Psmb1 (proteasome 20S subunit beta 1)

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Gene: Psmb1 (proteasome 20S subunit beta 1) Rattus norvegicus

Analyze

Symbol:

Psmb1

Name:

proteasome 20S subunit beta 1

RGD ID:

621092

Description:

Predicted to have endopeptidase activity. Predicted to be involved in proteasomal ubiquitin-independent protein catabolic process and proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to localize to cytoplasm; nucleoplasm; and proteasome core complex, beta-subunit complex. Orthologous to human PSMB1 (proteasome 20S subunit beta 1); PARTICIPATES IN ubiquitin/proteasome degradation pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1,3-dinitrobenzene; 17alpha-ethynylestradiol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

macropain subunit C5; multicatalytic endopeptidase complex subunit C5; proteasome (prosome, macropain) subunit, beta type 1; proteasome beta 1 subunit; proteasome component C5; proteasome gamma chain; proteasome subunit beta 1; proteasome subunit beta type-1; proteasome subunit RC5

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):	PSMB1 (proteasome 20S subunit beta 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Psmb1 (proteasome (prosome, macropain) subunit, beta type 1)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Psmb1 (proteasome 20S subunit beta 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PSMB1 (proteasome 20S subunit beta 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PSMB1 (proteasome 20S subunit beta 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Psmb1 (proteasome 20S subunit beta 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PSMB1 (proteasome 20S subunit beta 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	PSMB1 (proteasome 20S subunit beta 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Psmb1 (proteasome 20S subunit beta 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	PSMB1 (proteasome 20S subunit beta 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Psmb1 (proteasome (prosome, macropain) subunit, beta type 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	psmb1 (proteasome subunit beta 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Saccharomyces cerevisiae (baker's yeast):	PRE7	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Prosbeta6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	pbs-6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

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	1	56,442,432 - 56,463,544 (-)	NCBI
Rnor_6.0 Ensembl	1	57,470,632 - 57,489,727 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	57,470,878 - 57,491,359 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	58,399,237 - 58,419,917 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	54,369,775 - 54,388,816 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	54,372,719 - 54,391,761 (-)	NCBI
Celera	1	52,648,620 - 52,666,985 (-)	NCBI		Celera
Cytogenetic Map	1	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Acute Coronary Syndrome (ISO)

amenorrhea (ISO)

osteoarthritis (ISO)

peripheral nervous system disease (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane (EXP,ISO)

1,2-dimethylhydrazine (ISO)

1,3-dinitrobenzene (EXP)

17alpha-ethynylestradiol (EXP,ISO)

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

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

2,4-dibromophenyl 2,4,5-tribromophenyl ether (EXP)

2-hydroxypropanoic acid (ISO)

2-nitrofluorene (EXP)

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

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

4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one (EXP)

5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole (EXP)

6-propyl-2-thiouracil (EXP)

acrylamide (ISO)

aflatoxin B1 (EXP,ISO)

amiodarone (EXP)

ammonium chloride (EXP)

arsenous acid (ISO)

benzbromarone (EXP)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP)

bisphenol F (ISO)

cadmium dichloride (EXP,ISO)

carbon nanotube (ISO)

chloropicrin (ISO)

clofibrate (EXP)

cyclosporin A (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

dicrotophos (ISO)

diethylstilbestrol (EXP)

disodium selenite (ISO)

doxorubicin (ISO)

ethanol (ISO)

finasteride (EXP)

flutamide (EXP)

folic acid (ISO)

genistein (EXP)

hyaluronic acid (EXP)

hydralazine (ISO)

hydrogen peroxide (EXP,ISO)

indometacin (ISO)

L-ethionine (EXP)

leflunomide (EXP)

lithium atom (EXP)

lithium hydride (EXP)

maneb (ISO)

methapyrilene (EXP)

methoxychlor (EXP)

methylparaben (ISO)

N-nitrosodimethylamine (EXP)

nefazodone (EXP)

nimesulide (EXP)

omeprazole (EXP)

paclitaxel (ISO)

paracetamol (ISO)

paraquat (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

phenobarbital (EXP)

PhIP (EXP)

phlorizin (ISO)

piperonyl butoxide (EXP)

pirinixic acid (EXP,ISO)

pregnenolone 16alpha-carbonitrile (EXP)

rac-lactic acid (ISO)

rotenone (ISO)

sodium arsenite (ISO)

sodium fluoride (ISO)

stattic (ISO)

sunitinib (ISO)

theophylline (EXP)

thioacetamide (EXP)

tungsten (ISO)

valdecoxib (EXP)

valproic acid (EXP,ISO)

vincaleukoblastine (ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

proteasomal ubiquitin-independent protein catabolic process (IBA)

proteasome-mediated ubiquitin-dependent protein catabolic process (IBA)

proteolysis involved in cellular protein catabolic process (IEA)

Cellular Component

cytoplasm (IBA,IEA)

nucleoplasm (IEA,ISO)

nucleus (IBA)

proteasome complex (ISO)

proteasome core complex (IBA,IEA,ISO,ISS)

proteasome core complex, beta-subunit complex (ISS)

Molecular Function

endopeptidase activity (IBA)

protein binding (ISO)

threonine-type endopeptidase activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

ubiquitin/proteasome degradation pathway (IEA)

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.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
4.	Pipeline to import KEGG annotations from KEGG into RGD
5.	RGD automated data pipeline
6.	RGD automated import pipeline for gene-chemical interactions
7.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
8.	Tamura T, etal., FEBS Lett 1990 May 7;264(1):91-4.

Additional References at PubMed

PMID:2335242	PMID:16857966	PMID:17323924	PMID:17540904	PMID:19056867	PMID:20458337	PMID:20498273	PMID:21630459	PMID:22793692	PMID:23376485	PMID:31505169

Genomics

Comparative Map Data

Psmb1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	56,442,432 - 56,463,544 (-)	NCBI
Rnor_6.0 Ensembl	1	57,470,632 - 57,489,727 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	57,470,878 - 57,491,359 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	58,399,237 - 58,419,917 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	54,369,775 - 54,388,816 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	54,372,719 - 54,391,761 (-)	NCBI
Celera	1	52,648,620 - 52,666,985 (-)	NCBI		Celera
Cytogenetic Map	1	q12	NCBI

PSMB1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	6	170,535,120 - 170,553,307 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	6	170,535,120 - 170,553,307 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	6	170,844,208 - 170,862,395 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	170,686,134 - 170,704,312 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	6	170,761,840 - 170,780,019	NCBI
Celera	6	171,639,464 - 171,657,679 (-)	NCBI
Cytogenetic Map	6	q27	NCBI
HuRef	6	168,349,261 - 168,367,473 (-)	NCBI		HuRef
CHM1_1	6	171,105,483 - 171,123,692 (-)	NCBI		CHM1_1

Psmb1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	15,695,983 - 15,718,538 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	17	15,695,283 - 15,720,013 (-)	Ensembl
GRCm38	17	15,475,721 - 15,498,276 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	15,475,021 - 15,499,751 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	15,612,685 - 15,635,240 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	17	15,180,922 - 15,203,243 (-)	NCBI			mm8
Celera	17	16,263,619 - 16,283,553 (-)	NCBI		Celera
Cytogenetic Map	17	A2	NCBI
cM Map	17	8.95	NCBI

Psmb1
(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_004955411	3,286,835 - 3,304,931 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955411	3,285,610 - 3,304,210 (+)	NCBI	ChiLan1.0	ChiLan1.0

PSMB1
(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	6	173,781,040 - 173,799,243 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	173,781,040 - 173,799,342 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	6	168,695,047 - 168,713,257 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

PSMB1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	12	72,440,224 - 72,456,304 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	12	72,440,224 - 72,456,284 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	12	72,202,460 - 72,218,544 (-)	NCBI
ROS_Cfam_1.0	12	73,425,690 - 73,441,776 (-)	NCBI
UMICH_Zoey_3.1	12	72,698,433 - 72,714,512 (-)	NCBI
UNSW_CanFamBas_1.0	12	72,520,615 - 72,536,698 (-)	NCBI
UU_Cfam_GSD_1.0	12	72,911,637 - 72,927,722 (-)	NCBI

Psmb1
(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_024404946	151,224,293 - 151,246,522 (+)	NCBI
SpeTri2.0	NW_004937098	67,298 - 80,019 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PSMB1
(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	23,782 - 40,033 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	23,827 - 40,033 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

PSMB1
(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	13	97,682,501 - 97,701,339 (+)	NCBI
ChlSab1.1 Ensembl	13	97,682,369 - 97,701,799 (+)	Ensembl

Psmb1
(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_004624850	6,339,918 - 6,357,925 (-)	NCBI

Position Markers

RH136917

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	57,470,765 - 57,470,974	NCBI	Rnor6.0
Rnor_5.0	1	58,399,124 - 58,399,333	UniSTS	Rnor5.0
RGSC_v3.4	1	54,369,661 - 54,369,870	UniSTS	RGSC3.4
Celera	1	52,648,506 - 52,648,715	UniSTS
RH 3.4 Map	1	672.2	UniSTS
Cytogenetic Map	1	q12	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
738020	Pia8	Pristane induced arthritis QTL 8	4.7		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	1	64407321	Rat
1554320	Bmd1	Bone mineral density QTL 1	12.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	254393	86904217	Rat
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	5655769	122614963	Rat
4889451	Eae29	Experimental allergic encephalomyelitis QTL 29	5.51		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	1	5655772	85706974	Rat
1300167	Hrtrt2	Heart rate QTL 2	4.35		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	11314489	75844121	Rat
2313062	Bmd73	Bone mineral density QTL 73	3.9	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	1	11314489	83657083	Rat
2313065	Bss67	Bone structure and strength QTL 67	3.1	0.0001	tibia area (VT:1000281)	tibia total energy absorbed before break (CMO:0001736)	1	11314489	83657083	Rat
2313069	Bss68	Bone structure and strength QTL 68	2.9	0.0001	tibia size trait (VT:0100001)	tibia total energy absorbed before break (CMO:0001736)	1	11314489	83657083	Rat
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	11314489	83657083	Rat
2313077	Bss69	Bone structure and strength QTL 69	3.5	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	11314489	83657083	Rat
2313092	Bmd72	Bone mineral density QTL 72	2.5	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	11314489	83657083	Rat
2313097	Bss70	Bone structure and strength QTL 70	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	11314489	83657083	Rat
631508	Sald1	Serum aldosterone level QTL 1	3.7		blood aldosterone amount (VT:0005346)	serum aldosterone level (CMO:0000487)	1	12493439	57493439	Rat
2302038	Pia31	Pristane induced arthritis QTL 31	5.5	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)	1	13629251	58629251	Rat
634353	Rends2	Renal damage susceptibility QTL 2		0.05	kidney blood vessel morphology trait (VT:0000530)	organ lesion measurement (CMO:0000677)	1	20341560	58000154	Rat
724520	Bp145	Blood pressure QTL 145	2.1	0.0024	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	21079305	66079305	Rat
1357400	Bw62	Body weight QTL62	4.05		inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	1	23406428	68406428	Rat
631495	Bp96	Blood pressure QTL 96	4.52		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	23406428	108057505	Rat
1358192	Ept13	Estrogen-induced pituitary tumorigenesis QTL 13	3.4		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	24297799	78748000	Rat
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	25951907	130917265	Rat
1331785	Rf27	Renal function QTL 27	4.643		urine sodium amount (VT:0006274)	urine sodium level (CMO:0000129)	1	31489454	79689689	Rat
1354643	Foco2	Food consumption QTL 2	7.17	0.0001	eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	1	34449112	79449112	Rat
1354599	Bw29	Body weight QTL 29	3.46	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	34449112	79449112	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34993530	173445086	Rat
1300172	Bp172	Blood pressure QTL 172	3.56		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	35377508	94364229	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	35377692	217372257	Rat
9589820	Insglur3	Insulin/glucose ratio QTL 3	10.75	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	1	35854167	80854167	Rat
8552900	Pigfal1	Plasma insulin-like growth factor 1 level QTL 1	7.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	35854167	80854167	Rat
8552948	Pigfal11	Plasma insulin-like growth factor 1 level QTL 11	4.7		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	35854167	80854167	Rat
1331732	Srn4	Serum renin concentration QTL 4	4.467		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	1	36033165	79689689	Rat
1331792	Rf29	Renal function QTL 29	4.589		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	1	36033165	79689689	Rat
2302059	Pia36	Pristane induced arthritis QTL 36	3.8	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G1 level (CMO:0002115)	1	41907249	86907249	Rat
2313051	Bss57	Bone structure and strength QTL 57	3.7	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	43579208	126240667	Rat
2313059	Bss55	Bone structure and strength QTL 55	3.2	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	1	43579208	126240667	Rat
2313072	Bss53	Bone structure and strength QTL 53	4.3	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	43579208	126240667	Rat
2313078	Bss54	Bone structure and strength QTL 54	3.5	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	1	43579208	126240667	Rat
2313094	Bss58	Bone structure and strength QTL 58	3.7	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	43579208	126240667	Rat
2313098	Bmd70	Bone mineral density QTL 70	3.6	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	1	43579208	126240667	Rat
2313099	Bss56	Bone structure and strength QTL 56	2.4	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	1	43579208	126240667	Rat
1331778	Rf28	Renal function QTL 28	4.66		urine potassium amount (VT:0010539)	urine potassium excretion rate (CMO:0000761)	1	46113461	79689689	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	49147799	156446783	Rat
4889962	Bss94	Bone structure and strength QTL 94	3.8		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	49547328	83657083	Rat
1578649	Bmd8	Bone mineral density QTL 8	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	49578577	94578577	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	49578577	169852184	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49578693	217054291	Rat
1578756	Iddm22	Insulin dependent diabetes mellitus QTL 22	2.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	50522714	57861469	Rat
6903308	Scl36	Serum cholesterol QTL 36	2	0.0125	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	50522714	94225616	Rat
4889919	Bss86	Bone structure and strength QTL 86	4.1		tibia area (VT:1000281)	tibia midshaft total cross-sectional area (CMO:0001715)	1	53851348	83657083	Rat
4889929	Bss87	Bone structure and strength QTL 87	6.7		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	53851348	83657083	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	55
Count of miRNA genes:	50
Interacting mature miRNAs:	53
Transcripts:	ENSRNOT00000002037
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	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_053590	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006227981	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039093141	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039093143	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC121701	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC058455	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474033	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ211516	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ214442	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ214574	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ214726	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ218426	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220680	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222870	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225328	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ229756	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230094	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000023	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X52783	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000002037 ⟹ ENSRNOP00000002037

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	57,470,632 - 57,489,727 (-)	Ensembl

RefSeq Acc Id:

NM_053590 ⟹ NP_446042

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	56,442,681 - 56,461,680 (-)	NCBI
Rnor_6.0	1	57,470,879 - 57,489,705 (-)	NCBI
Rnor_5.0	1	58,399,237 - 58,419,917 (-)	NCBI
RGSC_v3.4	1	54,369,775 - 54,388,816 (-)	RGD
Celera	1	52,648,620 - 52,666,985 (-)	RGD

Sequence:

show sequence

CAGCAGGAGTTAGGCGCGATGCTTTCCACTGCCGCTTACCGGGACCCGGACCGAGAGCTGGTAA
TGGGGCCTCAGGGCTCCGCCGGCCCTGTGCAGATGCGTTTCTCGCCTTATGCCTTCAACGGAGG
TACTGTATTGGCAATTGCTGGAGAAGATTTTTCCATCGTTGCTTCAGACACTCGGTTGAGTGAA
GGGTTTTCAATTCATACCCGAGATAGCCCCAAATGTTACAAACTAACAGACAAAACAGTAATTG
GCTGCAGTGGCTTTCATGGAGATTGTCTCACCTTGACAAAGATTATTGAAGCAAGATTAAAGAT
GTACAAGCATTCCAATAACAAGGCCATGACAACAGGGGCGATTGCTGCAATGCTGTCTACCATC
CTGTACTCACGGCGTTTCTTCCCTTACTATGTCTACAACATCATTGAGGGACTTGATGAAGAAG
GAAAGGGAGCCGTGTACAGCTTTGACCCAGTAGGCTCTTACCAGAGAGACTCTTTCAAAGCCGG
AGGCTCAGCAAGTGCCATGCTGCAGCCGCTGCTCGACAACCAGGTTGGCTTCAAAAATATGCAG
AATGTGGAGCATGTCCCCCTGACTCTGGACAGAGCCATGAGGCTGGTGAAAGACGTCTTCATTT
CTGCAGCCGAGAGGGATGTGTACACTGGAGACGCCCTCAGGATCTGCATCGTGACCAAAGAGGG
CATCAGGGAGGAGACTGTTCCCCTTCGGAAAGACTGATGTGGGGCCAGGGTTTGGAGCTGTGGC
ACGTTTGTTTTATTAAAAAGAAATGTAAAGG

hide sequence

RefSeq Acc Id:

XM_006227981 ⟹ XP_006228043

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	56,442,432 - 56,463,329 (-)	NCBI
Rnor_6.0	1	57,470,878 - 57,491,359 (-)	NCBI
Rnor_5.0	1	58,399,237 - 58,419,917 (-)	NCBI

Sequence:

show sequence

AGTTGCGCTCTCGACTGGAGCCCGGCTTGTTGTGCTTAAACTGAAACCACAGAAGACTGGGGAA
TTAAGAAAACTTAACAAAGGCCTGACAAGAGACAATTTATGGTCTCTCGGAATCGGCAGATCCA
GGTTGTGCGGTAGTTGGATGCAGGCGTGGACCTCCAAGAGCAGCGACGAGTACAGGCTAGAGGA
GCCCAAGGGGCGGGGCGAGGGAGGCGGAAGTGGACCGGTCCCAGCGGCCATTTTGCCGTGAGAC
AGCAGGAGTTAGGCGCGATGCTTTCCACTGCCGCTTACCGGGACCCGGACCGAGAGCTGGTAAT
GGGGCCTCAGGGCTCCGCCGGCCCTGTGCAGATGCGTTTCTCGCCTTATGCCTTCAACGGAGGT
ACTGTATTGGCAATTGCTGGAGAAGATTTTTCCATCGTTGCTTCAGACACTCGGTTGAGTGAAG
GGTTTTCAATTCATACCCGAGATAGCCCCAAATGTTACAAACTAACAGACAAAACAGTAATTGG
CTGCAGTGGCTTTCATGGAGATTGTCTCACCTTGACAAAGATTATTGAAGCAAGATTAAAGATG
TACAAGCATTCCAATAACAAGGCCATGACAACAGGGGCGATTGCTGCAATGCTGTCTACCATCC
TGTACTCACGGCGTTTCTTCCCTTACTATGTCTACAACATCATTGGAGGACTTGATGAAGAAGG
AAAGGGAGCCGTGTACAGCTTTGACCCAGTAGGCTCTTACCAGAGAGACTCTTTCAAAGCCGGA
GGCTCAGCAAGTGCCATGCTGCAGCCGCTGCTCGACAACCAGGTTGGCTTCAAAAATATGCAGA
ATGTGGAGCATGTCCCCCTGACTCTGGACAGAGCCATGAGGCTGGTGAAAGACGTCTTCATTTC
TGCAGCCGAGAGGGATGTGTACACTGGAGACGCCCTCAGGATCTGCATCGTGACCAAAGAGGGC
ATCAGGGAGGAGACTGTTCCCCTTCGGAAAGACTGATGTGGGGCCAGGGTTTGGAGCTGTGGCA
CGTTTGTTTTATTAAAAAGAAATGTAAAGGA

hide sequence

RefSeq Acc Id:

XM_039093141 ⟹ XP_038949069

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	56,442,432 - 56,463,544 (-)	NCBI

RefSeq Acc Id:

XM_039093143 ⟹ XP_038949071

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	56,442,432 - 56,459,918 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_446042	(Get FASTA)	NCBI Sequence Viewer
	XP_006228043	(Get FASTA)	NCBI Sequence Viewer
	XP_038949069	(Get FASTA)	NCBI Sequence Viewer
	XP_038949071	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH58455	(Get FASTA)	NCBI Sequence Viewer
	CAA36987	(Get FASTA)	NCBI Sequence Viewer
	EDL99819	(Get FASTA)	NCBI Sequence Viewer
	EDL99820	(Get FASTA)	NCBI Sequence Viewer
	EDL99821	(Get FASTA)	NCBI Sequence Viewer
	P18421	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_446042 ⟸ NM_053590
- Peptide Label:	precursor
- UniProtKB:	P18421 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MLSTAAYRDPDRELVMGPQGSAGPVQMRFSPYAFNGGTVLAIAGEDFSIVASDTRLSEGFSIHT RDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRF FPYYVYNIIEGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVP LTLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEGIREETVPLRKD hide sequence

RefSeq Acc Id:	XP_006228043 ⟸ XM_006227981
- Peptide Label:	isoform X1
- UniProtKB:	Q6PDW4 (UniProtKB/TrEMBL)
- Sequence:	show sequence MLSTAAYRDPDRELVMGPQGSAGPVQMRFSPYAFNGGTVLAIAGEDFSIVASDTRLSEGFSIHT RDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRF FPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVP LTLDRAMRLVKDVFISAAERDVYTGDALRICIVTKEGIREETVPLRKD hide sequence

RefSeq Acc Id:

ENSRNOP00000002037 ⟸ ENSRNOT00000002037

RefSeq Acc Id:	XP_038949069 ⟸ XM_039093141
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038949071 ⟸ XM_039093143
- Peptide Label:	isoform X3

Transcriptome

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

Promoters

RGD ID:

13689645

Promoter ID:

EPDNEW_R169

Type:

initiation region

Name:

Psmb1_1

Description:

proteasome subunit beta 1

SO ACC ID:

SO:0000170

Source:

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

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	57,489,720 - 57,489,780	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

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 (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/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 (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)

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

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

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/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

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 (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

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

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

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

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

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 (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

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

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 (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 (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

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 (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 (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 (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:621092	AgrOrtholog
Ensembl Genes	ENSRNOG00000001488	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000002037	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000002037	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.60.20.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:6922317	IMAGE-MGC_LOAD
InterPro	Ntn_hydrolases_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Proteasome_beta1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Proteasome_bsu_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Proteasome_sua/b	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Proteasome_suB-type	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:94198	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:72741	IMAGE-MGC_LOAD
NCBI Gene	94198	ENTREZGENE
PANTHER	PTHR11599:SF59	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Proteasome	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Psmb1	PhenoGen
PROSITE	PROTEASOME_BETA_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PROTEASOME_BETA_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF56235	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	P18421	ENTREZGENE, UniProtKB/Swiss-Prot
	Q6PDW4	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2019-09-13	Psmb1	proteasome 20S subunit beta 1	Psmb1	proteasome subunit beta 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2015-08-19	Psmb1	proteasome subunit beta 1	Psmb1	proteasome (prosome, macropain) subunit, beta type 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-20	Psmb1	proteasome (prosome, macropain) subunit, beta type 1			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Psmb1	proteasome (prosome, macropain) subunit, beta type 1			Symbol and Name status set to provisional	70820	PROVISIONAL

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

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

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

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

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)