Psmb9 (proteasome 20S subunit beta 9) - Rat Genome Database

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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: Enables proteasome binding activity. Involved in several processes, including cellular response to electrical stimulus; hematopoietic or lymphoid organ development; and response to benzene. Located in cytosol. Part of 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
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,667,044 - 4,672,512 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl204,666,046 - 4,672,512 (+)Ensembl
Rnor_6.0203,973,424 - 3,978,845 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,973,420 - 3,978,845 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,052,972 - 6,058,393 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,801,187 - 4,806,608 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1204,801,449 - 4,806,835 (+)NCBI
Celera206,268,113 - 6,273,528 (+)NCBICelera
RH 3.4 Map2058.54RGD
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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)
arsenite(3-)  (ISO)
atrazine  (EXP)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
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)
Cuprizon  (EXP)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
fulvestrant  (ISO)
gentamycin  (EXP)
glycidol  (EXP)
haloperidol  (EXP)
heptachlor  (EXP)
hydralazine  (ISO)
hydrogen peroxide  (ISO)
ivermectin  (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)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
theophylline  (EXP)
thioacetamide  (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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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  
PMID:34857032  


Genomics

Comparative Map Data
Psmb9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2204,667,044 - 4,672,512 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl204,666,046 - 4,672,512 (+)Ensembl
Rnor_6.0203,973,424 - 3,978,845 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl203,973,420 - 3,978,845 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,052,972 - 6,058,393 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4204,801,187 - 4,806,608 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1204,801,449 - 4,806,835 (+)NCBI
Celera206,268,113 - 6,273,528 (+)NCBICelera
RH 3.4 Map2058.54RGD
Cytogenetic Map20p12NCBI
PSMB9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38632,854,192 - 32,859,851 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl632,844,136 - 32,859,851 (+)EnsemblGRCh38hg38GRCh38
GRCh37632,821,969 - 32,827,628 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36632,929,916 - 32,935,606 (+)NCBINCBI36hg18NCBI36
Build 34632,929,933 - 32,935,336NCBI
Celera634,370,831 - 34,376,521 (+)NCBI
Cytogenetic Map6p21.32NCBI
HuRef632,564,144 - 32,569,834 (+)NCBIHuRef
CHM1_1632,822,763 - 32,828,450 (+)NCBICHM1_1
Psmb9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,400,961 - 34,406,304 (-)NCBIGRCm39mm39
GRCm39 Ensembl1734,400,961 - 34,406,738 (-)Ensembl
GRCm381734,182,030 - 34,187,330 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,181,987 - 34,187,764 (-)EnsemblGRCm38mm10GRCm38
MGSCv371734,319,044 - 34,324,275 (-)NCBIGRCm37mm9NCBIm37
MGSCv361733,792,387 - 33,797,618 (-)NCBImm8
Celera1736,935,695 - 36,940,923 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.98NCBI
Psmb9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554371,513,418 - 1,516,164 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554371,513,425 - 1,516,164 (+)NCBIChiLan1.0ChiLan1.0
PSMB9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1633,539,060 - 33,544,541 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl633,539,060 - 33,564,402 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0632,423,614 - 32,429,062 (+)NCBIMhudiblu_PPA_v0panPan3
PSMB9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1122,432,287 - 2,438,920 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl122,432,505 - 2,438,069 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha122,514,269 - 2,519,652 (+)NCBI
ROS_Cfam_1.0122,714,362 - 2,719,981 (+)NCBI
ROS_Cfam_1.0 Ensembl122,714,362 - 2,719,981 (+)Ensembl
UMICH_Zoey_3.1122,431,658 - 2,437,234 (+)NCBI
UNSW_CanFamBas_1.0122,513,127 - 2,518,651 (+)NCBI
UU_Cfam_GSD_1.0122,587,464 - 2,593,086 (+)NCBI
Psmb9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494638,061,110 - 38,065,954 (+)NCBI
SpeTri2.0NW_00493647625,894,313 - 25,899,132 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PSMB9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl725,055,594 - 25,078,594 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1725,072,133 - 25,077,508 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2729,438,756 - 29,444,131 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PSMB9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11739,246,356 - 39,251,852 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1739,245,854 - 39,251,842 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604432,640,507 - 32,645,947 (+)NCBIVero_WHO_p1.0
Psmb9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475423,811,008 - 23,815,432 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH142199  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,666,717 - 4,666,900 (-)MAPPERmRatBN7.2
Rnor_6.0203,979,036 - 3,979,218NCBIRnor6.0
Rnor_5.0206,058,584 - 6,058,766UniSTSRnor5.0
RGSC_v3.4204,800,814 - 4,800,996UniSTSRGSC3.4
Celera206,267,740 - 6,267,922UniSTS
RH 3.4 Map2060.6UniSTS
Cytogenetic Map20p12UniSTS
RH128991  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,672,241 - 4,672,451 (-)MAPPERmRatBN7.2
Rnor_6.0203,973,485 - 3,973,694NCBIRnor6.0
Rnor_5.0206,053,033 - 6,053,242UniSTSRnor5.0
RGSC_v3.4204,806,338 - 4,806,547UniSTSRGSC3.4
Celera206,273,258 - 6,273,467UniSTS
RH 3.4 Map2057.94UniSTS
Cytogenetic Map20p12UniSTS
RH94492  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,672,360 - 4,672,455 (-)MAPPERmRatBN7.2
Rnor_6.0203,973,481 - 3,973,575NCBIRnor6.0
Rnor_5.0206,053,029 - 6,053,123UniSTSRnor5.0
RGSC_v3.4204,806,457 - 4,806,551UniSTSRGSC3.4
Celera206,273,377 - 6,273,471UniSTS
RH 3.4 Map2058.54UniSTS
Cytogenetic Map20p12UniSTS
D17Dgm5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,670,159 - 4,670,234 (-)MAPPERmRatBN7.2
Rnor_6.0203,975,702 - 3,975,776NCBIRnor6.0
Rnor_5.0206,055,250 - 6,055,324UniSTSRnor5.0
RGSC_v3.4204,804,256 - 4,804,330UniSTSRGSC3.4
Celera206,271,176 - 6,271,250UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
7175099Tcs2T cell selection QTL 2T cell selectionexpression2045025574693102Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2046066076691706Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat

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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000532   ⟹   ENSRNOP00000000532
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,667,091 - 4,672,512 (+)Ensembl
Rnor_6.0 Ensembl203,973,420 - 3,978,845 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081162
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl203,975,480 - 3,976,214 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091362   ⟹   ENSRNOP00000093912
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl204,666,046 - 4,672,512 (+)Ensembl
RefSeq Acc Id: NM_012708   ⟹   NP_036840
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,667,091 - 4,672,512 (+)NCBI
Rnor_6.0203,973,424 - 3,978,845 (-)NCBI
Rnor_5.0206,052,972 - 6,058,393 (-)NCBI
RGSC_v3.4204,801,187 - 4,806,608 (+)RGD
Celera206,268,113 - 6,273,528 (+)RGD
Sequence:
RefSeq Acc Id: XM_039098423   ⟹   XP_038954351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2204,667,044 - 4,672,502 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036840   ⟸   NM_012708
- UniProtKB: P28077 (UniProtKB/Swiss-Prot),   Q6MGA6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000532   ⟸   ENSRNOT00000000532
RefSeq Acc Id: XP_038954351   ⟸   XM_039098423
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000093912   ⟸   ENSRNOT00000091362

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P28077-F1-model_v2 AlphaFold P28077 1-219 view protein structure

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 AssemblyChrPosition (strand)Source
Rnor_6.0203,978,824 - 3,978,884EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 3974588 3974589 A G snv M520/N (MCW), Buf/N (MCW), ACI/N (MCW), MR/N (MCW)
20 3975685 3975686 G C snv WN/N (MCW), M520/N (MCW), F344/NRrrc (MCW), Buf/N (MCW), ACI/N (MCW), WKY/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3427 AgrOrtholog
BioCyc Gene G2FUF-4552 BioCyc
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