Best1 (bestrophin 1) - Rat Genome Database

Name: Best1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Best1 (bestrophin 1) Rattus norvegicus

Analyze

Symbol:

Best1

Name:

bestrophin 1

RGD ID:

1311656

Description:

Predicted to enable identical protein binding activity. Predicted to contribute to chloride channel activity. Predicted to be involved in transepithelial chloride transport. Predicted to act upstream of or within chloride transport; detection of light stimulus involved in visual perception; and regulation of calcium ion transport. Predicted to be located in basolateral plasma membrane. Predicted to be part of chloride channel complex. Human ortholog(s) of this gene implicated in autosomal dominant vitreoretinochoroidopathy; bestrophinopathy; macular degeneration; retinitis pigmentosa 50; and vitelliform macular dystrophy. Orthologous to human BEST1 (bestrophin 1); PARTICIPATES IN retinitis pigmentosa pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

bestrophin-1; LOC293735; vitelliform macular dystrophy (Best disease, bestrophin); vitelliform macular dystrophy 2 homolog; vitelliform macular dystrophy 2 homolog (human); Vmd2

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):	BEST1 (bestrophin 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Best1 (bestrophin 1)	HGNC	Treefam, EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Best1 (bestrophin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	BEST1 (bestrophin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	BEST1 (bestrophin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Best1 (bestrophin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	BEST1 (bestrophin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	BEST1 (bestrophin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Best1 (bestrophin 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	BEST1 (bestrophin 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Best1 (bestrophin 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	best1 (bestrophin 1)	Alliance	DIOPT (OrthoFinder\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Best2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Best3	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Best4	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	best-13	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	best-14	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	best-23	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	best-3	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	best-4	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	best-7	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	best-9	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	best-1	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	best-15	Alliance	DIOPT (OMA\|OrthoFinder\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	best-18	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	best-2	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	best-20	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	best-21	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	best-22	Alliance	DIOPT (OMA\|OrthoFinder\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	best-12	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	best-6	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	best-5	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	best-8	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	best-17	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	best-16	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	C09B9.85	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	best-25	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)

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	1	206,629,340 - 206,646,085 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	1	206,629,500 - 206,646,063 (-)	Ensembl
Rnor_6.0	1	226,033,146 - 226,049,893 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	226,030,875 - 226,049,929 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	232,981,264 - 232,998,090 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	212,432,811 - 212,449,374 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	212,591,240 - 212,607,804 (-)	NCBI
Celera	1	204,125,034 - 204,141,598 (-)	NCBI		Celera
Cytogenetic Map	1	q43	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autosomal dominant vitreoretinochoroidopathy (ISO)

bestrophinopathy (ISO)

cone-rod dystrophy (ISO)

cone-rod dystrophy 6 (ISO)

familial temporal lobe epilepsy 8 (ISO)

fundus dystrophy (ISO)

hemochromatosis type 5 (ISO)

intellectual disability (ISO)

Iron Overload (ISO)

macular degeneration (ISO)

retinitis pigmentosa (ISO)

retinitis pigmentosa 50 (ISO)

Stargardt disease (ISO)

vitelliform macular dystrophy (ISO)

Vitelliform Macular Dystrophy 2 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

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

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

5-aza-2'-deoxycytidine (ISO)

5-Nitro-2-(3-phenylpropylamino)benzoic acid (ISO)

acrolein (ISO)

acrylamide (EXP,ISO)

aflatoxin B1 (ISO)

alpha-pinene (ISO)

antirheumatic drug (ISO)

aristolochic acid (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

calcium atom (ISO)

calcium(0) (ISO)

choline (ISO)

cisplatin (ISO)

copper atom (EXP)

copper(0) (EXP)

Cuprizon (EXP)

dexamethasone (ISO)

dextran sulfate (ISO)

flufenamic acid (ISO)

folic acid (ISO)

genistein (ISO)

indometacin (ISO)

iodide salt (ISO)

L-methionine (ISO)

Niflumic acid (ISO)

ozone (ISO)

paracetamol (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sodium dichromate (ISO)

sunitinib (ISO)

thapsigargin (ISO)

titanium dioxide (ISO)

tunicamycin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

chloride transmembrane transport (IEA)

chloride transport (ISO)

detection of light stimulus involved in visual perception (ISO)

regulation of calcium ion transport (ISO)

transepithelial chloride transport (ISO)

Cellular Component

basal plasma membrane (ISO)

basolateral plasma membrane (ISO)

cellular_component (ND)

chloride channel complex (ISO)

Molecular Function

chloride channel activity (ISO)

identical protein binding (ISO)

molecular_function (ND)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

retinitis pigmentosa pathway (ISO)

References

References - curated


1.	Daiger SP, etal., Clin Genet. 2013 Aug;84(2):132-41. doi: 10.1111/cge.12203. Epub 2013 Jun 19.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	GOA data from the GO Consortium
4.	MGD data from the GO Consortium
5.	OMIM Disease Annotation Pipeline
6.	Petrukhin K, etal., Nat Genet. 1998 Jul;19(3):241-7.
7.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	RGD automated import pipeline for gene-chemical interactions
9.	RGD comprehensive gene curation

Additional References at PubMed

PMID:11050159	PMID:12477932	PMID:16282372	PMID:16636205	PMID:17003041	PMID:19372599	PMID:19853238	PMID:21498420	PMID:26130088

Genomics

Candidate Gene Status

Best1 is a candidate Gene for QTL Arrd2

Comparative Map Data

Best1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	206,629,340 - 206,646,085 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	1	206,629,500 - 206,646,063 (-)	Ensembl
Rnor_6.0	1	226,033,146 - 226,049,893 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	226,030,875 - 226,049,929 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	232,981,264 - 232,998,090 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	212,432,811 - 212,449,374 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	212,591,240 - 212,607,804 (-)	NCBI
Celera	1	204,125,034 - 204,141,598 (-)	NCBI		Celera
Cytogenetic Map	1	q43	NCBI

BEST1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	11	61,950,063 - 61,965,515 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	11	61,946,722 - 61,965,515 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	11	61,717,293 - 61,732,987 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	61,474,408 - 61,488,981 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	11	61,474,423 - 61,488,495	NCBI
Celera	11	59,052,654 - 59,067,236 (+)	NCBI
Cytogenetic Map	11	q12.3	NCBI
HuRef	11	58,045,346 - 58,059,923 (+)	NCBI		HuRef
CHM1_1	11	61,600,555 - 61,615,131 (+)	NCBI		CHM1_1

Best1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	9,962,536 - 9,978,997 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	19	9,962,538 - 9,978,997 (-)	Ensembl
GRCm38	19	9,985,172 - 10,001,633 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	9,985,174 - 10,001,633 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	10,059,662 - 10,076,123 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	19	10,052,219 - 10,064,259 (-)	NCBI			mm8
Celera	19	10,682,499 - 10,706,936 (-)	NCBI		Celera
Cytogenetic Map	19	A	NCBI

Best1
(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_004955511	5,773,670 - 5,780,540 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955511	5,773,025 - 5,783,800 (-)	NCBI	ChiLan1.0	ChiLan1.0

BEST1
(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	11	60,672,835 - 60,687,417 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	60,672,835 - 60,687,417 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	11	57,314,430 - 57,329,450 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

BEST1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	18	54,468,844 - 54,483,565 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	18	54,468,844 - 54,480,311 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	18	53,051,324 - 53,062,626 (-)	NCBI
ROS_Cfam_1.0	18	55,522,441 - 55,534,952 (-)	NCBI
UMICH_Zoey_3.1	18	54,584,036 - 54,595,144 (-)	NCBI
UNSW_CanFamBas_1.0	18	54,205,089 - 54,216,350 (-)	NCBI
UU_Cfam_GSD_1.0	18	55,071,126 - 55,082,395 (-)	NCBI

Best1
(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_024404947	11,006,856 - 11,018,414 (-)	NCBI
SpeTri2.0	NW_004936581	1,120,681 - 1,132,226 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

BEST1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	9,538,084 - 9,553,247 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	9,538,082 - 9,550,975 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	8,986,192 - 9,001,827 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

BEST1
(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	1	11,841,052 - 11,857,694 (-)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	1	11,837,837 - 11,857,233 (-)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666038	109,214,720 - 109,230,905 (-)	NCBI	Vero_WHO_p1.0

Best1
(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_004624926	471,073 - 478,436 (-)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

BF387442

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	206,629,585 - 206,629,735 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	226,033,384 - 226,033,533	NCBI	Rnor6.0
Rnor_5.0	1	232,981,566 - 232,981,715	UniSTS	Rnor5.0
RGSC_v3.4	1	212,432,897 - 212,433,046	UniSTS	RGSC3.4
Celera	1	204,125,120 - 204,125,269	UniSTS
RH 3.4 Map	1	1520.4	UniSTS
Cytogenetic Map	1	q43	UniSTS

RH124242

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	206,629,181 - 206,629,285 (+)	MAPPER	mRatBN7.2
mRatBN7.2	1	23,638,719 - 23,638,823 (+)	MAPPER	mRatBN7.2
mRatBN7.2	3	136,915,508 - 136,915,612 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	226,032,980 - 226,033,083	NCBI	Rnor6.0
Rnor_6.0	1	25,077,959 - 25,078,062	NCBI	Rnor6.0
Rnor_5.0	1	232,981,162 - 232,981,265	UniSTS	Rnor5.0
Rnor_5.0	1	26,536,032 - 26,536,135	UniSTS	Rnor5.0
RGSC_v3.4	1	212,432,493 - 212,432,596	UniSTS	RGSC3.4
RGSC_v3.4	1	24,186,378 - 24,186,481	UniSTS	RGSC3.4
Celera	1	22,350,730 - 22,350,833	UniSTS
Celera	1	204,124,716 - 204,124,819	UniSTS
Cytogenetic Map	1	q43	UniSTS
Cytogenetic Map	1	p12	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
1578780	Cm52	Cardiac mass QTL 52	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	1	81591954	219808434	Rat
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	94642722	214537671	Rat
1354606	Bp246	Blood pressure QTL 246	3.6		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	102813953	218753816	Rat
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	115540693	238914717	Rat
7421630	Bp362	Blood pressure QTL 362		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	118608292	241799120	Rat
1598853	Memor3	Memory QTL 3	4.5		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	1	143506580	212458660	Rat
737828	Hcas3	Hepatocarcinoma susceptibility QTL 3	4.9		liver integrity trait (VT:0010547)	liver tumorous lesion volume to total liver volume ratio (CMO:0001082)	1	144267353	222987745	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	144267353	251128347	Rat
7771612	Cm80	Cardiac mass QTL 80	8.4		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	1	149448574	221264292	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	150700142	252085212	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	150700247	252085048	Rat
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	150700247	252085048	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	151162512	256448636	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	151162512	256448636	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	151162512	256448636	Rat
1358886	Bp260	Blood pressure QTL 260	3.67		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	151162766	225824951	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	153136852	260522016	Rat
2312420	Pur17	Proteinuria QTL 17	7.1	0.0001	urine protein amount (VT:0005160)	urine total protein excretion rate (CMO:0000756)	1	156677124	218753816	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	156677124	256448636	Rat
2292222	Bp307	Blood pressure QTL 307	3.06	0.0014	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	164310393	213533942	Rat
2292220	Bp306	Blood pressure QTL 306	3.47	0.00087	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	164310393	243914901	Rat
619613	Bp77	Blood pressure QTL 77		0.01	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	164747424	209747424	Rat
619613	Bp77	Blood pressure QTL 77		0.01	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	164747424	209747424	Rat
1354653	Despr9	Despair related QTL 9		0.00019	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	167909849	212909849	Rat
61341	Bp26	Blood pressure QTL 26			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	169537671	214537671	Rat
724562	Rends1	Renal damage susceptibility QTL 1		0.05	kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	1	169537671	214537671	Rat
1358294	Bw37	Body weight QTL 37	5	0.000011	body mass (VT:0001259)	body weight (CMO:0000012)	1	171310381	216310381	Rat
2293689	Bss47	Bone structure and strength QTL 47	7.25	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	1	171629477	216629477	Rat
2293693	Bss22	Bone structure and strength QTL 22	33.52	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	1	171629477	216629477	Rat
2300161	Bmd43	Bone mineral density QTL 43	8.4	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	171629477	216629477	Rat
2300174	Bmd42	Bone mineral density QTL 42	8.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	bone mineral density (CMO:0001226)	1	171629477	216629477	Rat
2300187	Bmd41	Bone mineral density QTL 41	8.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	171629477	216629477	Rat
2293654	Bss30	Bone structure and strength QTL 30	32.65	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	1	171629477	216629477	Rat
2293673	Bss27	Bone structure and strength QTL 27	18.63	0.0001	femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	1	171629477	216629477	Rat
2293677	Bss41	Bone structure and strength QTL 41	9.38	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra cross-sectional area (CMO:0001689)	1	171629477	216629477	Rat
1549830	Bss1	Bone structure and strength QTL 1	4.8		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	172609619	217609619	Rat
631214	Bw61	Body weight QTL61	3.4	0.0001	intramuscular adipose amount (VT:0010044)	intramuscular fat area (CMO:0001162)	1	173108781	218108781	Rat
70163	Bw20	Body weight QTL 20	5.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	174133260	219133260	Rat
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	176426412	257976495	Rat
1600380	Niddm70	Non-insulin dependent diabetes mellitus QTL 70	3.1	0.0008	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	176550523	221550523	Rat
10059600	Bp378	Blood pressure QTL 378	3.08	0.05	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	176869060	221869060	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	177227632	256448636	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	177227632	256448636	Rat
1558658	Bw59	Body weight QTL 59	3.5	0.0003	body mass (VT:0001259)	body weight (CMO:0000012)	1	178784622	223784622	Rat
634321	Hc1	Hypercalciuria QTL 1	2.91		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	178810256	240830002	Rat
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	179567751	260522016	Rat
1302787	Stl25	Serum triglyceride level QTL 25	2.7	0.0073	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	1	180359209	210702199	Rat
6903303	Scl34	Serum cholesterol QTL 34	2.5	0.0033	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	180359209	218108781	Rat
737977	Bp160	Blood pressure QTL 160		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	181133855	226133855	Rat
724559	Pancm1	Pancreatic morphology QTL 1	7.1		islet of Langerhans morphology trait (VT:0005215)	pancreatic islet damage composite score (CMO:0001156)	1	181759564	214537555	Rat
2293083	Iddm25	Insulin dependent diabetes mellitus QTL 25	4.18		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	181829673	224569684	Rat
634312	Bp143	Blood pressure QTL 143	3	0.0002	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	182623426	219932796	Rat
8655655	Arrd2	Age-related retinal degeneration QTL 2	7.79		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	183970203	243914901	Rat
8655855	Arrd3	Age-related retinal degeneration QTL 3	3.07		lens clarity trait (VT:0001304)	cataract incidence/prevalence measurement (CMO:0001585)	1	183970203	243914901	Rat
631838	Niddm36	Non-insulin dependent diabetes mellitus QTL 36		0.01	insulin secretion trait (VT:0003564)	calculated pancreatic islet insulin release measurement (CMO:0001217)	1	184550676	229550676	Rat
1300145	Rf7	Renal function QTL 7	2.96		urine creatinine amount (VT:0010540)	urine creatinine level (CMO:0000125)	1	185145134	221264292	Rat
2312564	Glom18	Glomerulus QTL 18	2.4	0.003	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	1	185356336	231689108	Rat
1582206	Kidm33	Kidney mass QTL 33	6.9		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	188377360	224054420	Rat
1358898	Bp255	Blood pressure QTL 255	3.6		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	191019702	246062233	Rat
10059590	Kidm44	Kidney mass QTL 44	3.42	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	191033875	236033875	Rat
1358191	Ept10	Estrogen-induced pituitary tumorigenesis QTL 10	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	192825253	243914732	Rat
8552891	Epfw5	Epididymal fat weight QTL 5	4.4		epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	1	193113876	238113876	Rat
634338	Hcar4	Hepatocarcinoma resistance QTL 4	4.6		liver integrity trait (VT:0010547)	liver tumorous lesion number to liver area ratio (CMO:0001210)	1	193422268	214537671	Rat
1600388	Niddm67	Non-insulin dependent diabetes mellitus QTL 67	5.84	0.000004	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	195804352	257091168	Rat
1600395	Niddm69	Non-insulin dependent diabetes mellitus QTL 69	4.14	0.0002	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	195804352	257091168	Rat
1600396	Niddm68	Non-insulin dependent diabetes mellitus QTL 68	4.97	0.0003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	195804352	257091168	Rat
631658	Cm7	Cardiac mass QTL 7	5.32	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	1	196248093	241248093	Rat
1358292	Cm37	Cardiac mass QTL 37	6.2	0.00000081	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	1	196248093	241248093	Rat
1600374	Mcs17	Mammary carcinoma susceptibility QTL 17	3		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	197670404	242670404	Rat
1641926	Teswt2	Testicular weight QTL 2	2.82		testis mass (VT:1000644)	both testes wet weight (CMO:0000175)	1	197697768	238755659	Rat
2302375	Bw83	Body weight QTL 83	4.87	0.0002	body mass (VT:0001259)	body weight (CMO:0000012)	1	197697768	242697768	Rat
61376	Bp42	Blood pressure QTL 42	23.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	197814409	242814409	Rat
1298084	Thym4	Thymus enlargement QTL 4	10.68		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	197814409	242814409	Rat
1357335	Bw39	Body weight QTL 39	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	1	197814409	242814409	Rat
1331790	Bp201	Blood pressure QTL 201	3.127		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	198211513	225126682	Rat
634313	Niddm43	Non-insulin dependent diabetes mellitus QTL 43			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	199050459	259647894	Rat
2292218	Kidm35	Kidney mass QTL 35			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	199368955	224569684	Rat
2293694	Bss38	Bone structure and strength QTL 38	7.05	0.0001	femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	1	201554356	246554356	Rat
7394701	Uae46	Urinary albumin excretion QTL 46	3.6	0.0056	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	201554356	246554356	Rat
2300175	Bmd40	Bone mineral density QTL 40	15.4	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	1	201554356	246554356	Rat
2293655	Bss36	Bone structure and strength QTL 36	10.66	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	201554356	246554356	Rat
2293674	Bss39	Bone structure and strength QTL 39	7.1	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	1	201554356	246554356	Rat
10059587	Bw173	Body weight QTL 173	3.23	0.025	body mass (VT:0001259)	body weight (CMO:0000012)	1	202069611	247069611	Rat
1600363	Hc6	Hypercalciuria QTL 6	2.7		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	203995416	244113296	Rat
1600397	Edcs4	Endometrial carcinoma susceptibility QTL 4	2.2		uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	1	206081677	251081677	Rat
61403	Niddm4	Non-insulin dependent diabetes mellitus QTL 4			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	206329708	222745518	Rat
1357399	Bw45	Body weight QTL 45	3.05		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	1	206329708	251329708	Rat
1357404	Bw42	Body weight QTL 42	4.49	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	206329708	251329708	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	30
Count of miRNA genes:	28
Interacting mature miRNAs:	30
Transcripts:	ENSRNOT00000007320
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	2	2	2	2	8	2		2	2	2	7	4
Low	1	9	35	19	11	19	8	9	30	11	16	7	8
Below cutoff		32	20	20		20			42	22	18

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001011940	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017589024	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039108615	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039108619	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC079048	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000046	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000007320 ⟹ ENSRNOP00000007320

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	206,629,500 - 206,646,063 (-)	Ensembl
Rnor_6.0 Ensembl	1	226,030,875 - 226,049,929 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000100670 ⟹ ENSRNOP00000095084

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	206,630,192 - 206,646,063 (-)	Ensembl

RefSeq Acc Id:

NM_001011940 ⟹ NP_001011940

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	206,629,500 - 206,646,063 (-)	NCBI
Rnor_6.0	1	226,033,298 - 226,049,859 (-)	NCBI
Rnor_5.0	1	232,981,264 - 232,998,090 (-)	NCBI
RGSC_v3.4	1	212,432,811 - 212,449,374 (-)	RGD
Celera	1	204,125,034 - 204,141,598 (-)	RGD

Sequence:

show sequence

CTGACATGACTCTGTACCAGGGGGCAGGAGAGCATGTGCTCTTCTACCATCAAAGTCTTCTCTG
CACACCCCTCATTCCTCAGACCTCCCTTCAACCCCAACAGAAACCCTAACAGGACCCAAGCCCA
CCGACTGCTACTCAGTGCCAAGCCATGACTATCACCTACACAAACGAAGTGGCCAATGCCCGCC
TTGGTTCCTTCTCGTGCCTCCTCCTGCGCTGGCGAGGCAGCATCTACAAGCTGCTGTACGGAGA
ATTCCTTGTCTTCATATTCCTCTACTATTGCATCCGTGGACTCTACAGAATGGTTCTCTCGAAT
CATCAGCAGCAGCAGTTTGAGAAGTTGGCTCTGTACTGCAACAGCTACATTCAGTTCATCCCTA
TATCCTTCGTTCTGGGTTTCTATGTTACATTGGTGGTGAGCCGATGGTGGAACCAGTACGAGAA
CTTGCCGTGGCCCGACCGCCTCATGATGCAGGTATCTAGCTTCGTGGAGGGCAAGGACGAGCAA
GGCCGGTTGCTGCGGCGCACGCTCATCCGCTACGCCATCCTGGGCCAAGTGCTCATCCTGCGCA
GCATCAGCACCTCGGTCTACAAGCGCTTTCCCAGTCTTCAACACCTGATGCAAGCAGGCTTTAT
GACTCCTGGGGAATATAAGCAGTTGCAGAGGTTGGGCCTACCACACAACACATTCTGGGTACCC
TGGGTGTGGTTTGCCAACCTGTCAATGAAAGCCTATCTTGGAGGTCGAATCAGGGACACTGTCC
TGCTCCAGAGCCTGATGAATGAGGTGTGCACCTTGCGTACTCAGTGTGGACACCTATATGCCTA
TGACTGGATCAATATCCCATTGGTGTACACACAGGTGGTGACAGTGGCGGTTTACAGCTTTTTC
CTTGCATGCTTGATCGGGAGGCAGTTTCTGAACCCACTCAAGAACTACCCAGGCCACGAGATGG
ATCTGGTTGTGCCTGTCTTCACAATCCTGCAGTTCTTATTCTACATGGGCTGGCTCAAGGTGGC
AGAACAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTGAGACCAACTGGATCATTGAC
AGAAACCTGCAGGTGTCCCTGTTGTCTGTGGATGGGATGCACCACGACGTGCCTCCCCTGGAGC
GAGACCTGTACTGGAATGAGGCGGCGCCTCAGCCGCCCTACACAGCTGCTTCTGCCGGGTCTCA
CCGACAATCCTTCATGGGCTCCACCTTCAACATGAGTCTGAAGAAAAAAGACTCAGAGGAGGAG
AGTGACACTTATGACAAGAAAGAGAATGATTACGGCAGCACCATTGGACGCTTCTTAGGACTGC
AATCCAATGACTACCATCCTCCCAAGACAGACTTAAAGACCAAACTGTTGTGGTCTAAGAAGGA
CCCCTTCCTCGAGGACCAGTCTAAGAATGACAAGCAGAAAGACCAGAAAAATGATGTCTGGAAA
CCAAAGGACCTCTTCAGAGCTATACCAAAGTTTAAGAGGCCAAGTTACCGCCAGGCCCCACAGC
CACTTGGCAGCCACCTTCCCATGGTCTTCCCTCCTCAGCAGTCAGCACCCTCAGTGCGTTACTC
AGACACAGGTGGTGGGCCTTCCGCACAGTACCAAGAGGCCTGTCACATGAAGAAGAAAACAGTG
GAGTTTAACTTGAACATTCCAGAGTGCCCTACGGAACATGAACAACCCCATTTGGACCAGATGC
ACACGATCCTGAAGGAGCCTGGAGAATCCTATCCTGTCAGTGATAAAGCTGACACCAATCCTGT
TTCCTATAAGTGATGCTTCACAGCTTGGTTCTCACCTGCATGGATGCCAGCAGGGCACTGACCC
AGTCAGAGGCACACAGCAGCGACACTCAAGAATATGTTCCCATGGCAGTCTGGCAGGTAACTCA
GAACCAGGACTGCTTAGTCCTGTCTGAACACACCTGTCTTTCACTATCTTTCCCCAAACTAGCG
AGTTTAATAAATATTCTTTCAGGCAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_039108615 ⟹ XP_038964543

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	206,629,340 - 206,646,085 (-)	NCBI

RefSeq Acc Id:

XM_039108619 ⟹ XP_038964547

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	206,629,340 - 206,646,085 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001011940	(Get FASTA)	NCBI Sequence Viewer
	XP_038964543	(Get FASTA)	NCBI Sequence Viewer
	XP_038964547	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH79048	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001011940 ⟸ NM_001011940

- UniProtKB:

Q6AYG9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MTITYTNEVANARLGSFSCLLLRWRGSIYKLLYGEFLVFIFLYYCIRGLYRMVLSNHQQQQFEK
LALYCNSYIQFIPISFVLGFYVTLVVSRWWNQYENLPWPDRLMMQVSSFVEGKDEQGRLLRRTL
IRYAILGQVLILRSISTSVYKRFPSLQHLMQAGFMTPGEYKQLQRLGLPHNTFWVPWVWFANLS
MKAYLGGRIRDTVLLQSLMNEVCTLRTQCGHLYAYDWINIPLVYTQVVTVAVYSFFLACLIGRQ
FLNPLKNYPGHEMDLVVPVFTILQFLFYMGWLKVAEQLINPFGEDDDDFETNWIIDRNLQVSLL
SVDGMHHDVPPLERDLYWNEAAPQPPYTAASAGSHRQSFMGSTFNMSLKKKDSEEESDTYDKKE
NDYGSTIGRFLGLQSNDYHPPKTDLKTKLLWSKKDPFLEDQSKNDKQKDQKNDVWKPKDLFRAI
PKFKRPSYRQAPQPLGSHLPMVFPPQQSAPSVRYSDTGGGPSAQYQEACHMKKKTVEFNLNIPE
CPTEHEQPHLDQMHTILKEPGESYPVSDKADTNPVSYK

hide sequence

RefSeq Acc Id:

ENSRNOP00000007320 ⟸ ENSRNOT00000007320

RefSeq Acc Id:	XP_038964547 ⟸ XM_039108619
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038964543 ⟸ XM_039108615
- Peptide Label:	isoform X1

RefSeq Acc Id:

ENSRNOP00000095084 ⟸ ENSRNOT00000100670

Transcriptome

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

Promoters

RGD ID:

13690763

Promoter ID:

EPDNEW_R1288

Type:

multiple initiation site

Name:

Best1_1

Description:

bestrophin 1

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	226,049,887 - 226,049,947	EPDNEW

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:1311656	AgrOrtholog
Ensembl Genes	ENSRNOG00000020346	Ensembl, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000007320	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000007320	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7115295	IMAGE-MGC_LOAD
InterPro	Best1	UniProtKB/TrEMBL
	Bestrophin	UniProtKB/TrEMBL
	Bestrophin-like	UniProtKB/TrEMBL
KEGG Report	rno:293735	UniProtKB/TrEMBL
MGC_CLONE	MGC:93985	IMAGE-MGC_LOAD
NCBI Gene	293735	ENTREZGENE
PANTHER	Bestrophin	UniProtKB/TrEMBL
	PTHR10736:SF4	UniProtKB/TrEMBL
Pfam	Bestrophin	UniProtKB/TrEMBL
PhenoGen	Best1	PhenoGen
UniProt	Q6AYG9	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-04	Best1	bestrophin 1	Vmd2	vitelliform macular dystrophy 2 homolog (human)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Vmd2	vitelliform macular dystrophy 2 homolog (human)		vitelliform macular dystrophy (Best disease, bestrophin)	Name updated	1299863	APPROVED
2005-12-06	Vmd2	vitelliform macular dystrophy (Best disease, bestrophin)	Vmd2_predicted	vitelliform macular dystrophy (Best disease, bestrophin) (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Vmd2_predicted	vitelliform macular dystrophy (Best disease, bestrophin) (predicted)			Symbol and Name status set to approved	70820	APPROVED

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

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

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

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

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Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

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