Rpn1 (ribophorin I) - Rat Genome Database

Name: Rpn1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Rpn1 (ribophorin I) Rattus norvegicus

Analyze

Symbol:

Rpn1

Name:

ribophorin I

RGD ID:

3594

Description:

Predicted to be involved in protein N-linked glycosylation via asparagine. Located in rough endoplasmic reticulum. Orthologous to human RPN1 (ribophorin I); PARTICIPATES IN Endoplasmic Reticulum-associated degradation pathway; N-linked glycan biosynthetic pathway; INTERACTS WITH 2,4,6-trinitrotoluene; 2,6-dinitrotoluene; acrylamide.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kDa subunit; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1-like; LOC100363329; RIBI; ribophorin-1; ribophorin1; RPN-I

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):	RPN1 (ribophorin I)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther
Mus musculus (house mouse):	Rpn1 (ribophorin I)	HGNC	EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Rpn1 (ribophorin I)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	RPN1 (ribophorin I)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	RPN1 (ribophorin I)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Rpn1 (ribophorin I)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	RPN1 (ribophorin I)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	RPN1 (ribophorin I)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Rpn1 (ribophorin I)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	RPN1 (ribophorin I)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Mus musculus (house mouse):	Rpn1 (ribophorin I)	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	OST1	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG33303	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	ribo-1	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	4	120,543,667 - 120,565,069 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	4	120,543,667 - 120,565,069 (+)	Ensembl
Rnor_6.0	4	119,997,232 - 120,018,687 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	119,997,268 - 120,018,679 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	185,243,182 - 185,264,593 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	4	109,501,306 - 109,522,708 (+)	NCBI		Celera
Cytogenetic Map	4	q34	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

hereditary breast ovarian cancer syndrome (ISO)

Primary Lymphedema with Myelodysplasia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

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

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

2,4,6-trinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

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

3H-1,2-dithiole-3-thione (ISO)

4-hydroxyphenyl retinamide (ISO)

acetylsalicylic acid (ISO)

acrylamide (EXP)

aflatoxin B2 (ISO)

ammonium chloride (EXP)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

bucladesine (ISO)

buspirone (EXP)

cadmium atom (ISO)

cadmium dichloride (EXP)

caffeine (ISO)

carbon nanotube (ISO)

chromium(6+) (ISO)

clofibrate (ISO)

coumestrol (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dibutyl phthalate (EXP)

doxorubicin (ISO)

endosulfan (EXP)

folic acid (ISO)

folpet (ISO)

gentamycin (EXP)

glafenine (EXP)

indometacin (ISO)

isoprenaline (ISO)

ivermectin (ISO)

lead diacetate (ISO)

medroxyprogesterone acetate (ISO)

methapyrilene (EXP)

miconazole (ISO)

nimesulide (EXP)

ozone (EXP)

paracetamol (ISO)

pirinixic acid (ISO)

sodium dichromate (ISO)

sodium fluoride (ISO)

tacrolimus hydrate (ISO)

tetrachloromethane (ISO)

thapsigargin (ISO)

titanium dioxide (ISO)

triptonide (ISO)

tunicamycin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

peptide transport (NAS)

protein glycosylation (ISO)

protein N-linked glycosylation (ISO)

protein N-linked glycosylation via asparagine (IBA,IEA,ISO)

Cellular Component

cytosol (IEA,ISO)

endoplasmic reticulum (ISO)

endoplasmic reticulum membrane (ISO)

integral component of membrane (IEA)

melanosome (IEA)

oligosaccharyltransferase complex (IBA,IEA,ISO)

rough endoplasmic reticulum (IDA,IEA,ISO)

Molecular Function

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

Endoplasmic Reticulum-associated degradation pathway (IEA)

N-linked glycan biosynthetic pathway (IEA)

References

References - curated


1.	Farah CA, etal., J Biol Chem. 2005 Mar 11;280(10):9439-49. Epub 2004 Dec 28.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	GOA data from the GO Consortium
4.	Harnik-Ort V, etal., J Cell Biol 1987 Apr;104(4):855-63.
5.	KEGG
6.	MGD data from the GO Consortium
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
12.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
13.	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data

Additional References at PubMed

PMID:2335524	PMID:9642163	PMID:9930704	PMID:12887896	PMID:15978772	PMID:17264154	PMID:19182904	PMID:19946888	PMID:21949367	PMID:22082260	PMID:22658674	PMID:23831032
PMID:23979707	PMID:24625528	PMID:25009997

Genomics

Comparative Map Data

Rpn1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	4	120,543,667 - 120,565,069 (+)	NCBI	mRatBN7.2
mRatBN7.2 Ensembl	4	120,543,667 - 120,565,069 (+)	Ensembl
Rnor_6.0	4	119,997,232 - 120,018,687 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	119,997,268 - 120,018,679 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	185,243,182 - 185,264,593 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	4	109,501,306 - 109,522,708 (+)	NCBI		Celera
Cytogenetic Map	4	q34	NCBI

RPN1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	3	128,619,969 - 128,681,075 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	3	128,619,969 - 128,650,818 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	3	128,338,812 - 128,369,661 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	3	129,821,503 - 129,852,409 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	3	129,821,510 - 129,852,378	NCBI
Celera	3	126,767,445 - 126,799,199 (-)	NCBI
Cytogenetic Map	3	q21.3	NCBI
HuRef	3	125,722,987 - 125,753,880 (-)	NCBI		HuRef
CHM1_1	3	128,301,823 - 128,332,696 (-)	NCBI		CHM1_1

Rpn1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	88,061,455 - 88,082,286 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	6	88,061,464 - 88,082,286 (+)	Ensembl
GRCm38	6	88,084,473 - 88,105,304 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	88,084,482 - 88,105,304 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	88,034,467 - 88,055,298 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	6	88,050,157 - 88,070,945 (+)	NCBI			mm8
Celera	6	90,021,709 - 90,042,660 (+)	NCBI		Celera
Cytogenetic Map	6	D1	NCBI
cM Map	6	39.13	NCBI

Rpn1
(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_004955429	15,204,453 - 15,232,476 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955429	15,204,848 - 15,231,547 (+)	NCBI	ChiLan1.0	ChiLan1.0

RPN1
(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	3	133,032,098 - 133,056,733 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	3	133,032,560 - 133,058,666 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	3	125,666,844 - 125,697,922 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

RPN1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	20	2,611,316 - 2,640,047 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	20	2,611,551 - 2,639,983 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	20	2,647,475 - 2,676,092 (-)	NCBI
ROS_Cfam_1.0	20	2,631,950 - 2,660,570 (-)	NCBI
UMICH_Zoey_3.1	20	2,352,624 - 2,381,238 (-)	NCBI
UNSW_CanFamBas_1.0	20	2,679,052 - 2,707,535 (-)	NCBI
UU_Cfam_GSD_1.0	20	2,639,667 - 2,668,086 (-)	NCBI

Rpn1
(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_024404942	20,305,933 - 20,313,522 (+)	NCBI
SpeTri2.0	NW_004936798	347,803 - 355,392 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RPN1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	13	71,884,282 - 71,941,263 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	13	71,892,600 - 71,908,772 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	13	79,273,302 - 79,289,569 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RPN1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	22	52,391,793 - 52,417,341 (+)	NCBI	ChlSab1.1		chlSab2
ChlSab1.1 Ensembl	22	52,391,813 - 52,417,575 (+)	Ensembl	ChlSab1.1		chlSab2
Vero_WHO_p1.0	NW_023666041	113,942,601 - 113,968,226 (-)	NCBI	Vero_WHO_p1.0

Rpn1
(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_004624961	9,482 - 45,569 (+)	NCBI	HetGla_female_1.0		hetGla2

Position Markers

RH134572

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	120,564,776 - 120,564,989 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	120,018,395 - 120,018,607	NCBI	Rnor6.0
Rnor_5.0	4	185,264,309 - 185,264,521	UniSTS	Rnor5.0
Celera	4	109,522,416 - 109,522,628	UniSTS
RH 3.4 Map	4	716.41	UniSTS

D6Wsu137e

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	120,564,802 - 120,564,997 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	120,018,421 - 120,018,615	NCBI	Rnor6.0
Rnor_5.0	4	185,264,335 - 185,264,529	UniSTS	Rnor5.0
Celera	4	109,522,442 - 109,522,636	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
2303168	Bp330	Blood pressure QTL 330	4.25	0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	5214602	146446691	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	11320076	180699135	Rat
1358352	Srcrt3	Stress Responsive Cort QTL 3	2.29		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	38465774	146803430	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	44463720	155883716	Rat
1354612	Foco1	Food consumption QTL 1	8.87		eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	4	44463908	148090542	Rat
1354660	Salc1	Saline consumption QTL 1	11.26		drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	4	44463908	148090542	Rat
2312567	Glom19	Glomerulus QTL 19	1.9	0.006	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	4	45456990	146803430	Rat
1298082	Stresp4	Stress response QTL 4			blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	50119848	146803430	Rat
70200	Alc18	Alcohol consumption QTL 18	9.2		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	4	56647873	149491524	Rat
1641833	Alc21	Alcohol consumption QTL 21	8.6	0.0001	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	56698790	126192555	Rat
738009	Sach4	Saccharine consumption QTL 4	4.9	0.000016	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	59948935	154902892	Rat
738016	Alc16	Alcohol consumption QTL 16	3.6	0.00015	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	59948935	154902892	Rat
738031	Alc14	Alcohol consumption QTL 14	7.6	0.00003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	59948935	154902892	Rat
61418	Pia5	Pristane induced arthritis QTL 5	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	62277855	128289560	Rat
631674	Iddm14	Insulin dependent diabetes mellitus QTL 14			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	4	64528739	157573521	Rat
61330	Eau1	Experimental allergic uveoretinitis QTL 1		0.0003	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	4	70362013	132642728	Rat
631646	Stl4	Serum triglyceride level QTL 4	6.5	0.0001	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	4	73169846	132642728	Rat
631662	Hcar2	Hepatocarcinoma resistance QTL 2	3.1	0.0003	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	78878504	123878504	Rat
738015	Pia9	Pristane induced arthritis QTL 9	4.5	0.048	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	80694870	125694870	Rat
1641919	Alc22	Alcohol consumption QTL 22		0.0005	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	81192555	126192555	Rat
70177	Xhs1	X-ray hypersensitivity QTL 1	25.1		intestine integrity trait (VT:0010554)	post-insult time to onset of moribundity (CMO:0001896)	4	82798864	152731274	Rat
1576316	Ept5	Estrogen-induced pituitary tumorigenesis QTL 5	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	4	83428419	177635233	Rat
634334	Xhs3	X-ray hypersensitivity QTL 3	10		intestine integrity trait (VT:0010554)	post-insult time to onset of moribundity (CMO:0001896)	4	84728680	129854654	Rat
1582232	Gluco25	Glucose level QTL 25	3.6	0.0023	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	85253748	148090731	Rat
12798523	Anxrr56	Anxiety related response QTL 56	2.83	0.05	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	85253748	150276390	Rat
1358202	Gluco11	Glucose level QTL 11	2.4	0.02	adipocyte glucose uptake trait (VT:0004185)	absolute change in adipocyte glucose uptake (CMO:0000873)	4	85379421	167139601	Rat
61476	Aia3	Adjuvant induced arthritis QTL 3	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	86730991	131730991	Rat
1578662	Bss15	Bone structure and strength QTL 15	19.6		femur width (VT:1000666)	femoral neck width (CMO:0001695)	4	87327165	132327165	Rat
1578670	Bss14	Bone structure and strength QTL 14	16.4		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	4	87327165	132327165	Rat
1578655	Bmd11	Bone mineral density QTL 11	11		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	4	90850165	135850165	Rat
634335	Anxrr16	Anxiety related response QTL 16	7.22		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	4	93308457	167139447	Rat
631689	Scl4	Serum cholesterol level QTL 4	1.9	0.008	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	4	95174120	140174120	Rat
61434	Cia3	Collagen induced arthritis QTL 3	4.8		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	103194656	148194656	Rat
2302049	Pia32	Pristane induced arthritis QTL 32	5.1	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)	4	105789505	150789505	Rat
731165	Uae21	Urinary albumin excretion QTL 21	2.4	0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	4	106649412	151649412	Rat
61406	Scwia1	Streptococcal cell wall induced arthritis QTL 1	2.3		joint integrity trait (VT:0010548)	experimental arthritis severity measurement (CMO:0001459)	4	106805662	151805662	Rat
7207480	Bss105	Bone structure and strength QTL 105	8.1		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	4	109827074	154827074	Rat
1549832	Bss3	Bone structure and strength QTL 3	11		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	4	109827074	154827074	Rat
737821	Hcar9	Hepatocarcinoma resistance QTL 9	3.7		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	109866907	167139601	Rat
1331759	Hrtrt13	Heart rate QTL 13	3.54628		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	110275411	168266883	Rat
6478760	Anxrr45	Anxiety related response QTL 45		0.06717	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	110870972	155870972	Rat
6478763	Anxrr46	Anxiety related response QTL 46		0.07428	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	110870972	155870972	Rat
12798519	Anxrr54	Anxiety related response QTL 54	2.54	0.05	locomotor behavior trait (VT:0001392)	distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)	4	114627026	159627026	Rat
1300116	Hrtrt5	Heart rate QTL 5	3.76		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	116179486	151161268	Rat
724535	Cm18	Cardiac mass QTL 18	2.6		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	4	118856416	163856416	Rat
1331802	Srn5	Serum renin concentration QTL 5	3.045		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	4	119428175	157578333	Rat
12798527	Anxrr58	Anxiety related response QTL 58	4.11	0.05	locomotor behavior trait (VT:0001392)	distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)	4	119463257	147278687	Rat
70201	Gcr1	Gastric cancer resistance QTL 1	2.7		stomach morphology trait (VT:0000470)	stomach tumor susceptibility score (CMO:0002043)	4	120260281	147278687	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	351
Count of miRNA genes:	214
Interacting mature miRNAs:	254
Transcripts:	ENSRNOT00000073429
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	43	57	41	19	41	8	11	74	35	41	11	8
Low
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_013067	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB100593	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AB100594	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC061756	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473957	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220145	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ229660	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230735	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000148	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M33508	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X05300	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000073429 ⟹ ENSRNOP00000066002

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	4	120,543,667 - 120,565,069 (+)	Ensembl
Rnor_6.0 Ensembl	4	119,997,268 - 120,018,679 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000095042 ⟹ ENSRNOP00000085043

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	4	120,546,479 - 120,565,069 (+)	Ensembl

RefSeq Acc Id:

NM_013067 ⟹ NP_037199

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	4	120,543,667 - 120,565,069 (+)	NCBI
Rnor_6.0	4	119,997,232 - 120,018,687 (+)	NCBI
Rnor_5.0	4	185,243,182 - 185,264,593 (+)	NCBI
Celera	4	109,501,306 - 109,522,708 (+)	NCBI

Sequence:

show sequence

GGGGGGGGGGCGGGGCGCGTGTCGGTGGCGCTCAGCTCGCGGTCATGGAGGCGCCGATCGTCTT
GCTGCTGCTGCTATGGCTCGGGGCCTTGGCCCCGACGCCCGGCAGCGCCTCTTCGGAGGCTCCG
CCGCTGGTCAACGAGGACGTGAAGCGCACGGTGGACCTGAGCAGCCACCTAGCCAAGGTGACGG
CTGAGGTGGTCCTGGCGCACCCGGGCGGCGGCTCTACAGCACGAGCCAGCTCTTTCGTTCTGGC
CCTGGAGCCCGAACTGGAGTCGCGACTTGCACACCTAGGCGTGCAGGTAAAGGGAGAAGATGAG
GAAGACAACAACCTAGAAGTACGAGAAACCAAAATGAAGGGGAAAAGTGGGAGGTTTTTCACCG
TCAAGCTCCCAGTTGCTCTTGATCCTGGGTCCAAGATCTCAATCGTTGTGGAAACTGTCTACAC
CCATGTGCTTCATCCATACCCGACTCAGATAACTCAGTCAGAGAAACAGTTTGTGGTGTTTGAG
GGCAACCATTACTTCTACTCTCCCTATCCAACAAAGACCCAGACCATGCGAGTGAGACTTGCTT
CCCGAAATGTGGAGAGCCATACCAAGCTGGGGAACCCCTCAAGGTCTGAGGACATCCTGGACTA
TGGGCCTTTTAAAGACATCCCTGCCTACAGTCAGGATACTTTCAAAGTACATTATGAGAACAAT
AGCCCTTTCCTGACCATCACCAGTATGACCCGGGTCATTGAGGTTTCTCACTGGGGCAATATTG
CTGTGGAAGAGAACGTGGACTTGAAGCATACAGGTGCGGTGCTGAAGGGACCTTTCTCCCGCTA
CGATTACCAGAGGCAGCCTGACAGTGGGATCTCCTCCATTCGTTCTTTTAAGACCATCCTTCCT
GCTGCTGCCCAGGATGTGTATTACCGGGATGAAATCGGTAATGTTTCCACCAGCCACCTCCTTA
TTTTGGATGACTCCGTGGAAATGGAAATCCGGCCTCGATTTCCTCTCTTTGGAGGGTGGAAGAC
ACACTACATCGTTGGTTACAACCTCCCAAGCTATGAGTACCTCTATAATCTGGGTGACCAGTAT
GCACTGAAGATGCGGTTTGTAGACCACGTGTTTGATGAGCAAGTGATAGATTCTCTGACAGTGA
AGATCATCCTTCCTGAGGGAGCCAAGAACATCCAGGTAGACAGTCCCTACGATATTAGCCGGGC
CCCAGATGAGCTGCATTACACCTACCTAGACACATTCGGCCGCCCGGTGATTGTTGCTTACAAG
AAGAATCTAGTTGAACAGCACATTCAGGACATTGTGGTGCACTACACATTCAACAAGGTGCTCA
TGCTGCAGGAGCCTCTGCTGGTTGTGGCCGCCTTCTACATCCTGTTCTTCACCGTCATCATCTA
CGTCCGTCTAGACTTTTCCATCACCAAGGACCCAGCAGCAGAAGCCAGGATGAAAGTGGCCTGT
ATCACAGAGCAGGTCTTAACCCTGGTCAACAAGAGGTTAGGCCTCTACCGTCACTTTGATGAGA
CTGTCAATAGATACAAGCAGTCCCGGGACATCTCTACCCTCAATAGTGGCAAGAAGAGCCTAGA
GACAGAGCACAAAGCTGTGACCAGTGAGATTGCTGTGCTGCAGTCTAGGCTGAAGACGGAGGGC
TCTGACCTGTGTGACAGGGTGAGCGAAATGCAGAAGCTGGACGCGCAGGTCAAGGAGCTGGTAC
TGAAGTCTGCGGTGGAGGCAGAGAGGCTGGTGGCTGGCAAGCTCAAGAAGGACACATACATCGA
GAATGAAAAGCTCAGCTCAGGAAAACGCCAGGAGCTGGTCACCAAGATCGACCACATCCTGGAC
GCTCTGTAGCTCTTGTCTCCAGAGCAGGCCTGGGTTGCCTACACTTCTGGATGGAATAGGTAGA
GGGAGGAAGTTGTGATTAGCCTAAGACCTCAAGAAAAAAGCTGAGGCCCATCCATGGCTGTGTA
AGAAGCTTGTCCCTTATTTCTGAATGGTTCTCTTTTTTACAAAAACAAAAACCTAAACAAAAAT
CCTGTTTAAAAAACAAACTTGGTTGTGTTTTGAGCAAAAGCATTTTCAGTAGTTGATTGCTGTT
TTGTTTTGATACCTGGGTATTTTTTCTGTCTGTAAGCCCTGTTTTATGGCCTTCTGATTCCTAA
TGTTTGGTTCTTTTGTGAGCGTATGCATGGTTTTTTAAAAGTGTGTATGACCAAATAAAAATAA
AGGAGGGACTGTGAACATTGG

hide sequence

Protein Sequences


Protein RefSeqs	NP_037199	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA42043	(Get FASTA)	NCBI Sequence Viewer
	AAH61756	(Get FASTA)	NCBI Sequence Viewer
	BAE16987	(Get FASTA)	NCBI Sequence Viewer
	BAE16988	(Get FASTA)	NCBI Sequence Viewer
	CAA28919	(Get FASTA)	NCBI Sequence Viewer
	EDL91305	(Get FASTA)	NCBI Sequence Viewer
	EDL91306	(Get FASTA)	NCBI Sequence Viewer
	P07153	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_037199 ⟸ NM_013067
- Peptide Label:	precursor
- UniProtKB:	Q6P7A7 (UniProtKB/TrEMBL)
- Sequence:	show sequence MEAPIVLLLLLWLGALAPTPGSASSEAPPLVNEDVKRTVDLSSHLAKVTAEVVLAHPGGGSTAR ASSFVLALEPELESRLAHLGVQVKGEDEEDNNLEVRETKMKGKSGRFFTVKLPVALDPGSKISI VVETVYTHVLHPYPTQITQSEKQFVVFEGNHYFYSPYPTKTQTMRVRLASRNVESHTKLGNPSR SEDILDYGPFKDIPAYSQDTFKVHYENNSPFLTITSMTRVIEVSHWGNIAVEENVDLKHTGAVL KGPFSRYDYQRQPDSGISSIRSFKTILPAAAQDVYYRDEIGNVSTSHLLILDDSVEMEIRPRFP LFGGWKTHYIVGYNLPSYEYLYNLGDQYALKMRFVDHVFDEQVIDSLTVKIILPEGAKNIQVDS PYDISRAPDELHYTYLDTFGRPVIVAYKKNLVEQHIQDIVVHYTFNKVLMLQEPLLVVAAFYIL FFTVIIYVRLDFSITKDPAAEARMKVACITEQVLTLVNKRLGLYRHFDETVNRYKQSRDISTLN SGKKSLETEHKAVTSEIAVLQSRLKTEGSDLCDRVSEMQKLDAQVKELVLKSAVEAERLVAGKL KKDTYIENEKLSSGKRQELVTKIDHILDAL hide sequence

RefSeq Acc Id:

ENSRNOP00000066002 ⟸ ENSRNOT00000073429

RefSeq Acc Id:

ENSRNOP00000085043 ⟸ ENSRNOT00000095042

Transcriptome

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

Promoters

RGD ID:

13693227

Promoter ID:

EPDNEW_R3752

Type:

multiple initiation site

Name:

Rpn1_1

Description:

ribophorin I

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	4	119,997,261 - 119,997,321	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (2019)

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

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (2020)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN-Lx/CubMcwi (2019)

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

BN/NHsdMcwi (2019)

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

BN/NHsdMcwi (2020)

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

BN/SsN (2020)

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

BN/SsN (MCW)

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

BUF/N (2020)

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

BXH2/CubMcwi (2020)

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

BXH3/CubMcwi (2020)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

DA/OlaHsd (2019)

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

F344/DuCrl (2019)

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

F344/N (2020)

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

F344/NCrl (2019)

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

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

F344/Stm (2019)

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

FHH/EurMcwi (2019)

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

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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

FXLE16/Stm (2020)

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

FXLE18/Stm (2020)

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

GH/OmrMcwi (MCW)

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

GK/FarMcwi (2019)

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

GK/Ox (RGD)

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

HXB10/IpcvMcwi (2019)

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

HXB2/IpcvMcwi (2019)

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

HXB20/IpcvMcwi (2020)

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

HXB31/IpcvMcwi (2019)

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

HXB4/IpcvMcwi (2020)

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

LE/Stm (2019)

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

LE/Stm (RGD)

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

LEW/Crl (2019)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LEXF10A/StmMcwi (2020)

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

LEXF11/Stm (2020)

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

LEXF1A/Stm (2019)

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

LEXF1C/Stm (2019)

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

LEXF2B/Stm (2019)

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

LEXF3/Stm (2020)

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

LEXF4/Stm (2020)

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

LH/MavRrrc (RGD)

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

LH/MavRrrcAek (2020)

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

LL/MavRrrc (RGD)

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

LL/MavRrrcAek (2020)

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

LN/MavRrrc (RGD)

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

LN/MavRrrcAek (2020)

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

M520/N (2020)

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

M520/N (MCW)

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

M520/NRrrcMcwi (2019)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (2020)

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

MR/N (MCW)

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

MWF/Hsd (2019)

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

PVG/Seac (2019)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHR/OlalpcvMcwi (2019)

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

SHRSP/A3NCrl (2019)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (2020)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (2019)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WAG/RijCrl (2020)

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

WKY/Gcrc (RGD)

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

WKY/N (2020)

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

WKY/N (MCW)

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

WKY/NCrl (2019)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (2020)

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

WN/N (MCW)

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3594	AgrOrtholog
Ensembl Genes	ENSRNOG00000046345	Ensembl, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000066002	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000073429	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:5600029	IMAGE-MGC_LOAD
InterPro	Ribophorin_I	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:25596	UniProtKB/TrEMBL
MGC_CLONE	MGC:72518	IMAGE-MGC_LOAD
NCBI Gene	25596	ENTREZGENE
PANTHER	PTHR21049	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Ribophorin_I	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Rpn1	PhenoGen
TIGR	TC216574
UniProt	P07153	ENTREZGENE
	Q6P7A7	ENTREZGENE, UniProtKB/TrEMBL
	RPN1_RAT	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-04-12	Rpn1	ribophorin I	LOC100363329	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1-like	Data Merged	737654	PROVISIONAL
2010-05-06	LOC100363329	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1-like			Symbol and Name status set to provisional	70820	PROVISIONAL
2002-06-10	Rpn1	Ribophorin I			Symbol and Name status set to approved	70586	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)

Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)