Psmb9 (proteasome 20S subunit beta 9)

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Gene: Psmb9 (proteasome 20S subunit beta 9) Rattus norvegicus

Analyze

Symbol:

Psmb9

Name:

proteasome 20S subunit beta 9

RGD ID:

3427

Description:

Exhibits proteasome binding activity. Involved in several processes, including cellular response to electrical stimulus; hematopoietic or lymphoid organ development; and response to benzene. Localizes to cytosol and proteasome complex. Biomarker of breast carcinoma and peptic esophagitis. Human ortholog(s) of this gene implicated in autoimmune disease (multiple); lymphoma; and renal cell carcinoma. Orthologous to human PSMB9 (proteasome 20S subunit beta 9); PARTICIPATES IN ubiquitin/proteasome degradation pathway; INTERACTS WITH (+)-schisandrin B; 1,3-dinitrobenzene; 1-naphthyl isothiocyanate.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

large multifunctional protease 2; Lmp2; low molecular mass polypeptide 2; low molecular mass protein 2; macropain chain 7; multicatalytic endopeptidase complex chain 7; proteasome (prosome, macropain) subunit, beta type 9 (large multifunctional peptidase 2); proteasome (prosome, macropain) subunit, beta type, 9; proteasome chain 7; proteasome subunit beta 9; proteasome subunit beta type-9; proteasome subunit beta-1i; proteosome (prosome macropain) subunit beta type 9 (large multifunctional protease 2); proteosome (prosome, macropain) subunit, beta type 9; really interesting new gene 12 protein; RING12 protein

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	20	4,667,044 - 4,672,512 (+)	NCBI
Rnor_6.0 Ensembl	20	3,973,420 - 3,978,845 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	20	3,973,424 - 3,978,845 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	20	6,052,972 - 6,058,393 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	4,801,187 - 4,806,608 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	20	4,801,449 - 4,806,835 (+)	NCBI
Celera	20	6,268,113 - 6,273,528 (+)	NCBI		Celera
RH 3.4 Map	20	58.54	RGD
Cytogenetic Map	20	p12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

acrodermatitis (ISO)

adult respiratory distress syndrome (ISO)

ankylosing spondylitis (ISO)

autoimmune thyroiditis (ISO)

breast carcinoma (IEP)

colorectal carcinoma (ISO)

esophagus squamous cell carcinoma (ISO)

Experimental Diabetes Mellitus (IEP)

Experimental Liver Cirrhosis (ISO)

Hashimoto Disease (ISO)

Huntington's disease (ISO)

hypothyroidism (ISO)

lymphoma (ISO)

multiple sclerosis (ISO)

peptic esophagitis (IEP)

Proteasome-Associated Autoinflammatory Syndrome 3 (ISO)

psoriasis (ISO)

renal cell carcinoma (ISO)

Spondylarthritis (ISO)

thyroid gland Hurthle cell carcinoma (ISO)

Transplant Rejection (IEP)

type 1 diabetes mellitus (ISO)

Uterine Neoplasms (ISO)

vitiligo (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,3-dinitrobenzene (EXP)

1-naphthyl isothiocyanate (EXP)

1-nitropyrene (ISO)

17alpha-ethynylestradiol (EXP)

17beta-estradiol (ISO)

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

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

2-nitrofluorene (EXP)

3,3',4,4',5-pentachlorobiphenyl (EXP)

4,4'-diaminodiphenylmethane (EXP)

4-(ethoxymethylene)-2-phenyloxazol-5-one (EXP)

4-hydroxyphenyl retinamide (ISO)

acetamide (EXP)

aflatoxin B1 (ISO)

Aflatoxin G1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

Aroclor 1254 (ISO)

atrazine (EXP)

azathioprine (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (EXP,ISO)

bisphenol A (EXP)

buspirone (EXP)

C60 fullerene (EXP)

cadmium dichloride (EXP)

calcitriol (ISO)

carbon nanotube (ISO)

chloroprene (EXP,ISO)

chromium(6+) (ISO)

ciguatoxin CTX1B (ISO)

cisplatin (ISO)

clofibrate (ISO)

cobalt dichloride (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

dicrotophos (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

entinostat (ISO)

gentamycin (EXP)

glycidol (EXP)

haloperidol (EXP)

heptachlor (EXP)

hydralazine (ISO)

hydrogen peroxide (ISO)

lead diacetate (ISO)

leflunomide (EXP)

lipopolysaccharide (ISO)

lithium atom (EXP)

lithium hydride (EXP)

methotrexate (ISO)

methylmercury chloride (ISO)

microcystin RR (ISO)

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

N-nitrosodimethylamine (EXP)

nefazodone (EXP)

nickel atom (ISO)

nickel sulfate (ISO)

nimesulide (EXP)

paracetamol (EXP,ISO)

pentachlorophenol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phenobarbital (EXP)

phenylmercury acetate (ISO)

PhIP (EXP)

pirinixic acid (ISO)

quercitrin (ISO)

rotenone (EXP)

salicylic acid (ISO)

SB 431542 (ISO)

serpentine asbestos (ISO)

silicon dioxide (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

sodium dodecyl sulfate (ISO)

Soman (EXP)

sulfasalazine (EXP)

tamibarotene (ISO)

tamoxifen (ISO)

tert-butyl hydroperoxide (ISO)

tetrachloromethane (EXP,ISO)

theophylline (EXP)

titanium dioxide (ISO)

tolfenamic acid (ISO)

trichloroethene (EXP)

trichostatin A (ISO)

trimellitic anhydride (EXP)

Triptolide (EXP)

triptonide (ISO)

valproic acid (EXP,ISO)

vancomycin (ISO)

vitamin E (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

antigen processing and presentation (ISO)

cellular response to electrical stimulus (IEP)

cellular response to interleukin-1 (IEP)

cellular response to virus (IEP)

immune system process (IEA)

liver development (IEP)

muscle atrophy (IEP)

proteasomal ubiquitin-independent protein catabolic process (IBA)

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

proteolysis involved in cellular protein catabolic process (IEA)

regulation of cysteine-type endopeptidase activity (IEA,ISO)

response to alkaloid (IEP)

response to bacterium (ISO)

response to benzene (IEP)

response to drug (IEP)

spleen development (IEP)

thymus development (IEP)

Cellular Component

cytoplasm (IBA)

cytosol (IDA,IEA,ISO)

nucleus (IBA,IEA)

proteasome complex (IDA)

proteasome core complex (IBA,IEA,ISO)

proteasome core complex, beta-subunit complex (ISS)

spermatoproteasome complex (ISO,ISS)

Molecular Function

endopeptidase activity (IBA)

proteasome binding (IDA)

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.	Atkins D, etal., Int J Cancer. 2004 Mar 20;109(2):265-73.
2.	Bollard CM, etal., Blood. 2007 Oct 15;110(8):2838-45. Epub 2007 Jul 3.
3.	Casp CB, etal., Genes Immun. 2003 Oct;4(7):492-9.
4.	Dahlmann B, etal., Biochimie. 2001 Mar-Apr;83(3-4):295-9.
5.	Diaz-Hernandez M, etal., J Neurosci. 2003 Dec 17;23(37):11653-61.
6.	Ding H, etal., Zhonghua Nei Ke Za Zhi. 2002 Jul;41(7):465-7.
7.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8.	GOA data from the GO Consortium
9.	Haroon N, etal., Arthritis Rheum. 2012 Apr;64(4):1119-26. doi: 10.1002/art.33430. Epub 2011 Oct 27.
10.	Hayashi T and Faustman DL, Cancer Res. 2002 Jan 1;62(1):24-7.
11.	Hayashi T and Faustman DL, J Appl Physiol. 2001 Dec;91(6):2804-15.
12.	Hohler T, etal., Ann Rheum Dis. 1997 Dec;56(12):741-3.
13.	Husom AD, etal., Arch Biochem Biophys. 2004 Jan 1;421(1):67-76.
14.	James AB, etal., J Neurosci. 2006 Feb 1;26(5):1624-34.
15.	Karpova IaD, etal., Bioorg Khim. 2013 Jul-Aug;39(4):400-10.
16.	Karpova IaD, etal., Izv Akad Nauk Ser Biol. 2012 May-Jun;(3):296-302.
17.	Kimura HJ, etal., PLoS One. 2009 Nov 17;4(11):e7857.
18.	Kramer U, etal., Genes Immun. 2007 Sep;8(6):513-7. Epub 2007 Jun 21.
19.	Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
20.	Lebid' IuV, etal., Fiziol Zh. 2010;56(4):66-75.
21.	Liu Q, etal., Scand J Gastroenterol. 2009;44(8):960-9.
22.	Melnikova VI, etal., Biochemistry (Mosc). 2008 Apr;73(4):451-7.
23.	MGD data from the GO Consortium
24.	Mishto M, etal., PLoS One. 2010 Feb 18;5(2):e9287.
25.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
26.	Pipeline to import KEGG annotations from KEGG into RGD
27.	Proffitt JA and Blair GE, FEBS Lett. 1997 Jan 3;400(2):141-4.
28.	RGD automated data pipeline
29.	RGD automated import pipeline for gene-chemical interactions
30.	Seliger B, etal., Int J Oncol. 2002 Feb;20(2):349-53.
31.	Sharova NP, etal., Cell Immunol. 2009;256(1-2):47-55. doi: 10.1016/j.cellimm.2009.01.004. Epub 2009 Feb 23.
32.	Sixt SU, etal., Mediators Inflamm. 2012;2012:204250. Epub 2012 Jan 29.
33.	Sun H, etal., Biochem J. 2012 Aug 1;445(3):377-82. doi: 10.1042/BJ20120820.
34.	Suzuki K, etal., Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):2285-90.
35.	Tamura T, etal., J Biochem (Tokyo) 1992 Oct;112(4):530-4.
36.	Tengowski MW, etal., Biol Reprod. 2007 Jan;76(1):149-63. Epub 2006 Sep 20.
37.	Tong PZ, etal., Mol Med Rep. 2013 Oct;8(4):1043-8. doi: 10.3892/mmr.2013.1631. Epub 2013 Aug 14.
38.	Vargas-Alarcon G, etal., Hum Immunol. 2004 Dec;65(12):1437-42.
39.	Zakharova LA, etal., Cell Immunol. 2011;271(2):385-91. doi: 10.1016/j.cellimm.2011.08.005. Epub 2011 Aug 17.

Additional References at PubMed

PMID:2335214	PMID:12477932	PMID:15356141	PMID:16512786	PMID:16857966	PMID:17540904	PMID:20458337	PMID:20888554	PMID:23012479	PMID:23706739	PMID:24586191	PMID:26524591

Genomics

Comparative Map Data

Psmb9
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	20	4,667,044 - 4,672,512 (+)	NCBI
Rnor_6.0 Ensembl	20	3,973,420 - 3,978,845 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	20	3,973,424 - 3,978,845 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	20	6,052,972 - 6,058,393 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	4,801,187 - 4,806,608 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	20	4,801,449 - 4,806,835 (+)	NCBI
Celera	20	6,268,113 - 6,273,528 (+)	NCBI		Celera
RH 3.4 Map	20	58.54	RGD
Cytogenetic Map	20	p12	NCBI

PSMB9
(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	32,844,136 - 32,859,851 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	6	32,854,192 - 32,859,851 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	6	32,821,969 - 32,827,628 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	32,929,916 - 32,935,606 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	6	32,929,933 - 32,935,336	NCBI
Celera	6	34,370,831 - 34,376,521 (+)	NCBI
Cytogenetic Map	6	p21.32	NCBI
HuRef	6	32,564,144 - 32,569,834 (+)	NCBI		HuRef
CHM1_1	6	32,822,763 - 32,828,450 (+)	NCBI		CHM1_1

Psmb9
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	34,400,961 - 34,406,304 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	17	34,400,961 - 34,406,738 (-)	Ensembl
GRCm38	17	34,182,030 - 34,187,330 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	34,181,987 - 34,187,764 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	34,319,044 - 34,324,275 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	17	33,792,387 - 33,797,618 (-)	NCBI			mm8
Celera	17	36,935,695 - 36,940,923 (-)	NCBI		Celera
Cytogenetic Map	17	B1	NCBI
cM Map	17	17.98	NCBI

Psmb9
(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_004955437	1,513,418 - 1,516,164 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955437	1,513,425 - 1,516,164 (+)	NCBI	ChiLan1.0	ChiLan1.0

PSMB9
(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	33,539,060 - 33,544,541 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	33,539,060 - 33,564,402 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	6	32,423,614 - 32,429,062 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

PSMB9
(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	2,432,287 - 2,438,920 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	12	2,432,505 - 2,438,069 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	12	2,514,269 - 2,519,652 (+)	NCBI
ROS_Cfam_1.0	12	2,714,362 - 2,719,981 (+)	NCBI
UMICH_Zoey_3.1	12	2,431,658 - 2,437,234 (+)	NCBI
UNSW_CanFamBas_1.0	12	2,513,127 - 2,518,651 (+)	NCBI
UU_Cfam_GSD_1.0	12	2,587,464 - 2,593,086 (+)	NCBI

Psmb9
(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	38,061,110 - 38,065,954 (+)	NCBI
SpeTri2.0	NW_004936476	25,894,313 - 25,899,132 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PSMB9
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	25,055,594 - 25,078,594 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	25,072,133 - 25,077,508 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	29,438,756 - 29,444,131 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PSMB9
(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	17	39,246,356 - 39,251,852 (-)	NCBI
ChlSab1.1 Ensembl	17	39,245,854 - 39,251,842 (-)	Ensembl
Vero_WHO_p1.0	NW_023666044	32,640,507 - 32,645,947 (+)	NCBI

Psmb9
(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_004624754	23,811,008 - 23,815,432 (-)	NCBI

Position Markers

RH142199

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	4,666,717 - 4,666,900 (-)	MAPPER
Rnor_6.0	20	3,979,036 - 3,979,218	NCBI	Rnor6.0
Rnor_5.0	20	6,058,584 - 6,058,766	UniSTS	Rnor5.0
RGSC_v3.4	20	4,800,814 - 4,800,996	UniSTS	RGSC3.4
Celera	20	6,267,740 - 6,267,922	UniSTS
RH 3.4 Map	20	60.6	UniSTS
Cytogenetic Map	20	p12	UniSTS

RH128991

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	4,672,241 - 4,672,451 (-)	MAPPER
Rnor_6.0	20	3,973,485 - 3,973,694	NCBI	Rnor6.0
Rnor_5.0	20	6,053,033 - 6,053,242	UniSTS	Rnor5.0
RGSC_v3.4	20	4,806,338 - 4,806,547	UniSTS	RGSC3.4
Celera	20	6,273,258 - 6,273,467	UniSTS
RH 3.4 Map	20	57.94	UniSTS
Cytogenetic Map	20	p12	UniSTS

RH94492

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	4,672,360 - 4,672,455 (-)	MAPPER
Rnor_6.0	20	3,973,481 - 3,973,575	NCBI	Rnor6.0
Rnor_5.0	20	6,053,029 - 6,053,123	UniSTS	Rnor5.0
RGSC_v3.4	20	4,806,457 - 4,806,551	UniSTS	RGSC3.4
Celera	20	6,273,377 - 6,273,471	UniSTS
RH 3.4 Map	20	58.54	UniSTS
Cytogenetic Map	20	p12	UniSTS

D17Dgm5

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	4,670,159 - 4,670,234 (-)	MAPPER
Rnor_6.0	20	3,975,702 - 3,975,776	NCBI	Rnor6.0
Rnor_5.0	20	6,055,250 - 6,055,324	UniSTS	Rnor5.0
RGSC_v3.4	20	4,804,256 - 4,804,330	UniSTS	RGSC3.4
Celera	20	6,271,176 - 6,271,250	UniSTS
Cytogenetic Map	20	p12	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
724519	Bp144	Blood pressure QTL 144		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	20	1	5192000	Rat
1354642	Despr15	Despair related QTL 15		0.0027	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	20	1	24652101	Rat
1600382	Edcs3	Endometrial carcinoma susceptibility QTL3	3.5	0.003	uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	20	1	25653396	Rat
1641893	Alcrsp7	Alcohol response QTL 7			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	26305996	Rat
2317851	Alcrsp22	Alcohol response QTL 22	3.2	0.05	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	26305996	Rat
7387283	Uae44	Urinary albumin excretion QTL 44		0.1712	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	20	1	27357423	Rat
9590275	Scort15	Serum corticosterone level QTL 15	3.48	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	28375393	Rat
9589155	Insul32	Insulin level QTL 32	6.38	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	20	1	28375393	Rat
9590109	Sffal8	Serum free fatty acids level QTL 8	5.32	0.01	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	20	1	28375393	Rat
7411650	Foco23	Food consumption QTL 23	20.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	28375393	Rat
8694189	Bw153	Body weight QTL 153	3.13	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	20	1	28375393	Rat
6893685	Bw111	Body weight QTL 111	2.7	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	20	1	33300419	Rat
9590252	Scort12	Serum corticosterone level QTL 12	20.46	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	37550487	Rat
7411668	Foco32	Food consumption QTL 32	8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	37550487	Rat
2305926	Iddm37	Insulin dependent diabetes mellitus QTL 37	6		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	20	2018654	47018654	Rat
2306850	Pia40	Pristane induced arthritis QTL 40		0.0001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	20	2018770	6567419	Rat
1641915	Colcr9	Colorectal carcinoma resistance QTL 9	2.97	0.0024	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	20	2999707	47999707	Rat
61472	Aia1	Adjuvant induced arthritis QTL 1	18	0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	20	3151815	6896013	Rat
61448	Ciaa1	CIA Autoantibody QTL 1	30	0.001	blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	20	3151815	6896013	Rat
2317057	Aia27	Adjuvant induced arthritis QTL 27	2.83		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	20	3402111	27968216	Rat
7175096	Tcs1	T cell selection QTL 1			T cell selection	expression	20	3910555	5533640	Rat
7175099	Tcs2	T cell selection QTL 2			T cell selection	expression	20	3945383	4156365	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	148
Count of miRNA genes:	120
Interacting mature miRNAs:	125
Transcripts:	ENSRNOT00000000532
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	10	29	13	19	13				7	16	11
Low		25	28	28		28	8	11	66	28	24		8
Below cutoff		8							8		1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_012708	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039098423	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC098547	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC091161	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BP500440	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BX883043	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473988	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D10757	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ228039	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000324	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222887	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222888	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222889	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222890	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222891	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000000532 ⟹ ENSRNOP00000000532

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	3,973,420 - 3,978,845 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000081162

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	3,975,480 - 3,976,214 (-)	Ensembl

RefSeq Acc Id:

NM_012708 ⟹ NP_036840

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	4,667,091 - 4,672,512 (+)	NCBI
Rnor_6.0	20	3,973,424 - 3,978,845 (-)	NCBI
Rnor_5.0	20	6,052,972 - 6,058,393 (-)	NCBI
RGSC_v3.4	20	4,801,187 - 4,806,608 (+)	RGD
Celera	20	6,268,113 - 6,273,528 (+)	RGD

Sequence:

show sequence

CCTTCGCCGCACGCCGCTGCTGATTGGAAACCAGAGCTCCGCACTGCTAGGATGCTGCAAGCCG
GAGCACCTACCGCCGGCTCTTTCCGGACGGGAGAAGTCCACACCGGGACAACCATCATGGCTGT
GGAATTTGACGGGGGTGTCGTGGTGGGCTCTGATTCCCGAGTGTCAGCGGGAGCAGCCGTAGTG
AACCGCGTGTTTGACAAGCTCTCCCCTCTGCACCAGCGCATCTACTGTGCCCTCTCGGGTTCCG
CTGCTGATGCCCAAGCCATAGCGGACATGGCCGCCTACCAGCTGGAGCTGCACGGGTTGGAACT
GGAGGAGCCGCCCCTTGTTCTGGCTGCTGCAAACATAGTGAAGAACATCTCCTACAAGTACCGC
GAGGACTTGTTAGCGCATCTCATGGTAGCTGGTTGGGACCAACGTGAGGGGGGCCAGGTGTATG
GAACCATGGGAGGGATGCTAATTCGACAGCCCTTTGCAATCGGTGGTTCCGGAAGCACCTATAT
TTACGGTTATGTGGACGCAGCTTATAAACCAGGCATGACCCCCGAGGAGTGCCGGCGTTTCACC
ACAGACGCCATCACTCTGGCCATGAACCGAGATGGCTCCAGTGGGGGTGTCATCTACCTGGTCA
CCATTACAGCTGATGGTGTGGACCATCGCGTCATCCTGGGAGACGAGCTGCCAAAATTCTACGA
TGAGTGAAGTCCCTTCTTTGTTTGCAATAAACTTTATGGAGCCAGAGGTTGGTGTAATGGGCAG
AGGTGAAATGGGTATCAGAGAAACGCAGTGCGTGGAGGGAAGCTTCCTCCCGGCCCAGAGATCA
GCAAGCACCTCCCATTCTTTTTTAAAAAATAAACTTTATTATTAAAATAAAAAACTCTTATAAA
TAAAAAATAAGTAAAAC

hide sequence

RefSeq Acc Id:

XM_039098423 ⟹ XP_038954351

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	4,667,044 - 4,672,502 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_036840	(Get FASTA)	NCBI Sequence Viewer
	XP_038954351	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH91161	(Get FASTA)	NCBI Sequence Viewer
	AGV38984	(Get FASTA)	NCBI Sequence Viewer
	AGV38985	(Get FASTA)	NCBI Sequence Viewer
	AGV38986	(Get FASTA)	NCBI Sequence Viewer
	AGV38987	(Get FASTA)	NCBI Sequence Viewer
	AGV38988	(Get FASTA)	NCBI Sequence Viewer
	BAA01589	(Get FASTA)	NCBI Sequence Viewer
	CAE83940	(Get FASTA)	NCBI Sequence Viewer
	EDL96811	(Get FASTA)	NCBI Sequence Viewer
	P28077	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_036840 ⟸ NM_012708

- UniProtKB:

P28077 (UniProtKB/Swiss-Prot), Q6MGA6 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MLQAGAPTAGSFRTGEVHTGTTIMAVEFDGGVVVGSDSRVSAGAAVVNRVFDKLSPLHQRIYCA
LSGSAADAQAIADMAAYQLELHGLELEEPPLVLAAANIVKNISYKYREDLLAHLMVAGWDQREG
GQVYGTMGGMLIRQPFAIGGSGSTYIYGYVDAAYKPGMTPEECRRFTTDAITLAMNRDGSSGGV
IYLVTITADGVDHRVILGDELPKFYDE

hide sequence

RefSeq Acc Id:

ENSRNOP00000000532 ⟸ ENSRNOT00000000532

RefSeq Acc Id:	XP_038954351 ⟸ XM_039098423
- Peptide Label:	isoform X1

Transcriptome

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

Promoters

RGD ID:

13701322

Promoter ID:

EPDNEW_R11846

Type:

initiation region

Name:

Psmb9_1

Description:

proteasome subunit beta 9

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	20	3,978,824 - 3,978,884	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:3427	AgrOrtholog
Ensembl Genes	ENSRNOG00000000459	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000000532	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000000532	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.60.20.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7366097	IMAGE-MGC_LOAD
InterPro	Ntn_hydrolases_N	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Pept_T1A_subB	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Proteasome_beta9	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:24967	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:108740	IMAGE-MGC_LOAD
NCBI Gene	24967	ENTREZGENE
PANTHER	PTHR11599:SF50	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Proteasome	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Psmb9	PhenoGen
PRINTS	PROTEASOME	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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	A0A023ILN9_RAT	UniProtKB/TrEMBL
	P28077	ENTREZGENE, UniProtKB/Swiss-Prot
	Q6MGA6	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2019-09-13	Psmb9	proteasome 20S subunit beta 9	Psmb9	proteasome subunit beta 9	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2015-08-19	Psmb9	proteasome subunit beta 9	Psmb9	proteasome (prosome, macropain) subunit, beta type, 9	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2013-04-04	Psmb9	proteasome (prosome, macropain) subunit, beta type, 9	Psmb9	proteasome (prosome, macropain) subunit, beta type 9 (large multifunctional peptidase 2)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-02-15	Psmb9	proteasome (prosome, macropain) subunit, beta type 9 (large multifunctional peptidase 2)	Psmb9	proteosome (prosome, macropain) subunit, beta type 9	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2001-10-24	Psmb9	proteosome (prosome, macropain) subunit, beta type 9 (large multifunctional protease 2)			Name updated to reflect Human and Mouse nomenclature	68913	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_mapping	found in the major histocompatibility RT1 complex	1300431

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 Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)