Psmb6 (proteasome 20S subunit beta 6)

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Gene: Psmb6 (proteasome 20S subunit beta 6) Rattus norvegicus

Analyze

Symbol:

Psmb6

Name:

proteasome 20S subunit beta 6

RGD ID:

61881

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 cytosol; nucleoplasm; and proteasome core complex, beta-subunit complex. Orthologous to human PSMB6 (proteasome 20S subunit beta 6); PARTICIPATES IN ubiquitin/proteasome degradation pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

macropain delta chain; multicatalytic endopeptidase complex delta chain; proteasome (prosome, macropain) subunit, beta type 6; proteasome beta 6 subunit; proteasome chain 5; proteasome delta chain; proteasome subunit beta 6; proteasome subunit beta type 6-like; proteasome subunit beta type-6; proteasome subunit Y; Psmb6l

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

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	10	55,239,274 - 55,241,581 (+)	NCBI
Rnor_6.0 Ensembl	10	57,131,386 - 57,133,637 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	57,131,339 - 57,133,685 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	56,888,972 - 56,891,279 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	57,370,397 - 57,372,704 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	57,384,019 - 57,386,327 (+)	NCBI
Celera	10	54,385,536 - 54,387,843 (+)	NCBI		Celera
Cytogenetic Map	10	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(S)-nicotine (ISO)

1,2,4-trimethylbenzene (EXP)

1,3-dinitrobenzene (EXP)

17beta-estradiol (ISO)

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

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

2-hydroxypropanoic acid (ISO)

2-naphthylamine (ISO)

3-methylcholanthrene (ISO)

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

aflatoxin B1 (ISO)

ammonium chloride (EXP)

arsane (ISO)

arsenic atom (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

bis(2-chloroethyl) sulfide (EXP)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP)

chloropicrin (ISO)

cisplatin (ISO)

clofibrate (EXP)

cobalt dichloride (ISO)

cyclosporin A (ISO)

diarsenic trioxide (ISO)

dibenzo[a,l]pyrene (ISO)

dibutyl phthalate (ISO)

dichlorine (EXP)

doxorubicin (ISO)

epoxomicin (ISO)

finasteride (EXP)

flavonoids (EXP)

flutamide (EXP)

heparin (ISO)

hydralazine (ISO)

isobutanol (ISO)

L-ascorbic acid (ISO)

leflunomide (EXP)

microcystin RR (ISO)

N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal (ISO)

nefazodone (EXP)

nicotine (ISO)

nimesulide (EXP)

O-acetyl-L-carnitine (EXP)

ochratoxin A (EXP)

ouabain (ISO)

ozone (EXP)

paclitaxel (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

phenobarbital (EXP)

PhIP (EXP)

piperonyl butoxide (EXP)

pirinixic acid (ISO)

pregnenolone 16alpha-carbonitrile (EXP)

quercitrin (ISO)

rac-lactic acid (ISO)

rotenone (ISO)

stattic (ISO)

sulforaphane (ISO)

tetrachloromethane (ISO)

tungsten (ISO)

tunicamycin (ISO)

valdecoxib (EXP)

valproic acid (EXP,ISO)

vinclozolin (EXP)

vitamin E (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)

Cellular Component

cytoplasm (IBA)

cytosol (ISO)

nucleoplasm (ISO)

nucleus (IBA)

proteasome complex (ISO)

proteasome core complex (IBA,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.	Puente XS and Lopez-Otin C, Genome Res 2004 Apr;14(4):609-22.
6.	RGD automated data pipeline
7.	RGD automated import pipeline for gene-chemical interactions
8.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
9.	Tamura T, etal., J Biochem (Tokyo) 1992 Oct;112(4):530-4.

Additional References at PubMed

PMID:2335214	PMID:9688553	PMID:15057822	PMID:15489334	PMID:16857966	PMID:17323924	PMID:19056867	PMID:20458337	PMID:20498273	PMID:21630459	PMID:22793692	PMID:23376485
PMID:23844134	PMID:25468996	PMID:30361391

Genomics

Comparative Map Data

Psmb6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	10	55,239,274 - 55,241,581 (+)	NCBI
Rnor_6.0 Ensembl	10	57,131,386 - 57,133,637 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	10	57,131,339 - 57,133,685 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	10	56,888,972 - 56,891,279 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	57,370,397 - 57,372,704 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	10	57,384,019 - 57,386,327 (+)	NCBI
Celera	10	54,385,536 - 54,387,843 (+)	NCBI		Celera
Cytogenetic Map	10	q24	NCBI

PSMB6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	17	4,796,144 - 4,798,502 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	17	4,796,164 - 4,798,495 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	17	4,699,459 - 4,701,790 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	4,646,415 - 4,648,748 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	17	4,646,414 - 4,648,746	NCBI
Celera	17	4,714,866 - 4,717,199 (+)	NCBI
Cytogenetic Map	17	p13.2	NCBI
HuRef	17	4,587,894 - 4,590,253 (+)	NCBI		HuRef
CHM1_1	17	4,708,411 - 4,710,770 (+)	NCBI		CHM1_1

Psmb6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	70,416,116 - 70,418,684 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	11	70,416,193 - 70,418,684 (+)	Ensembl
GRCm38	11	70,525,324 - 70,527,858 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	70,525,367 - 70,527,858 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	70,338,859 - 70,341,360 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	11	70,341,595 - 70,343,844 (+)	NCBI			mm8
Celera	11	78,073,676 - 78,076,176 (+)	NCBI		Celera
Cytogenetic Map	11	B3	NCBI
cM Map	11	42.99	NCBI

Psmb6
(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_004955467	10,220,285 - 10,222,659 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955467	10,220,435 - 10,222,470 (+)	NCBI	ChiLan1.0	ChiLan1.0

PSMB6
(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	17	4,832,225 - 4,834,549 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	4,831,981 - 4,834,549 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	17	4,842,978 - 4,845,321 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

PSMB6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	5	31,776,286 - 31,778,789 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	5	31,776,293 - 31,778,682 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	5	31,915,750 - 31,918,255 (-)	NCBI
ROS_Cfam_1.0	5	31,881,502 - 31,884,007 (-)	NCBI
UMICH_Zoey_3.1	5	31,847,683 - 31,850,185 (-)	NCBI
UNSW_CanFamBas_1.0	5	31,807,355 - 31,809,858 (-)	NCBI
UU_Cfam_GSD_1.0	5	31,983,746 - 31,986,251 (-)	NCBI

Psmb6
(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_024405602	53,005,091 - 53,007,195 (+)	NCBI
SpeTri2.0	NW_004936677	2,893,780 - 2,895,870 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PSMB6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	12	52,096,009 - 52,098,164 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	12	54,317,056 - 54,319,039 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3
Pig Cytomap	12	q13	NCBI

PSMB6
(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	16	4,272,009 - 4,274,451 (+)	NCBI
ChlSab1.1 Ensembl	16	4,272,081 - 4,274,555 (+)	Ensembl

Psmb6
(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_004624786	8,679,442 - 8,681,547 (+)	NCBI

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
631554	Bp133	Blood pressure QTL 133		0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	764421	66221621	Rat
2298544	Neuinf9	Neuroinflammation QTL 9	4.6		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	10	5877536	64401490	Rat
8662860	Vetf10	Vascular elastic tissue fragility QTL 10			artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	10	6229095	75983805	Rat
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6429075	99492409	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9841807	108540162	Rat
9590310	Scort19	Serum corticosterone level QTL 19	6.3	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	12639513	57639513	Rat
9590268	Scort13	Serum corticosterone level QTL 13	3.26	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	12639513	57639513	Rat
9589136	Insul27	Insulin level QTL 27	10.46	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	10	12639513	57639513	Rat
2301967	Cm73	Cardiac mass QTL 73	4.55		heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	10	14827894	92423564	Rat
631268	Cia21	Collagen induced arthritis QTL 21	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	14827894	107857673	Rat
2316949	Gluco60	Glucose level QTL 60	3.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	10	14827894	110992275	Rat
1354587	Kidm21	Kidney mass QTL 21	3.3		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	10	15375474	62469074	Rat
631564	Apr3	Acute phase response QTL 3	3.9		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	10	16468736	61468736	Rat
6893350	Bw99	Body weight QTL 99	0.87	0.16	body mass (VT:0001259)	body weight (CMO:0000012)	1	17121542	62121542	Rat
6893352	Bw100	Body weight QTL 100	0.33	0.6	body mass (VT:0001259)	body weight (CMO:0000012)	1	17121542	62121542	Rat
1598852	Anxrr19	Anxiety related response QTL 19	5.07		body movement coordination trait (VT:0005424)	number of rearing movements in an experimental apparatus (CMO:0001752)	10	19402814	64402814	Rat
1554317	Bmd4	Bone mineral density QTL 4	9.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	20170031	102897474	Rat
70223	Bp57	Blood pressure QTL 57	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	21523906	83549467	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	21523906	90312401	Rat
70188	BpQTLcluster1	Blood pressure QTL cluster 1	4.864		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	21523906	90312401	Rat
70198	BpQTLcluster9	Blood pressure QTL cluster 9	2.94		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	21523906	90312401	Rat
1581497	Esta1	Estrogen-induced thymic atrophy QTL 1			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	21707766	64648311	Rat
724556	Pur2	Proteinuria QTL 2	5.5		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	10	22901497	93886300	Rat
1331762	Rf40	Renal function QTL 40	3.873		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	10	23861015	66539843	Rat
1331791	Cm31	Cardiac mass QTL 31	3.84606		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	10	23861015	112626471	Rat
631267	Cia20	Collagen induced arthritis QTL 20	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61325	Aia5	Adjuvant induced arthritis QTL 5		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
61354	Pia10	Pristane induced arthritis QTL 10		0.01	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	24483076	107857673	Rat
70224	Eae3	Experimental allergic encephalomyelitis QTL 3	4.1		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	10	27237530	64648311	Rat
1298069	Bp168	Blood pressure QTL 168	5.5		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	10	27237530	101482600	Rat
631542	Bp82	Blood pressure QTL 82	6.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	27237530	102427718	Rat
2300171	Bmd58	Bone mineral density QTL 58	4.9	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	10	28789280	73789280	Rat
2292441	Bp308	Blood pressure QTL 308			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
10402859	Bp381	Blood pressure QTL 381		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30099909	75099909	Rat
724527	Bp148	Blood pressure QTL 148		0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	10	30983805	75983805	Rat
1576311	Pia26	Pristane induced arthritis QTL 26			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	31919397	78343192	Rat
1578779	Tcas10	Tongue tumor susceptibility QTL 10	3.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	10	33179030	78179030	Rat
631557	Bp136	Blood pressure QTL 136		0.003	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	33343192	78343192	Rat
1576319	Cia29	Collagen induced arthritis QTL 29			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	35139424	80139424	Rat
6893342	Cm78	Cardiac mass QTL 78	0.1	0.88	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	10	36185929	82675365	Rat
631552	Vetf2	Vascular elastic tissue fragility QTL 2	4.5	0.0002	aorta elastic tissue integrity trait (VT:0010556)	artery internal elastic lamina non-tumorous lesion count (CMO:0001913)	10	36185929	95845311	Rat
1358897	Stresp6	Stress response QTL 6	4.17	0.022	blood norepinephrine amount (VT:0005663)	plasma norepinephrine level (CMO:0001010)	10	36584373	66539843	Rat
61441	Btemp1	Thermal response to stress QTL 1	4		body temperature trait (VT:0005535)	core body temperature (CMO:0001036)	10	36584560	66015527	Rat
2317042	Aia20	Adjuvant induced arthritis QTL 20	3.38		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	10	40514044	85514044	Rat
2317043	Aia7	Adjuvant induced arthritis QTL 7	3.82		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	10	40514044	85514044	Rat
1576308	Schws1	Schwannoma susceptibility QTL 1		0.0041	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	10	41260363	106105607	Rat
631269	Cia22	Collagen induced arthritis QTL 22	8.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
631270	Cia23	Collagen induced arthritis QTL 23	3.9		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	41260363	107857673	Rat
8552805	Bw145	Body weight QTL 145	2.2		body mass (VT:0001259)	change in body weight to body weight ratio (CMO:0002216)	10	43188659	81042642	Rat
1298078	Stresp5	Stress response QTL 5	2.99	0.00025	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	43289657	108540162	Rat
61463	Bp12	Blood pressure QTL 12	6.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	43704955	88704955	Rat
2300218	Hpcl2	Hepatic cholesterol level QTL 2			liver cholesterol amount (VT:0010498)	liver cholesterol level (CMO:0001597)	10	46593021	98939209	Rat
9589030	Epfw9	Epididymal fat weight QTL 9	19.24	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	10	46848346	91848346	Rat
7411614	Foco18	Food consumption QTL 18		0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	10	46848346	91848346	Rat
8694173	Bw149	Body weight QTL 149	4.38	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	10	46848346	91848346	Rat
631547	Bp87	Blood pressure QTL 87	4.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	50638337	95638337	Rat
2293652	Bmd22	Bone mineral density QTL 22	4.9	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	10	51289203	84596393	Rat
2293669	Bmd33	Bone mineral density QTL 33	4.5	0.0001	femur strength trait (VT:0010010)	femoral neck polar moment of inertia (CMO:0001670)	10	51289203	84596393	Rat
2293679	Bmd30	Bone mineral density QTL 30	3.5	0.0001	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	10	51289203	84596393	Rat
2293705	Bmd25	Bone mineral density QTL 25	7.1	0.0001	femur mineral mass (VT:0010011)	cortical volumetric bone mineral density (CMO:0001730)	10	51289203	84596393	Rat
7207811	Bmd90	Bone mineral density QTL 90	5.2		femur size trait (VT:1000369)	femoral neck cross-sectional area (CMO:0001697)	10	51289203	84596393	Rat
1549846	Scl47	Serum cholesterol level QTL 47	3.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	10	53104718	98104718	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	53621375	112626471	Rat
61387	Bp1	Blood pressure QTL 1	5.1		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	10	53621375	112626471	Rat
631530	Tls3	T-lymphoma susceptibility QTL 3	0	0.0001	thymus integrity trait (VT:0010555)	percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)	10	53625815	98939209	Rat
631535	Cm51	Cardiac mass QTL 51	3		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	10	53637485	94807701	Rat
1578762	Toxo1	Toxoplasma gondii resistance QTL 1			brain integrity trait (VT:0010579)	percentage of study population displaying Toxoplasma gondii brain cysts at a point in time (CMO:0002028)	10	54057616	61300905	Rat
1359017	Hrtrt21	Heart rate QTL 21	2.4		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	10	55224855	100224855	Rat
1354585	Eae18a	Experimental allergic encephalomyelitis QTL 18a	7.5	0.0004	nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	10	55678976	60404791	Rat
2306787	Ean3	Experimental allergic neuritis QTL 3	3.1		nervous system integrity trait (VT:0010566)	body weight loss (CMO:0001399)	10	55678976	69385767	Rat
70171	Cari1	Carrageenan-induced inflammation QTL 1	4.9	0.0005	hypodermis integrity trait (VT:0010550)	inflammatory exudate volume (CMO:0001429)	10	55678976	112626471	Rat
70164	Bw21	Body weight QTL 21	4.36	0.00005	body mass (VT:0001259)	body weight (CMO:0000012)	10	55679084	102427604	Rat
1354608	Cm33	Cardiac mass QTL 33	2.8		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	10	56698730	101698730	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	80
Count of miRNA genes:	67
Interacting mature miRNAs:	71
Transcripts:	ENSRNOT00000026507
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_057099	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008767811	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC058451	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D10754	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ209811	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ217385	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ224639	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000220	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000026507 ⟹ ENSRNOP00000026507

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	10	57,131,386 - 57,133,637 (+)	Ensembl

RefSeq Acc Id:

NM_057099 ⟹ NP_476440

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	10	55,239,274 - 55,241,581 (+)	NCBI
Rnor_6.0	10	57,131,378 - 57,133,685 (+)	NCBI
Rnor_5.0	10	56,888,972 - 56,891,279 (+)	NCBI
RGSC_v3.4	10	57,370,397 - 57,372,704 (+)	RGD
Celera	10	54,385,536 - 54,387,843 (+)	RGD

Sequence:

show sequence

AGAGGAAGATGGCGGCCGCCTTAGCTGTTCGTGGAGCCGTCTCTGCACCGGCCTTTGGGCCGGA
GGCGCTCACTCCAGACTGGGAAAACCGAGAAGTCTCCACAGGGACCACGATCATGGCTGTGCAA
TTTGACGGGGGCGTGGTTCTAGGAGCAGACTCCAGAACAACCACTGGGTCGTACATCGCCAATC
GAGTGACTGACAAGCTGACCCCTATCCACGATCACATCTTCTGCTGCCGCTCAGGCTCGGCAGC
TGATACCCAAGCAGTAGCTGATGCTGTCACGTACCAGCTTGGTTTCCACAGTATTGAGCTGAAC
GAGCCTCCACTAGTGCACACAGCTGCCAGTCTCTTTAAGGAGATGTGTTACCGCTACAGAGAAG
ATCTGATGGCAGGAATCATCATCGCAGGCTGGGACCCTCAAGAAGGAGGGCAGGTGTACTCTGT
TCCCATGGGAGGTATGATGGTAAGACAGTCCTTTGCCATCGGAGGCTCCGGGAGCTCATATATC
TATGGCTATGTTGATGCTACCTATCGGGAAGGCATGACCAAGGATGAATGTCTGCAATTCACTG
CCAATGCTCTTGCTTTGGCTATGGAACGGGATGGCTCCAGTGGAGGAGTGATCCGCTTGGCAGC
CATTCAACAGTCGGGGGTAGAGCGGCAGGTGCTTTTGGGAGACCAGATCCCCAAGGTCACCATC
TCCACTTTGCCACCTCCCTGAAGCCTAGGATTCCCATCCCGACGCACAAGCTAATAAACAGATT
GTCAATGAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_008767811 ⟹ XP_008766033

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	57,131,339 - 57,133,539 (+)	NCBI

Sequence:

show sequence

CGGAGCGCTTTACGACCGTTGCTTTGTGGCAGCTGTAGAAGAGGAAGATGGCGGCCGCCTTAGC
TGTTCGTGGAGCCGTCTCTGCACCGGCCTTTGGGCCGGAGGCGCTCACTCCAGACTGGGAAAAC
CGAGAAGTCTCCACAGGGACCACGATCATGGCTGTGCAATTTGACGGGGGCGTGGTTCTAGGAG
CAGACTCCAGAACAACCACTGGGTCGTACATCGCCAATCGAGTGACTGACAAGCTGACCCCTAT
CCACGATCACATCTTCTGCTGCCGCTCAGGCTCGGCAGCTGATACCCAAGCAGTAGCTGATGCT
GTCACGTACCAGCTTGGTTTCCACAGTATTGAGCTGAACGAGCCTCCACTAGTGCACACAGCCG
CCAGTCTCTTTAAGGAGATGTGTTACCGCTACAGAGAAGATCTGATGGCAGGAATCATCATCGC
AGGCTGGGACCCTCAAGAAGGAGGGCAGGTGTACTCTGTTCCCATGGGAGGTATGATGGTAAGA
CAGTCCTTTGCCATCGGAGGCTCCGGGAGCTCATATATCTATGGCTATGTTGATGCTACCTATC
GGGAAGGCATGACCAAGGATGAATGTCTGCAATTCACTGCCAATGTCTCCCTGTTTTCTCTACA
GCTCTTGCTTTGGCTATGGAACGGGATGGCTCCAGTGGAGGAGTGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_476440	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH58451	(Get FASTA)	NCBI Sequence Viewer
	BAA01586	(Get FASTA)	NCBI Sequence Viewer
	EDM05016	(Get FASTA)	NCBI Sequence Viewer
	P28073	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_476440 ⟸ NM_057099

- UniProtKB:

P28073 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MAAALAVRGAVSAPAFGPEALTPDWENREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIANRVT
DKLTPIHDHIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLM
AGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKDECLQFTANA
LALAMERDGSSGGVIRLAAIQQSGVERQVLLGDQIPKVTISTLPPP

hide sequence

RefSeq Acc Id:

XP_008766033 ⟸ XM_008767811

- Peptide Label:

isoform X1

- Sequence:

show sequence

MAAALAVRGAVSAPAFGPEALTPDWENREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIANRVT
DKLTPIHDHIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLM
AGIIIAGWDPQEGGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKDECLQFTANV
SLFSLQLLLWLWNGMAPVEE

hide sequence

RefSeq Acc Id:

ENSRNOP00000026507 ⟸ ENSRNOT00000026507

Transcriptome

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

Promoters

RGD ID:

13697362

Promoter ID:

EPDNEW_R7886

Type:

multiple initiation site

Name:

Psmb6_1

Description:

proteasome subunit beta 6

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	10	57,131,373 - 57,131,433	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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
10	56891176	56891177	T	G	snv	FHH/EurMcwi (MCW), ACI/EurMcwi (MCW)

Assembly: RGSC_v3.4

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
10	57372601	57372602	T	G	snv	FHH/EurMcwi (MCW), ACI/EurMcwi (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:61881	AgrOrtholog
Ensembl Genes	ENSRNOG00000019551	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000026507	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000026507	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	3.60.20.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:6891542	IMAGE-MGC_LOAD
InterPro	Ntn_hydrolases_N	UniProtKB/Swiss-Prot
	Pept_T1A_subB	UniProtKB/Swiss-Prot
	Proteasome_beta6	UniProtKB/Swiss-Prot
	Proteasome_bsu_CS	UniProtKB/Swiss-Prot
	Proteasome_sua/b	UniProtKB/Swiss-Prot
	Proteasome_suB-type	UniProtKB/Swiss-Prot
KEGG Report	rno:100360846	UniProtKB/Swiss-Prot
	rno:29666	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:72726	IMAGE-MGC_LOAD
NCBI Gene	29666	ENTREZGENE
PANTHER	PTHR11599:SF46	UniProtKB/Swiss-Prot
Pfam	Proteasome	UniProtKB/Swiss-Prot
PhenoGen	Psmb6	PhenoGen
PRINTS	PROTEASOME	UniProtKB/Swiss-Prot
PROSITE	PROTEASOME_BETA_1	UniProtKB/Swiss-Prot
	PROTEASOME_BETA_2	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF56235	UniProtKB/Swiss-Prot
UniProt	P28073	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	Q6IE68	UniProtKB/Swiss-Prot
	Q6PDW5	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2019-09-13	Psmb6	proteasome 20S subunit beta 6	Psmb6	proteasome subunit beta 6	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2015-08-19	Psmb6	proteasome subunit beta 6	Psmb6	proteasome (prosome, macropain) subunit, beta type 6	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-06-10	Psmb6	proteasome (prosome, macropain) subunit, beta type 6			Name updated	70584	APPROVED

RGD Curation Notes

Note Type	Note	Reference

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

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

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

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

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Imported Annotations - KEGG (archival)