCGCGGGAG
CCACTTATGCGCAGGTCACCGTGTCCACCGGACCCGGGGCCATTCCACCGTGAACAAGCCAATC
TGGGCTACACACTCTCTTAGGTCTTCAAACCACAGAATGAGACTGAAGGATGAGAAACAAGCAG
GACGAGGTAAACTGGGAAGGCAAGGGAGGCTTTCCCTCCCAGTAGGCAATGAAAGTGAGAGAAG
CCTGGGCCAGATATTCTCCCTAAGCCTCTGGTCCCACCAAGACTCTGAATCCTCAAGCCCCACA
GGCCACGCCCACATCTAACCCCTGATCCCCCTATGCA

hide sequence

RefSeq Acc Id:

XM_039109629 ⟹ XP_038965557

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	137,139,625 - 137,175,637 (+)	NCBI

RefSeq Acc Id:

XM_039109630 ⟹ XP_038965558

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	137,139,597 - 137,170,957 (+)	NCBI

RefSeq Acc Id:

XR_005504407

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	137,139,604 - 137,171,779 (+)	NCBI

RefSeq Acc Id:

XR_005504408

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	137,139,589 - 137,159,529 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001129181	(Get FASTA)	NCBI Sequence Viewer
	NP_001382024	(Get FASTA)	NCBI Sequence Viewer
	XP_006238920	(Get FASTA)	NCBI Sequence Viewer
	XP_017448782	(Get FASTA)	NCBI Sequence Viewer
	XP_038965557	(Get FASTA)	NCBI Sequence Viewer
	XP_038965558	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL80410	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001129181 ⟸ NM_001135709

- Peptide Label:

precursor

- Sequence:

show sequence

METGAGPHPLRLFVCLMPLCLALLLGPGRPGTAEEVTLLDSKASQAELGWTALPSTGWEEISGV
DEHDRPIRTYQVCNVLEPNQDNWLQTGWISRGRGQRIFVELQFTLRDCSSIPGATGTCKETFNA
YYLETEADLGRGHPHLGGNRPRKIDTIAADESFTQGDLGERKMKLNTEVREIGPLSRQGFHLAF
QDVGACVALVSVRVYYKQCRATVRGLAAFPATAAESAFSTLVEVAGTCVAHSEGEPSSPPRMHC
GADGEWLVPVGRCSCSAGFQERGDICEACPPGFYKVSPRRPLCSPCPEHSLALENASTFCVCQD
TYARSPTDPPSASCTRPPSAPRDLQYSLSRSPLALRLRWLPPEDSGGRSDVTYSLLCLRCGRDG
PAGACQPCGPRVAFVPRQAGLRERAATLLHLRPGARYTVRVAALNGVSGPAAAAGATYAQVTVS
TGPGAPWEEDEIRRDRVEPQSVSLSWREPVPAGASGTNRTEYEIRYYEKGLGDRFQSWVHLGSP
LATQVGGQPRLRDSPFQNRNQNLTKSWETNPSYLDSCLLPELGCIAPGSRDQSPAVVVTVVTIS
ALLVLGSVMSVLAIWRRPCDGKGSGNAHDEEELYFHFKVPTRRTFLDPQSCGDPLQAVHLFAKE
LDAKSVTLEKSLGAGRFGDLCCGCLQLPGRQELPVAVHTLREGCSDSQKLSFLAEALTLGQFDH
SHIVRLEGVVTRGNPLMIVTEYMNLGALDDFLRHHEAELVTAQLMGLLPGLASAMKYLSEMGYV
HRGLAARRVLLSSGLICKISGFGRGPRDRAEAVYTTMSGRSPALWAAPETLQFGHFSSASDVWS
FGIVMWEVMAFGERPYWDMSGQDVIKAVEDGFRLPPPRNCPSQLHRLMLECWQKDPGERPRFSQ
IHSILSKMGQEPEPSKCASTTCLRPPTPLADRAFSAFPSFGSVGAWLEALDLCRYKDNFSAAGY
GSLEAVTEMTAQDLGSLGISSAEHREALLSGISALQTRVLQLQGQGVQV

hide sequence

RefSeq Acc Id:	XP_006238920 ⟸ XM_006238858
- Peptide Label:	isoform X2
- UniProtKB:	F1LX55 (UniProtKB/TrEMBL)
- Sequence:	show sequence METGAGPHPLRLFVCLMPLCLALLLGPGRPGTAEEVTLLDSKASQAELGWTALPSTGWEEISGV DEHDRPIRTYQVCNVLEPNQDNWLQTGWISRGRGQRIFVELQFTLRDCSSIPGATGTCKETFNA YYLETEADLGRGHPHLGGNRPRKIDTIAADESFTQGDLGERKMKLNTEVREIGPLSRQGFHLAF QDVGACVALVSVRVYYKQCRATVRGLAAFPATAAESAFSTLVEVAGTCVAHSEGEPSSPPRMHC GADGEWLVPVGRCSCSAGFQERGDICEACPPGFYKVSPRRPLCSPCPEHSLALENASTFCVCQD TYARSPTDPPSASCTRPPSAPRDLQYSLSRSPLALRLRWLPPEDSGGRSDVTYSLLCLRCGRDG PAGACQPCGPRVAFVPRQAGLRERAATLLHLRPGARYTVRVAALNGVSGPAAAAGATYAQVTVS TGPGAPWEEDEIRRDRVEPQSVSLSWREPVPAGASGTNRTEYEIRYYEKGQSEQTYSTVKTGAP AVTVTNLKPATRYVFQIRAASPGPSWEAQSFSPSIEVQTPGEVAPGSRDQSPAVVVTVVTISAL LVLGSVMSVLAIWRRPCDGKGSGNAHDEEELYFHFKVPTRRTFLDPQSCGDPLQAVHLFAKELD AKSVTLEKSLGAGRFGDLCCGCLQLPGRQELPVAVHTLREGCSDSQKLSFLAEALTLGQFDHSH IVRLEGVVTRGNPLMIVTEYMNLGALDDFLRHHEAELVTAQLMGLLPGLASAMKYLSEMGYVHR GLAARRVLLSSGLICKISGFGRGPRDRAEAVYTTMSGRSPALWAAPETLQFGHFSSASDVWSFG IVMWEVMAFGERPYWDMSGQDVIKAVEDGFRLPPPRNCPSQLHRLMLECWQKDPGERPRFSQIH SILSKMGQEPEPSKCASTTCLRPPTPLADRAFSAFPSFGSVGAWLEALDLCRYKDNFSAAGYGS LEAVTEMTAQDLGSLGISSAEHREALLSGISALQTRVLQLQGQGVQV hide sequence

RefSeq Acc Id:

XP_017448782 ⟸ XM_017593293

- Peptide Label:

isoform X4

- Sequence:

show sequence

METGAGPHPLRLFVCLMPLCLALLLGPGRPGTAEEVTLLDSKASQAELGWTALPSTGWEEISGV
DEHDRPIRTYQVCNVLEPNQDNWLQTGWISRGRGQRIFVELQFTLRDCSSIPGATGTCKETFNA
YYLETEADLGRGHPHLGGNRPRKIDTIAADESFTQGDLGERKMKLNTEVREIGPLSRQGFHLAF
QDVGACVALVSVRVYYKQCRATVRGLAAFPATAAESAFSTLVEVAGTCVAHSEGEPSSPPRMHC
GADGEWLVPVGRCSCSAGFQERGDICEACPPGFYKVSPRRPLCSPCPEHSLALENASTFCVCQD
TYARSPTDPPSASCTRPPSAPRDLQYSLSRSPLALRLRWLPPEDSGGRSDVTYSLLCLRCGRDG
PAGACQPCGPRVAFVPRQAGLRERAATLLHLRPGARYTVRVAALNGVSGPAAAAGATYAQVTVS
TGPGAIPP

hide sequence

RefSeq Acc Id:

ENSRNOP00000068718 ⟸ ENSRNOT00000082120

RefSeq Acc Id:

ENSRNOP00000053334 ⟸ ENSRNOT00000056496

RefSeq Acc Id:	XP_038965558 ⟸ XM_039109630
- Peptide Label:	isoform X3

RefSeq Acc Id:	XP_038965557 ⟸ XM_039109629
- Peptide Label:	isoform X1

Protein Domains

Eph LBD Fibronectin type-III Protein kinase SAM

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
5	146650746	146650747	T	G	snv	ACI/EurMcwi (MCW), FHH/EurMcwi (MCW)
5	146676742	146676743	A	G	snv	FHL/EurMcwi (MCW), ACI/EurMcwi (MCW), SR/JrHsd (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1562679	AgrOrtholog
Ensembl Genes	ENSRNOG00000037340	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000053334	UniProtKB/TrEMBL
	ENSRNOP00000068718	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000056496	UniProtKB/TrEMBL
	ENSRNOT00000082120	UniProtKB/TrEMBL
Gene3D-CATH	1.10.150.50	UniProtKB/TrEMBL
	2.60.40.10	UniProtKB/TrEMBL
InterPro	Eph_TM	UniProtKB/TrEMBL
	Ephrin_rcpt_lig-bd_dom	UniProtKB/TrEMBL
	Fibronectin_type3	UniProtKB/TrEMBL
	FN3_sf	UniProtKB/TrEMBL
	Galactose-bd-like	UniProtKB/TrEMBL
	Ig-like_fold	UniProtKB/TrEMBL
	Kinase-like_dom	UniProtKB/TrEMBL
	Prot_kinase_cat_dom	UniProtKB/TrEMBL
	SAM	UniProtKB/TrEMBL
	SAM_type	UniProtKB/TrEMBL
	Ser-Thr/Tyr_kinase	UniProtKB/TrEMBL
	Tyr_kinase_ephrin_rcpt	UniProtKB/TrEMBL
	Tyr_kinase_rcpt_V_CS	UniProtKB/TrEMBL
NCBI Gene	298528	ENTREZGENE
Pfam	EphA2_TM	UniProtKB/TrEMBL
	Ephrin_lbd	UniProtKB/TrEMBL
	fn3	UniProtKB/TrEMBL
	Pkinase_Tyr	UniProtKB/TrEMBL
	SAM_2	UniProtKB/TrEMBL
PhenoGen	Epha10	PhenoGen
PIRSF	TyrPK_ephrin_receptor	UniProtKB/TrEMBL
PRINTS	TYRKINASE	UniProtKB/TrEMBL
PROSITE	EPH_LBD	UniProtKB/TrEMBL
	FN3	UniProtKB/TrEMBL
	PROTEIN_KINASE_DOM	UniProtKB/TrEMBL
	RECEPTOR_TYR_KIN_V_1	UniProtKB/TrEMBL
	RECEPTOR_TYR_KIN_V_2	UniProtKB/TrEMBL
	SAM_DOMAIN	UniProtKB/TrEMBL
SMART	EPH_lbd	UniProtKB/TrEMBL
	FN3	UniProtKB/TrEMBL
	SAM	UniProtKB/TrEMBL
Superfamily-SCOP	FN_III-like	UniProtKB/TrEMBL
	Gal_bind_like	UniProtKB/TrEMBL
	Kinase_like	UniProtKB/TrEMBL
	SAM_homology	UniProtKB/TrEMBL
UniProt	A0A0G2JTH8_RAT	UniProtKB/TrEMBL
	F1LX55	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-12-01	Epha10	EPH receptor A10	RGD1562679	similar to Ephrin type-A receptor 10	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	RGD1562679	similar to Ephrin type-A receptor 10	RGD1562679_predicted	similar to Ephrin type-A receptor 10 (predicted)	'predicted' is removed	2292626	APPROVED
2006-03-07	RGD1562679_predicted	similar to Ephrin type-A receptor 10 (predicted)	LOC298528	similar to Ephrin type-A receptor 10	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC298528	similar to Ephrin type-A receptor 10			Symbol and Name status set to provisional	70820	PROVISIONAL

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

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

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

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

Send us a Message

Imported Disease Annotations - ClinVar