Stom (stomatin) - Rat Genome Database

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

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

Gene: Stom (stomatin) Rattus norvegicus

Analyze

Symbol:

Stom

Name:

stomatin

RGD ID:

1305109

Description:

Predicted to have RNA polymerase binding activity and protein homodimerization activity. Predicted to be involved in positive regulation by host of viral genome replication; positive regulation of viral process; and regulation of ion transport. Predicted to localize to several cellular components, including endoplasmic reticulum; membrane raft; and perinuclear region of cytoplasm. Orthologous to human STOM (stomatin); INTERACTS WITH acetamide; acrylamide; benzene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

erythrocyte band 7 integral membrane protein; LOC296655

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):	STOM (stomatin)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Stom (stomatin)	HGNC	Treefam, EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Stom (stomatin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	STOM (stomatin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	STOM (stomatin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Stom (stomatin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	STOM (stomatin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	STOM (stomatin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Stom (stomatin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	STOML3 (stomatin like 3)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	STOM (stomatin)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Stom (stomatin)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	stom (stomatin)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	mec-2	Alliance	DIOPT (Hieranoid\|OrthoInspector\|PANTHER\|TreeFam)
Drosophila melanogaster (fruit fly):	Mec2	Alliance	DIOPT (OMA\|PANTHER\|TreeFam)
Caenorhabditis elegans (roundworm):	sto-1	Alliance	DIOPT (OMA\|PANTHER\|TreeFam)
Caenorhabditis elegans (roundworm):	sto-4	Alliance	DIOPT (OMA\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	sto-6	Alliance	DIOPT (OMA\|PANTHER\|TreeFam)
Caenorhabditis elegans (roundworm):	unc-1	Alliance	DIOPT (OMA\|PANTHER\|TreeFam)
Drosophila melanogaster (fruit fly):	CG42540	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	sto-2	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	18,645,058 - 18,667,343 (-)	NCBI
Rnor_6.0 Ensembl	3	14,514,868 - 14,538,241 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	14,515,576 - 14,538,199 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	19,833,117 - 19,855,740 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	14,392,978 - 14,415,288 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	14,289,349 - 14,311,660 (-)	NCBI
Celera	3	13,358,166 - 13,380,297 (-)	NCBI		Celera
Cytogenetic Map	3	p11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1-dichloroethene (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

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

2,6-di-tert-butyl-4-methylphenol (ISO)

3,4-methylenedioxymethamphetamine (ISO)

5-fluorouracil (ISO)

acetamide (EXP)

acrylamide (EXP)

actinomycin D (ISO)

afimoxifene (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

benzene (EXP)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP,ISO)

cadmium dichloride (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

clofibrate (ISO)

copper(II) sulfate (ISO)

crocidolite asbestos (ISO)

cyclophosphamide (ISO)

cyclosporin A (ISO)

cytarabine (ISO)

dexamethasone (ISO)

dibutyl phthalate (EXP,ISO)

dichromium trioxide (ISO)

disodium selenite (ISO)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

ethyl methanesulfonate (ISO)

etoposide (ISO)

folic acid (ISO)

formaldehyde (ISO)

genistein (EXP)

lead diacetate (ISO)

medroxyprogesterone acetate (ISO)

methyl methanesulfonate (ISO)

methylmercury(1+) (EXP)

methylseleninic acid (ISO)

N-methyl-4-phenylpyridinium (ISO)

panobinostat (ISO)

paracetamol (ISO)

pentachlorophenol (ISO)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

quinolin-8-ol (ISO)

resveratrol (EXP)

SB 431542 (ISO)

serpentine asbestos (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sodium fluoride (ISO)

Soman (EXP)

tamoxifen (ISO)

testosterone (ISO)

tetrachloromethane (ISO)

titanium dioxide (ISO)

toluene (EXP)

trichloroethene (EXP)

trichostatin A (ISO)

tris(2-butoxyethyl) phosphate (ISO)

valproic acid (ISO)

vinclozolin (EXP)

vitamin E (ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

positive regulation by host of viral genome replication (ISO)

positive regulation of protein targeting to membrane (ISO)

positive regulation of viral process (ISO)

regulation of acid-sensing ion channel activity (ISO)

regulation of ion transmembrane transport (ISO)

Cellular Component

cellular_component (ND)

cytoplasm (ISO)

cytoskeleton (ISO)

endoplasmic reticulum (ISO)

integral component of plasma membrane (ISO)

membrane raft (ISO)

mitochondrion (ISO)

perinuclear region of cytoplasm (ISO)

plasma membrane (IBA,ISO)

Molecular Function

identical protein binding (ISO)

protein binding (IPI,ISO)

protein homodimerization activity (ISO)

RNA polymerase binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	MGD data from the GO Consortium
4.	RGD automated data pipeline
5.	RGD automated import pipeline for gene-chemical interactions
6.	RGD comprehensive gene curation
7.	Zhang JZ, etal., Arch Biochem Biophys. 1999 Dec 1;372(1):173-8.

Additional References at PubMed

PMID:1547348	PMID:9642292	PMID:12130500	PMID:12477932	PMID:16502470	PMID:19056867	PMID:19190083	PMID:19946888	PMID:21362503	PMID:22516433	PMID:22850675	PMID:23376485
PMID:23533145	PMID:25262680

Genomics

Comparative Map Data

Stom
(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	18,645,058 - 18,667,343 (-)	NCBI
Rnor_6.0 Ensembl	3	14,514,868 - 14,538,241 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	14,515,576 - 14,538,199 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	19,833,117 - 19,855,740 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	14,392,978 - 14,415,288 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	14,289,349 - 14,311,660 (-)	NCBI
Celera	3	13,358,166 - 13,380,297 (-)	NCBI		Celera
Cytogenetic Map	3	p11	NCBI

STOM
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	9	121,338,987 - 121,370,304 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	9	121,338,987 - 121,370,250 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	9	124,101,265 - 124,132,528 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	123,141,174 - 123,172,366 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	9	121,180,910 - 121,212,099	NCBI
Celera	9	94,749,842 - 94,781,033 (-)	NCBI
Cytogenetic Map	9	q33.2	NCBI
HuRef	9	93,719,010 - 93,750,325 (-)	NCBI		HuRef
CHM1_1	9	124,248,150 - 124,279,466 (-)	NCBI		CHM1_1

Stom
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	35,204,002 - 35,227,021 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	2	35,203,998 - 35,226,988 (-)	Ensembl
GRCm38	2	35,313,990 - 35,337,009 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	35,313,986 - 35,336,976 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	35,169,510 - 35,192,529 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	35,135,999 - 35,159,018 (-)	NCBI			mm8
Celera	2	35,008,711 - 35,031,730 (-)	NCBI		Celera
Cytogenetic Map	2	B	NCBI
cM Map	2	23.53	NCBI

Stom
(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_004955419	6,643,012 - 6,675,513 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955419	6,642,807 - 6,673,407 (+)	NCBI	ChiLan1.0	ChiLan1.0

STOM
(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	9	120,812,065 - 120,843,497 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	120,812,065 - 120,843,497 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	9	92,466,718 - 92,498,265 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

STOM
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	11	74,270,409 - 74,284,277 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	11	74,270,409 - 74,284,670 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	11	72,681,251 - 72,707,208 (-)	NCBI
ROS_Cfam_1.0	11	75,407,981 - 75,434,168 (-)	NCBI
UMICH_Zoey_3.1	11	73,914,858 - 73,940,571 (-)	NCBI
UNSW_CanFamBas_1.0	11	73,945,746 - 73,971,919 (-)	NCBI
UU_Cfam_GSD_1.0	11	74,685,417 - 74,711,398 (-)	NCBI

Stom
(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	190,040,059 - 190,069,001 (-)	NCBI
SpeTri2.0	NW_004936487	9,808,586 - 9,837,506 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

STOM
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	261,377,866 - 261,407,716 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	261,380,087 - 261,407,713 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	293,511,501 - 293,528,583 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

STOM
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	12	18,214,816 - 18,246,730 (+)	NCBI
ChlSab1.1 Ensembl	12	18,214,928 - 18,244,595 (+)	Ensembl

Stom
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624760	13,906,430 - 13,936,284 (+)	NCBI

Position Markers

RH132834

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	18,645,142 - 18,645,339 (+)	MAPPER
Rnor_6.0	3	14,515,661 - 14,515,857	NCBI	Rnor6.0
Rnor_5.0	3	19,833,202 - 19,833,398	UniSTS	Rnor5.0
RGSC_v3.4	3	14,393,063 - 14,393,259	UniSTS	RGSC3.4
Celera	3	13,358,251 - 13,358,447	UniSTS
Cytogenetic Map	3	p11	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
631679	Cm10	Cardiac mass QTL 10	7.34	0.0001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	1	25786001	Rat
70202	Alc19	Alcohol consumption QTL 19	2.5		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	3	1	28136884	Rat
631545	Bp85	Blood pressure QTL 85	3.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	1	28500807	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	diastolic blood pressure (CMO:0000005)	3	1	28500807	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	1	28500807	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	pulse pressure (CMO:0000292)	3	1	28500807	Rat
631831	Alc8	Alcohol consumption QTL 8	2.7		consumption behavior trait (VT:0002069)	calculated ethanol drink intake rate (CMO:0001615)	3	1	32972944	Rat
4889966	Bss95	Bone structure and strength QTL 95	4.4		tibia area (VT:1000281)	tibia-fibula cross-sectional area (CMO:0001718)	3	1	37891710	Rat
2312664	Scl62	Serum cholesterol level QTL 62		0.05	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	1	39773425	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	95176874	Rat
1298526	Arunc3	Aerobic running capacity QTL 3	2.2		exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	2631421	33477544	Rat
10401810	Kidm53	Kidney mass QTL 53			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	2631421	48562146	Rat
70203	Gcr2	Gastric cancer resistance QTL 2	2.6		stomach morphology trait (VT:0000470)	stomach tumor susceptibility score (CMO:0002043)	3	3285929	28136884	Rat
1358357	Srcrtb1	Stress Responsive Cort Basal QTL 1	6.36	0.002	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	3285929	28136884	Rat
8693641	Alc30	Alcohol consumption QTL 30	2	0.739	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	3	5654639	25105730	Rat
1558654	Bw56	Body weight QTL 56	4.5	0.0000171	body mass (VT:0001259)	body weight (CMO:0000012)	3	6000748	34394365	Rat
6893355	Bw101	Body weight QTL 101	0.4	0.38	body mass (VT:0001259)	body weight (CMO:0000012)	3	6000748	34394365	Rat
6893363	Bw105	Body weight QTL 105	2.6	0.0036	body mass (VT:0001259)	body weight (CMO:0000012)	3	6000748	34394365	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	3	6000748	51687917	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	3	6000748	51687917	Rat
1558647	Cm46	Cardiac mass QTL 46	5.4	0.0000055	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	6000866	34394121	Rat
1558650	Cm48	Cardiac mass QTL 48	4	0.0001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	3	6000866	34394121	Rat
1558657	Cm43	Cardiac mass QTL 43	6.6	0.0000000293	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	6000866	34394121	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10094081	93415837	Rat
2298542	Neuinf11	Neuroinflammation QTL 11	3.9		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	3	10119318	79772001	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	10639528	127023997	Rat
11528620	Bss113	Bone structure and strength QTL 113	9.75	0.00000000017	femur morphology trait (VT:0000559)	femoral neck width (CMO:0001695)	3	12236221	15217668	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	heart rate (CMO:0000002)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	heart rate (CMO:0000002)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	body weight (CMO:0000012)	3	13126914	36600143	Rat
634306	Bp140	Blood pressure QTL 140	3.3	0.0013	arterial blood pressure trait (VT:2000000)	body weight (CMO:0000012)	3	13126914	36600143	Rat
631568	Bp92	Blood pressure QTL 92	2.2	0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	13126914	41510346	Rat
2325840	Bp345	Blood pressure QTL 345		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14090411	29084626	Rat
731172	Bp151	Blood pressure QTL 151		0.04	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14090411	48562146	Rat
12879849	Bw180	Body weight QTL 180		0.037	body mass (VT:0001259)	body weight (CMO:0000012)	3	14090411	48562146	Rat
12879850	Cm91	Cardiac mass QTL 91		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	3	14090411	48562146	Rat
12879851	Cm92	Cardiac mass QTL 92		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	14090411	48562146	Rat
12879852	Cm93	Cardiac mass QTL 93		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	3	14090411	48562146	Rat
12879853	Am5	Aortic mass QTL 5		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	3	14090411	48562146	Rat
12879854	Kidm63	Kidney mass QTL 63		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	14090411	48562146	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	315
Count of miRNA genes:	180
Interacting mature miRNAs:	200
Transcripts:	ENSRNOT00000025904
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	3	40	45	29	19	29	4	6	41	33	37	11	4
Low		3	12	12		12	4	5	33	2	4		4
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001011965	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC083895	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000115	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000025904 ⟹ ENSRNOP00000025904

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	14,514,868 - 14,538,241 (-)	Ensembl

RefSeq Acc Id:

NM_001011965 ⟹ NP_001011965

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	18,645,058 - 18,667,343 (-)	NCBI
Rnor_6.0	3	14,515,576 - 14,538,199 (-)	NCBI
Rnor_5.0	3	19,833,117 - 19,855,740 (-)	NCBI
RGSC_v3.4	3	14,392,978 - 14,415,288 (-)	RGD
Celera	3	13,358,166 - 13,380,297 (-)	RGD

Sequence:

show sequence

CTGACGCCGTCAAGAGCGACTCCGACTCCAGCAGTATGTCTGACAAACGCCAGTCCGGCCATGT
CCAGTCTCAGCGGGTCCCCGAGTCCTTCAGGGATAATTCCAAGGCAGAACTGGGACCATGTGGA
TGGATTTTGGTGGCTGTCTCGTTCATCTTCGTGCTTATAACTTTCCCAATATCAATTTGGATTT
GCATAAAGATTGTGAAGGAGTATGAAAGAGTGATCATCTTCAGACTGGGCCGCATTTTGCAAGG
TGGCGCCAAAGGACCTGGGTTGTTTTTCATCCTGCCGTGCACTGACAGCTTCATCAAGGTGGAC
ATGAGGACCATCTCCTTCGATATTCCGCCACAGGAGGTGCTCACTAAGGACTCGGTGACCATCA
GCGTGGATGGTGTGGTCTATTACCGTGTTCAGAACGCAACCCTGGCTGTGGCAAATATCACCAA
TGCAGATTCGGCAACCCGTCTTTTGGCGCAAACTACCCTCAGGAATGCGCTGGGCACCAAGAAC
CTGTCTCAGATCCTCTCTGACAGAGAAGAGATCGCACACCACATGCAGAGTACGCTGGATGACG
CCACAGATGACTGGGGAATAAAGGTCGAGCGTGTGGAGATTAAGGACGTGAAGCTGCCAGTACA
GCTCCAGAGAGCCATGGCTGCAGAGGCAGAAGCCGCCCGGGAGGCTAGAGCCAAGGTGATTGCA
GCCGAAGGGGAAATGAATGCATCCAGGGCTCTGAAAGAAGCATCCATGGTTATCACGGAGTCTC
CTGCTGCCCTTCAGCTCCGGTACCTTCAAACCCTGACCACTATCGCTGCGGAGAAAAACTCCAC
CATTGTCTTCCCTCTGCCCATCGACATGTTGCAGGGCATCATGGGTTCCCACCACTGAGCAGTC
CAGCTCTATGGGAGAGCTGTGCTGAGTCCTTCCCAGGGTAAAGAGGGGACAAAGTTAGCCTTTA
ACTCTCGGGGAGATTAGCTGAAAGCTTGACTGTCCCCCTCCCTCTCCTTTCCTGTATGTGCACT
GTAGGGGCTCTTAGAATGGGCAGGGATCATAAAAGCAGATGAAGAGACTCGCTCTGGAGCCAGG
AGTGCAGCTCAGTTGCAGAGCACTGGCTTAGCCCGTTCAAGGCTCAGGGCTTCATCCTCAGCAC
CAACAAATAAACAAATAGGCAAGTCAGGGAAGGGACGCGTCTGAGCCCAGGTAAACACTCTGTG
ACACTGAAGAACTGTGCCACCCACTTCTCTGGCTGCCTGTGCCTTCCCTTCAGGGGATCCTTAG
GATCGTTTTGTTTTGTTTTGAGATAGGGTTTCTTAGAGTAGCCTTGGCTGTCCTGGCCTTGAAC
TCAGAGATCCCCCTGCCTCTGCCTCCCCAGTGCTGGGACTAAAGGTGTGGGCCACCACCACCTC
TCCCTTTAGGAAATCTTAAGGAAGGACATTTCCCCAAAGTTCATCCACCCACTCTAATCCTCTC
CCTCCTCCTGCTTGATCCTGTCAGAGCCAACAAAAAGGCTCACGCTGGCCCTTCCAAGACCGAA
GGTCACTCCTGTCATAGTCCTTTTGAAAATAGTTGCAGTTTTTAAAAACCGTCTTGGGCCTCCG
CCCCACAACCTAATGATCCCTGTGTGTGGCCTTGTTTAAAGCAGTGAATCTCTGCCACAGGAGT
GCTCCCTTCTCTCTCTCGCATATTTTCATGGATCAGGTTTTTAAATCGTTTTGAATTTTAAAAA
TAACTTTGAGTTCTATCAATAAACTTTATGTCCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001011965	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH83895	(Get FASTA)	NCBI Sequence Viewer
	EDL93146	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001011965 ⟸ NM_001011965

- UniProtKB:

Q5XI04 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSDKRQSGHVQSQRVPESFRDNSKAELGPCGWILVAVSFIFVLITFPISIWICIKIVKEYERVI
IFRLGRILQGGAKGPGLFFILPCTDSFIKVDMRTISFDIPPQEVLTKDSVTISVDGVVYYRVQN
ATLAVANITNADSATRLLAQTTLRNALGTKNLSQILSDREEIAHHMQSTLDDATDDWGIKVERV
EIKDVKLPVQLQRAMAAEAEAAREARAKVIAAEGEMNASRALKEASMVITESPAALQLRYLQTL
TTIAAEKNSTIVFPLPIDMLQGIMGSHH

hide sequence

RefSeq Acc Id:

ENSRNOP00000025904 ⟸ ENSRNOT00000025904

Protein Domains

PHB

Transcriptome

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

Promoters

RGD ID:

13692018

Promoter ID:

EPDNEW_R2542

Type:

multiple initiation site

Name:

Stom_1

Description:

stomatin

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	3	14,538,221 - 14,538,281	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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

ACI/EurMcwi (RGD)

Visual

CSV

TAB

Printer

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

ACI/N (MCW)

Visual

CSV

TAB

Printer

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

BBDP/Wor (RGD)

Visual

CSV

TAB

Printer

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

BN/SsN (MCW)

Visual

CSV

TAB

Printer

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

Buf/N (MCW)

Visual

CSV

TAB

Printer

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

COP/CrCrl (MCW & UW)

Visual

CSV

TAB

Printer

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

F344/NCrl (RGD)

Visual

CSV

TAB

Printer

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

F344/NRrrc (MCW)

Visual

CSV

TAB

Printer

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

FHH/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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

FHH/EurMcwi (RGD)

Visual

CSV

TAB

Printer

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

FHL/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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

FHL/EurMcwi (RGD)

Visual

CSV

TAB

Printer

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

GH/OmrMcwi (MCW)

Visual

CSV

TAB

Printer

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

GK/Ox (RGD)

Visual

CSV

TAB

Printer

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

LE/Stm (RGD)

Visual

CSV

TAB

Printer

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

LEW/Crl (RGD)

Visual

CSV

TAB

Printer

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

LEW/NCrlBR (RGD)

Visual

CSV

TAB

Printer

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

LH/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

LL/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

LN/MavRrrc (RGD)

Visual

CSV

TAB

Printer

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

M520/N (MCW)

Visual

CSV

TAB

Printer

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

MHS/Gib (RGD)

Visual

CSV

TAB

Printer

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

MNS/Gib (RGD)

Visual

CSV

TAB

Printer

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

MR/N (MCW)

Visual

CSV

TAB

Printer

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

SBH/Ygl (MCW)

Visual

CSV

TAB

Printer

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

SBH/Ygl (RGD)

Visual

CSV

TAB

Printer

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

SBN/Ygl (MCW)

Visual

CSV

TAB

Printer

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

SBN/Ygl (RGD)

Visual

CSV

TAB

Printer

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

SHR/NHsd (RGD)

Visual

CSV

TAB

Printer

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

SHRSP/Gcrc (RGD)

Visual

CSV

TAB

Printer

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

SR/JrHsd (MCW)

Visual

CSV

TAB

Printer

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

SR/JrHsd (RGD)

Visual

CSV

TAB

Printer

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

SS/Jr (RGD)

Visual

CSV

TAB

Printer

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

SS/JrHsdMcwi (MCW)

Visual

CSV

TAB

Printer

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

SS/JrHsdMcwi (RGD)

Visual

CSV

TAB

Printer

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

WAG/Rij (RGD)

Visual

CSV

TAB

Printer

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

WKY/Gcrc (RGD)

Visual

CSV

TAB

Printer

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

WKY/N (MCW)

Visual

CSV

TAB

Printer

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

WKY/NCrl (RGD)

Visual

CSV

TAB

Printer

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

WKY/NHsd (RGD)

Visual

CSV

TAB

Printer

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

WN/N (MCW)

Visual

CSV

TAB

Printer

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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
3	19839921	19839922	T	A	snv	BDIX.Cg-Tal/NemOda (KyushuU)
3	19839928	19839929	G	A	snv	BDIX.Cg-Tal/NemOda (KyushuU)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305109	AgrOrtholog
Ensembl Genes	ENSRNOG00000019147	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000025904	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000025904	ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7132959	IMAGE-MGC_LOAD
InterPro	Band-7_stomatin-like	UniProtKB/TrEMBL
	Band_7	UniProtKB/TrEMBL
	Band_7/SPFH_dom_sf	UniProtKB/TrEMBL
	Band_7/stomatin-like_CS	UniProtKB/TrEMBL
	Stomatin	UniProtKB/TrEMBL
	Stomatin	UniProtKB/TrEMBL
KEGG Report	rno:296655	UniProtKB/TrEMBL
MGC_CLONE	MGC:95236	IMAGE-MGC_LOAD
NCBI Gene	296655	ENTREZGENE
PANTHER	PTHR10264	UniProtKB/TrEMBL
	PTHR10264:SF115	UniProtKB/TrEMBL
Pfam	Band_7	UniProtKB/TrEMBL
PhenoGen	Stom	PhenoGen
PRINTS	STOMATIN	UniProtKB/TrEMBL
PROSITE	BAND_7	UniProtKB/TrEMBL
SMART	PHB	UniProtKB/TrEMBL
Superfamily-SCOP	SSF117892	UniProtKB/TrEMBL
UniProt	Q5XI04	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-12-06	Stom	stomatin	Stom_predicted	stomatin (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Stom_predicted	stomatin (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)

Send us a Message