Ryr3 (ryanodine receptor 3) - Rat Genome Database

Name: Ryr3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Ryr3 (ryanodine receptor 3) Rattus norvegicus

Analyze

Symbol:

Ryr3

Name:

ryanodine receptor 3

RGD ID:

68952

Description:

Enables calcium-induced calcium release activity and ryanodine-sensitive calcium-release channel activity. Involved in negative regulation of cytosolic calcium ion concentration. Located in endoplasmic reticulum and perinuclear region of cytoplasm. Orthologous to human RYR3 (ryanodine receptor 3); PARTICIPATES IN calcium transport pathway; calcium/calcium-mediated signaling pathway; Alzheimer's disease pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acrylamide.

Type:

protein-coding

RefSeq Status:

MODEL

Also known as:

LOW QUALITY PROTEIN: ryanodine receptor 3

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

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):	RYR3 (ryanodine receptor 3)	HGNC	Ensembl, HomoloGene, NCBI, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Ryr3 (ryanodine receptor 3)	HGNC	Treefam, OrthoMCL, NCBI, HomoloGene, Panther, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Ryr3 (ryanodine receptor 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	RYR3 (ryanodine receptor 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	RYR3 (ryanodine receptor 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Ryr3 (ryanodine receptor 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	RYR3 (ryanodine receptor 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Ryr3 (ryanodine receptor 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	RYR3 (ryanodine receptor 3)	Alliance	DIOPT (HGNC\|TreeFam)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	99,431,755 - 99,979,125 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	3	99,432,505 - 99,704,961 (-)	Ensembl
Rnor_6.0	3	104,117,307 - 104,665,151 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	104,118,063 - 104,504,204 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	110,710,040 - 111,249,930 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	98,476,626 - 98,872,629 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	98,375,910 - 98,382,386 (-)	NCBI
Celera	3	98,415,656 - 98,961,847 (-)	NCBI		Celera
Cytogenetic Map	3	q35	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

amenorrhea (ISO)

Bloom syndrome (ISO)

colon cancer (ISO)

Contracture (ISO)

epilepsy (ISO)

fetal akinesia deformation sequence syndrome 1 (ISO)

Generalized Epilepsy (ISO)

genetic disease (ISO)

primary ovarian insufficiency (ISO)

visual epilepsy (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17beta-estradiol (ISO)

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

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

3-methylcholanthrene (ISO)

8-Br-cAMP (ISO)

acrylamide (EXP)

aflatoxin B2 (ISO)

all-trans-retinoic acid (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

C60 fullerene (EXP)

cadmium dichloride (ISO)

clobetasol (ISO)

cocaine (EXP)

Cuprizon (EXP)

diarsenic trioxide (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

entinostat (ISO)

lead diacetate (EXP)

lead(0) (EXP)

lead(2+) (EXP)

methapyrilene (ISO)

methylmercury chloride (ISO)

nickel atom (ISO)

panobinostat (ISO)

paraquat (EXP)

phenylmercury acetate (ISO)

potassium dichromate (ISO)

progesterone (ISO)

SB 431542 (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

temozolomide (ISO)

tetrachloromethane (EXP)

thimerosal (ISO)

toluene (EXP)

trichostatin A (ISO)

trimellitic anhydride (ISO)

triptonide (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

calcium ion transport (ISO)

cellular calcium ion homeostasis (ISO)

negative regulation of cytosolic calcium ion concentration (IDA)

release of sequestered calcium ion into cytosol (IBA)

striated muscle contraction (ISO)

Cellular Component

calcium channel complex (IBA)

cytoplasmic vesicle membrane (IBA)

endoplasmic reticulum (IDA)

junctional membrane complex (ISO)

perinuclear region of cytoplasm (IDA)

plasma membrane (IBA)

sarcolemma (IBA)

sarcoplasmic reticulum membrane (IBA,ISO)

smooth endoplasmic reticulum (IBA)

Z disc (IBA)

Molecular Function

calcium ion binding (IBA)

calcium-induced calcium release activity (IBA,IDA)

calcium-release channel activity (ISO)

calmodulin binding (IEA)

ryanodine-sensitive calcium-release channel activity (IBA,IDA)

Molecular Pathway Annotations Click to see Annotation Detail View

Alzheimer's disease pathway (IEA)

calcium transport pathway (ISO)

calcium/calcium-mediated signaling pathway (IEA,ISO)

References

References - curated


1.	Bull R, etal., J Neurosci. 2008 Sep 17;28(38):9463-72.
2.	Clark JH, etal., J Biol Chem. 2010 Apr 30;285(18):13542-9. doi: 10.1074/jbc.M110.101485. Epub 2010 Feb 21.
3.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	GOA data from the GO Consortium
5.	Lanner JT, etal., Cold Spring Harb Perspect Biol. 2010 Nov;2(11):a003996. doi: 10.1101/cshperspect.a003996. Epub 2010 Oct 20.
6.	Mironneau J, etal., J Biol Chem 2001 Apr 6;276(14):11257-64.
7.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
8.	Pipeline to import KEGG annotations from KEGG into RGD
9.	RGD automated data pipeline
10.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:9384575	PMID:9395096	PMID:10444070	PMID:14592808	PMID:15795312	PMID:16645194	PMID:17360812	PMID:19116207	PMID:23943510

Genomics

Comparative Map Data

Ryr3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	99,431,755 - 99,979,125 (-)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	3	99,432,505 - 99,704,961 (-)	Ensembl
Rnor_6.0	3	104,117,307 - 104,665,151 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	104,118,063 - 104,504,204 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	110,710,040 - 111,249,930 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	98,476,626 - 98,872,629 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	98,375,910 - 98,382,386 (-)	NCBI
Celera	3	98,415,656 - 98,961,847 (-)	NCBI		Celera
Cytogenetic Map	3	q35	NCBI

RYR3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	15	33,310,962 - 33,866,121 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	15	33,310,773 - 33,866,103 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	15	33,603,168 - 34,158,303 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	31,390,469 - 31,945,595 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	15	31,390,468 - 31,945,594	NCBI
Celera	15	10,404,754 - 10,960,825 (+)	NCBI
Cytogenetic Map	15	q13.3-q14	NCBI
HuRef	15	10,464,756 - 11,021,191 (+)	NCBI		HuRef
CHM1_1	15	33,721,203 - 34,276,301 (+)	NCBI		CHM1_1

Ryr3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	112,461,699 - 113,047,755 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	2	112,461,700 - 113,047,441 (-)	Ensembl
GRCm38	2	112,631,354 - 113,217,405 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	112,631,355 - 113,217,096 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	112,471,537 - 112,870,488 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	112,432,219 - 112,831,170 (-)	NCBI			mm8
Celera	2	113,779,152 - 114,176,095 (-)	NCBI		Celera
Cytogenetic Map	2	E3- E4	NCBI

Ryr3
(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_004955416	713,373 - 1,259,885 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955416	712,506 - 1,260,111 (-)	NCBI	ChiLan1.0	ChiLan1.0

RYR3
(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	15	30,652,244 - 31,215,359 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	15	30,817,428 - 31,214,494 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	15	11,816,430 - 12,379,101 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

RYR3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	30	1,179,575 - 1,533,352 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	30	1,180,359 - 1,533,619 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	30	1,223,971 - 1,742,310 (-)	NCBI
ROS_Cfam_1.0	30	1,278,037 - 1,798,290 (-)	NCBI
UMICH_Zoey_3.1	30	1,224,326 - 1,741,522 (-)	NCBI
UNSW_CanFamBas_1.0	30	1,323,490 - 1,840,773 (-)	NCBI
UU_Cfam_GSD_1.0	30	1,451,015 - 1,969,019 (-)	NCBI

Ryr3
(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_024408640	79,716,961 - 80,219,351 (-)	NCBI
SpeTri2.0	NW_004936673	2,078,095 - 2,434,872 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RYR3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	80,640,245 - 81,208,334 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	80,640,030 - 81,208,576 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Pig Cytomap	7	q22-q23	NCBI

Ryr3
(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_004624804	467,207 - 1,030,873 (-)	NCBI

Position Markers

D3Rat73

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	99,783,911 - 99,784,115 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	104,470,998 - 104,471,201	NCBI	Rnor6.0
Rnor_5.0	3	111,056,716 - 111,056,919	UniSTS	Rnor5.0
RGSC_v3.4	3	98,838,741 - 98,838,945	RGD	RGSC3.4
RGSC_v3.4	3	98,838,742 - 98,838,945	UniSTS	RGSC3.4
RGSC_v3.1	3	98,735,170 - 98,735,373	RGD
Celera	3	98,766,428 - 98,766,631	UniSTS
RH 3.4 Map	3	782.3	RGD
RH 3.4 Map	3	782.3	UniSTS
RH 2.0 Map	3	535.2	RGD
FHH x ACI Map	3	57.2899	RGD
Cytogenetic Map	3	q34	UniSTS

D3Rat287

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	99,836,810 - 99,837,028 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	104,523,357 - 104,523,574	NCBI	Rnor6.0
Rnor_5.0	3	111,109,019 - 111,109,236	UniSTS	Rnor5.0
RGSC_v3.4	3	98,891,743 - 98,891,961	RGD	RGSC3.4
RGSC_v3.4	3	98,891,744 - 98,891,961	UniSTS	RGSC3.4
RGSC_v3.1	3	98,788,171 - 98,788,389	RGD
Celera	3	98,819,371 - 98,819,588	UniSTS
FHH x ACI Map	3	56.16	RGD
FHH x ACI Map	3	56.16	UniSTS
Cytogenetic Map	3	q34	UniSTS

D3Got51

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	99,678,306 - 99,678,454 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	104,367,228 - 104,367,377	NCBI	Rnor6.0
Rnor_5.0	3	110,953,330 - 110,953,479	UniSTS	Rnor5.0
RGSC_v3.4	3	98,730,778 - 98,730,928	RGD	RGSC3.4
RGSC_v3.4	3	98,730,779 - 98,730,928	UniSTS	RGSC3.4
RGSC_v3.1	3	98,627,207 - 98,627,356	RGD
Celera	3	98,661,749 - 98,661,898	UniSTS
RH 3.4 Map	3	865.3	UniSTS
RH 3.4 Map	3	865.3	RGD
RH 2.0 Map	3	540.2	RGD
Cytogenetic Map	3	q34	UniSTS

RH144535

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	99,950,537 - 99,950,775 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	104,637,484 - 104,637,721	NCBI	Rnor6.0
Rnor_5.0	3	111,222,292 - 111,222,529	UniSTS	Rnor5.0
RGSC_v3.4	3	99,007,632 - 99,007,869	UniSTS	RGSC3.4
Celera	3	98,933,602 - 98,933,839	UniSTS
RH 3.4 Map	3	784.0	UniSTS
Cytogenetic Map	3	q34	UniSTS

D38218

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	99,432,222 - 99,432,376 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	104,117,781 - 104,117,934	NCBI	Rnor6.0
Rnor_5.0	3	110,710,508 - 110,710,661	UniSTS	Rnor5.0
RGSC_v3.4	3	98,476,344 - 98,476,497	UniSTS	RGSC3.4
Celera	3	98,416,130 - 98,416,283	UniSTS
Cytogenetic Map	3	q34	UniSTS

BE101798

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	99,690,981 - 99,691,139 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	104,378,025 - 104,378,182	NCBI	Rnor6.0
Rnor_5.0	3	110,964,274 - 110,964,431	UniSTS	Rnor5.0
RGSC_v3.4	3	98,746,237 - 98,746,394	UniSTS	RGSC3.4
Celera	3	98,673,204 - 98,673,361	UniSTS
RH 3.4 Map	3	757.9	UniSTS
Cytogenetic Map	3	q34	UniSTS

AI072496

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	99,431,814 - 99,432,002 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	104,117,373 - 104,117,560	NCBI	Rnor6.0
Rnor_5.0	3	110,710,100 - 110,710,287	UniSTS	Rnor5.0
RGSC_v3.4	3	98,475,936 - 98,476,123	UniSTS	RGSC3.4
Celera	3	98,415,722 - 98,415,909	UniSTS
RH 3.4 Map	3	845.0	UniSTS
Cytogenetic Map	3	q34	UniSTS

AW526786

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	99,771,818 - 99,771,983 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	104,458,905 - 104,459,069	NCBI	Rnor6.0
Rnor_5.0	3	111,044,623 - 111,044,787	UniSTS	Rnor5.0
RGSC_v3.4	3	98,826,648 - 98,826,812	UniSTS	RGSC3.4
Celera	3	98,754,384 - 98,754,548	UniSTS
RH 3.4 Map	3	782.9	UniSTS
Cytogenetic Map	3	q34	UniSTS

BE120119

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	99,436,299 - 99,436,452 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	104,121,856 - 104,122,008	NCBI	Rnor6.0
Rnor_5.0	3	110,714,583 - 110,714,735	UniSTS	Rnor5.0
RGSC_v3.4	3	98,480,419 - 98,480,571	UniSTS	RGSC3.4
Celera	3	98,420,205 - 98,420,357	UniSTS
RH 3.4 Map	3	758.0	UniSTS
Cytogenetic Map	3	q34	UniSTS

RH138135

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	99,559,946 - 99,560,097 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	104,250,226 - 104,250,376	NCBI	Rnor6.0
Rnor_5.0	3	110,836,878 - 110,837,028	UniSTS	Rnor5.0
RGSC_v3.4	3	98,605,146 - 98,605,296	UniSTS	RGSC3.4
Celera	3	98,543,711 - 98,543,861	UniSTS
RH 3.4 Map	3	869.9	UniSTS
Cytogenetic Map	3	q34	UniSTS

Ryr3

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	99,440,333 - 99,441,268 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	104,125,890 - 104,126,824	NCBI	Rnor6.0
Rnor_5.0	3	110,718,617 - 110,719,551	UniSTS	Rnor5.0
RGSC_v3.4	3	98,484,453 - 98,485,387	UniSTS	RGSC3.4
Celera	3	98,424,239 - 98,425,173	UniSTS
Cytogenetic Map	3	q34	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
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	29463235	118376539	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	31172320	163586636	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	33703347	104104347	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	38192233	133483320	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	41874578	104104347	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	41874578	155617519	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	41874578	155617519	Rat
1581503	Cm58	Cardiac mass QTL 58	2.7	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	43827364	121056321	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	43827364	169034231	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	47233211	147415807	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	47233430	110362260	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	47233430	110362260	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	50437042	119183768	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	50437504	115638231	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
1582239	Epfw1	Epididymal fat weight QTL 1	4.5	0.0006	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	3	53184593	115665732	Rat
1581568	Rf53	Renal function QTL 53			total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	56395968	161299569	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	59242096	157323038	Rat
1300111	Rf12	Renal function QTL 12	3.78		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	61017749	121056321	Rat
1582210	Bw71	Body weight QTL 71	3.3	0.0012	body mass (VT:0001259)	body weight (CMO:0000012)	3	64655305	115665732	Rat
1582221	Kidm30	Kidney mass QTL 30	3.5	0.0008	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	3	64655305	115665732	Rat
12879848	Bw181	Body weght QTL 181		0.015	body mass (VT:0001259)	body weight (CMO:0000012)	3	70348525	121056321	Rat
2301414	Kidm37	Kidney mass QTL 37		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	70653097	121056321	Rat
1600376	Arunc5	Aerobic running capacity QTL 5		0.21	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	73376539	118376539	Rat
1581546	Pur13	Proteinuria QTL 13	2.93	0.0335	total urine protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	3	78196190	146592722	Rat
2302273	Gluco35	Glucose level QTL 35	5.3	0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	80800231	114297550	Rat
631649	Bp123	Blood pressure QTL 123	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	89772419	134772419	Rat
8694437	Bw167	Body weight QTL 167	22.46	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	3	91797474	136797474	Rat
631841	Niddm39	Non-insulin dependent diabetes mellitus QTL 39	3.36		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	94856903	159898684	Rat
724532	Cm17	Cardiac mass QTL 17	2		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	3	95735366	140735366	Rat
1582252	Sual1	Serum uric acid level QTL 1	3.4	0.0123	blood uric acid amount (VT:0010302)	blood uric acid level (CMO:0000501)	3	96127817	102200699	Rat
1582219	Bw63	Body weight QTL 63	3.8	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	3	96127817	115665732	Rat
1354611	Despr2	Despair related QTL 2	3.03	0.0028	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	3	97084464	142084464	Rat
2293087	Iddm27	Insulin dependent diabetes mellitus QTL 27	2.68		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	97551417	147415807	Rat
2312659	Slep7	Serum leptin concentration QTL 7		0.001	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	3	98535255	168026850	Rat
2312670	Bw94	Body weight QTL 94		0.01	inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	3	98535255	168026850	Rat
2312673	Scl63	Serum cholesterol level QTL 63		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	98535255	168026850	Rat
2302373	Gluco39	Glucose level QTL 39	5.01		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	3	98535386	161695835	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	124
Count of miRNA genes:	65
Interacting mature miRNAs:	72
Transcripts:	ENSRNOT00000027865, ENSRNOT00000040306, ENSRNOT00000049582
Prediction methods:	Microtar, 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									24		4	7
Low	3	41	17	1	19	1	8	9	50	20	32	4	8
Below cutoff		2	17	17		17		2		11	5

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_017592338	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601129	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039106806	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF011790	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF130881	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000118	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000040306 ⟹ ENSRNOP00000041223

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	99,432,505 - 99,704,961 (-)	Ensembl
Rnor_6.0 Ensembl	3	104,118,063 - 104,502,471 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000049582 ⟹ ENSRNOP00000040240

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	104,118,063 - 104,504,204 (-)	Ensembl

RefSeq Acc Id:

XM_039106806 ⟹ XP_038962734

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	99,431,755 - 99,979,125 (-)	NCBI

Protein Sequences


Protein RefSeqs	XP_038962734	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB65758	(Get FASTA)	NCBI Sequence Viewer
	AAD31272	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

ENSRNOP00000040240 ⟸ ENSRNOT00000049582

RefSeq Acc Id:

ENSRNOP00000041223 ⟸ ENSRNOT00000040306

RefSeq Acc Id:

XP_038962734 ⟸ XM_039106806

Protein Domains

B30.2/SPRY EF-hand Ion_trans MIR

Transcriptome

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (2019)

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

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (2020)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN-Lx/CubMcwi (2019)

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

BN/NHsdMcwi (2019)

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

BN/NHsdMcwi (2020)

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

BN/SsN (2020)

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

BN/SsN (MCW)

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

BUF/N (2020)

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

BXH2/CubMcwi (2020)

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

BXH3/CubMcwi (2020)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

DA/OlaHsd (2019)

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

F344/DuCrl (2019)

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

F344/N (2020)

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

F344/NCrl (2019)

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

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

F344/Stm (2019)

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

FHH/EurMcwi (2019)

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

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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

FXLE16/Stm (2020)

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

FXLE18/Stm (2020)

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

GH/OmrMcwi (MCW)

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

GK/FarMcwi (2019)

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

GK/Ox (RGD)

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

HXB10/IpcvMcwi (2019)

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

HXB2/IpcvMcwi (2019)

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

HXB20/IpcvMcwi (2020)

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

HXB31/IpcvMcwi (2019)

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

HXB4/IpcvMcwi (2020)

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

LE/Stm (2019)

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

LE/Stm (RGD)

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

LEW/Crl (2019)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LEXF10A/StmMcwi (2020)

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

LEXF11/Stm (2020)

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

LEXF1A/Stm (2019)

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

LEXF1C/Stm (2019)

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

LEXF2B/Stm (2019)

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

LEXF3/Stm (2020)

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

LEXF4/Stm (2020)

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

LH/MavRrrc (RGD)

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

LH/MavRrrcAek (2020)

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

LL/MavRrrc (RGD)

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

LL/MavRrrcAek (2020)

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

LN/MavRrrc (RGD)

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

LN/MavRrrcAek (2020)

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

M520/N (2020)

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

M520/N (MCW)

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

M520/NRrrcMcwi (2019)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (2020)

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

MR/N (MCW)

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

MWF/Hsd (2019)

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

PVG/Seac (2019)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHR/OlalpcvMcwi (2019)

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

SHRSP/A3NCrl (2019)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (2020)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (2019)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WAG/RijCrl (2020)

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

WKY/Gcrc (RGD)

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

WKY/N (2020)

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

WKY/N (MCW)

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

WKY/NCrl (2019)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (2020)

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

WN/N (MCW)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:68952	AgrOrtholog
Ensembl Genes	ENSRNOG00000006645	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000040240	UniProtKB/TrEMBL
	ENSRNOP00000041223	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000040306	UniProtKB/TrEMBL
	ENSRNOT00000049582	UniProtKB/TrEMBL
Gene3D-CATH	2.60.120.920	UniProtKB/TrEMBL
InterPro	ARM-type_fold	UniProtKB/TrEMBL
	B30.2/SPRY	UniProtKB/TrEMBL
	B30.2/SPRY_sf	UniProtKB/TrEMBL
	ConA-like_dom	UniProtKB/TrEMBL
	EF-hand-like_dom	UniProtKB/TrEMBL
	EF_hand_Ca-bd	UniProtKB/TrEMBL
	Ins145_P3_rcpt	UniProtKB/TrEMBL
	Ion_trans_dom	UniProtKB/TrEMBL
	IP3R_RIH_dom	UniProtKB/TrEMBL
	MIR_dom_sf	UniProtKB/TrEMBL
	MIR_motif	UniProtKB/TrEMBL
	RIH_assoc-dom	UniProtKB/TrEMBL
	RIH_dom	UniProtKB/TrEMBL
	Ryan_recept	UniProtKB/TrEMBL
	Ryanodine_rcpt	UniProtKB/TrEMBL
	Ryanrecept_TM4-6	UniProtKB/TrEMBL
	SPRY1_RyR	UniProtKB/TrEMBL
	SPRY2_RyR	UniProtKB/TrEMBL
	SPRY3_RyR	UniProtKB/TrEMBL
	SPRY_dom	UniProtKB/TrEMBL
NCBI Gene	170546	ENTREZGENE
Pfam	Ins145_P3_rec	UniProtKB/TrEMBL
	Ion_trans	UniProtKB/TrEMBL
	MIR	UniProtKB/TrEMBL
	RIH_assoc	UniProtKB/TrEMBL
	RR_TM4-6	UniProtKB/TrEMBL
	RYDR_ITPR	UniProtKB/TrEMBL
	RyR	UniProtKB/TrEMBL
	SPRY	UniProtKB/TrEMBL
PhenoGen	Ryr3	PhenoGen
PRINTS	RYANODINER	UniProtKB/TrEMBL
PROSITE	B302_SPRY	UniProtKB/TrEMBL
	EF_HAND_2	UniProtKB/TrEMBL
	MIR	UniProtKB/TrEMBL
SMART	MIR	UniProtKB/TrEMBL
	SPRY	UniProtKB/TrEMBL
Superfamily-SCOP	SSF100909	UniProtKB/TrEMBL
	SSF47473	UniProtKB/TrEMBL
	SSF48371	UniProtKB/TrEMBL
	SSF49899	UniProtKB/TrEMBL
	SSF82109	UniProtKB/TrEMBL
UniProt	F1LPJ2_RAT	UniProtKB/TrEMBL
	F1M7A1_RAT	UniProtKB/TrEMBL
	O35209_RAT	UniProtKB/TrEMBL
	Q9R273_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2002-06-10	Ryr3	ryanodine receptor 3			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_process	responsible for the increase of Ca++ release during caffeine- and neuromediator-induced global Ca++ response	67931

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

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

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

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

Imported Disease Annotations - ClinVar

RGD Manual Annotations

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

RGD Manual Annotations

Imported Annotations - KEGG (archival)