Psma3 (proteasome 20S subunit alpha 3)

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Gene: Psma3 (proteasome 20S subunit alpha 3) Rattus norvegicus

Analyze

Symbol:

Psma3

Name:

proteasome 20S subunit alpha 3

RGD ID:

61844

Description:

Predicted to have endopeptidase activity and ubiquitin protein ligase binding activity. Predicted to be involved in proteasomal ubiquitin-independent protein catabolic process; proteasome-mediated ubiquitin-dependent protein catabolic process; and regulation of endopeptidase activity. Localizes to synapse. Orthologous to human PSMA3 (proteasome 20S subunit alpha 3); PARTICIPATES IN ubiquitin/proteasome degradation pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 1,3-dinitrobenzene; 2,4-dibromophenyl 2,4,5-tribromophenyl ether.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

macropain subunit C8; multicatalytic endopeptidase complex subunit C8; multicatalytic proteinase subunit K; proteasome (prosome, macropain) subunit, alpha type 3; proteasome component C8; proteasome subunit alpha 3; proteasome subunit alpha type 3-like; proteasome subunit alpha type-3; proteasome subunit C8; proteasome subunit K; Psma3l

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	6	89,483,741 - 89,503,775 (+)	NCBI
Rnor_6.0 Ensembl	6	93,423,002 - 93,444,240 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	6	93,423,029 - 93,444,223 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	6	102,868,534 - 102,898,751 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	93,092,191 - 93,112,167 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	6	93,095,646 - 93,115,622 (+)	NCBI
Celera	6	87,965,854 - 87,985,832 (+)	NCBI		Celera
Cytogenetic Map	6	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

JMP syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2,4-trimethylbenzene (EXP)

1,2-dimethylhydrazine (ISO)

1,3-dinitrobenzene (EXP)

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

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

4,4'-diaminodiphenylmethane (ISO)

acrolein (ISO)

aflatoxin B1 (ISO)

alpha-pinene (ISO)

ammonium chloride (EXP)

ampicillin (EXP)

arsane (ISO)

arsenic atom (ISO)

bis(2-chloroethyl) sulfide (EXP)

bisphenol A (EXP,ISO)

bromobenzene (EXP)

bufalin (ISO)

clofibrate (ISO)

cyclosporin A (ISO)

dibenzo[a,l]pyrene (ISO)

dibutyl phthalate (EXP)

dicrotophos (ISO)

dimethylarsinous acid (ISO)

doxorubicin (ISO)

ethanol (ISO)

finasteride (EXP)

fluoxetine (EXP)

flutamide (EXP)

folic acid (ISO)

genistein (EXP,ISO)

gentamycin (EXP)

hydrogen peroxide (ISO)

isotretinoin (ISO)

lovastatin (ISO)

methoxychlor (EXP)

metronidazole (EXP)

monocrotaline (EXP)

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

nefazodone (EXP)

neomycin (EXP)

nickel atom (ISO)

nickel subsulfide (ISO)

nimesulide (EXP)

ozone (ISO)

p-menthan-3-ol (ISO)

paracetamol (EXP,ISO)

Pentoxifylline (EXP)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

phenethyl isothiocyanate (ISO)

phenobarbital (EXP)

picrotoxin (EXP)

pirinixic acid (ISO)

pregnenolone 16alpha-carbonitrile (EXP)

quinoline (ISO)

rotenone (EXP,ISO)

sarin (ISO)

sunitinib (ISO)

Tributyltin oxide (ISO)

tungsten (ISO)

valdecoxib (EXP)

vancomycin (EXP)

vorinostat (ISO)

warfarin (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)

regulation of endopeptidase activity (ISO)

Cellular Component

cytoplasm (IBA)

nucleus (IBA)

proteasome complex (ISO)

proteasome core complex (IBA,ISO,ISS)

proteasome core complex, alpha-subunit complex (IBA,ISS)

synapse (IBA,IDA)

Molecular Function

endopeptidase activity (IBA)

protein binding (ISO)

ubiquitin protein ligase binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

ubiquitin/proteasome degradation pathway (IEA)

References

References - curated


1.	Bingol B and Schuman EM, Nature. 2006 Jun 29;441(7097):1144-8.
2.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	GOA data from the GO Consortium
4.	MGD data from the GO Consortium
5.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	Pipeline to import KEGG annotations from KEGG into RGD
7.	Puente XS and Lopez-Otin C, Genome Res 2004 Apr;14(4):609-22.
8.	RGD automated data pipeline
9.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10.	RGD automated import pipeline for gene-chemical interactions
11.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
12.	Tanaka K, etal., Biochem Biophys Res Commun 1990 Sep 14;171(2):676-83.
13.	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data

Additional References at PubMed

PMID:2249692	PMID:2335242	PMID:9688553	PMID:15489334	PMID:16207813	PMID:16641100	PMID:16857966	PMID:17323924	PMID:19056867	PMID:19208651	PMID:20458337	PMID:20498273
PMID:21630459	PMID:22793692	PMID:23376485	PMID:25002582	PMID:26524591	PMID:30361391	PMID:31904090

Genomics

Comparative Map Data

Psma3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	6	89,483,741 - 89,503,775 (+)	NCBI
Rnor_6.0 Ensembl	6	93,423,002 - 93,444,240 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	6	93,423,029 - 93,444,223 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	6	102,868,534 - 102,898,751 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	93,092,191 - 93,112,167 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	6	93,095,646 - 93,115,622 (+)	NCBI
Celera	6	87,965,854 - 87,985,832 (+)	NCBI		Celera
Cytogenetic Map	6	q24	NCBI

PSMA3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	14	58,244,843 - 58,272,012 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	14	58,244,843 - 58,272,004 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	14	58,711,561 - 58,738,722 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	14	57,781,346 - 57,808,479 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	14	57,781,345 - 57,808,479	NCBI
Celera	14	38,761,540 - 38,788,685 (+)	NCBI
Cytogenetic Map	14	q23.1	NCBI
HuRef	14	38,877,058 - 38,904,216 (+)	NCBI		HuRef
CHM1_1	14	58,650,049 - 58,677,295 (+)	NCBI		CHM1_1

Psma3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	71,016,057 - 71,042,651 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	12	71,021,395 - 71,043,121 (+)	Ensembl
GRCm38	12	70,969,283 - 70,995,877 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	70,974,621 - 70,996,347 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	72,075,610 - 72,095,924 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	12	71,893,298 - 71,913,526 (+)	NCBI			mm8
Celera	12	72,078,082 - 72,098,500 (+)	NCBI		Celera
Cytogenetic Map	12	C2	NCBI

Psma3
(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_004955466	11,979,482 - 11,997,952 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955466	11,979,482 - 11,997,952 (+)	NCBI	ChiLan1.0	ChiLan1.0

PSMA3
(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	14	57,105,891 - 57,133,181 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	14	57,105,891 - 57,133,181 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	14	38,836,869 - 38,864,152 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

PSMA3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	8	33,616,735 - 33,642,434 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	8	33,616,480 - 33,642,404 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	8	33,378,219 - 33,403,729 (+)	NCBI
ROS_Cfam_1.0	8	33,858,343 - 33,884,028 (+)	NCBI
UMICH_Zoey_3.1	8	33,471,278 - 33,496,743 (+)	NCBI
UNSW_CanFamBas_1.0	8	33,538,435 - 33,564,256 (+)	NCBI
UU_Cfam_GSD_1.0	8	33,913,572 - 33,939,074 (+)	NCBI

Psma3
(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_024408640	71,519,504 - 71,541,053 (-)	NCBI
SpeTri2.0	NW_004936495	2,650,668 - 2,672,192 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PSMA3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	187,343,507 - 187,372,215 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	187,342,231 - 187,371,149 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	208,246,764 - 208,274,223 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PSMA3
(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	24	35,438,084 - 35,465,320 (+)	NCBI
ChlSab1.1 Ensembl	24	35,437,308 - 35,465,203 (+)	Ensembl

Psma3
(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_004624884	3,324,390 - 3,346,128 (+)	NCBI

Position Markers

RH127444

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	93,442,743 - 93,442,958	NCBI	Rnor6.0
Rnor_5.0	6	102,898,469 - 102,898,684	UniSTS	Rnor5.0
RGSC_v3.4	6	93,111,885 - 93,112,100	UniSTS	RGSC3.4
Celera	6	87,985,550 - 87,985,765	UniSTS
RH 3.4 Map	6	639.3	UniSTS
Cytogenetic Map	6	q24	UniSTS

RH138090

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	93,424,697 - 93,424,843	NCBI	Rnor6.0
Rnor_5.0	6	102,870,438 - 102,870,584	UniSTS	Rnor5.0
RGSC_v3.4	6	93,093,859 - 93,094,005	UniSTS	RGSC3.4
Celera	6	87,967,522 - 87,967,668	UniSTS
RH 3.4 Map	6	640.3	UniSTS
Cytogenetic Map	10	q25	UniSTS
Cytogenetic Map	6	q24	UniSTS

RH130667

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	93,443,835 - 93,444,035	NCBI	Rnor6.0
Rnor_5.0	6	102,899,561 - 102,899,761	UniSTS	Rnor5.0
RGSC_v3.4	6	93,112,977 - 93,113,177	UniSTS	RGSC3.4
Celera	6	87,986,642 - 87,986,842	UniSTS
RH 3.4 Map	6	639.5	UniSTS
Cytogenetic Map	6	q24	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
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	2537030	111715717	Rat
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	7009971	115379601	Rat
634330	Pia16	Pristane induced arthritis QTL 16	3.9		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	6	48432758	108268790	Rat
4889848	Pur25	Proteinuria QTL 25	14	0.003	total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	6	59803065	94001333	Rat
1558641	Cm47	Cardiac mass QTL 47	2.9	0.001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	6	60606431	108154445	Rat
6893332	Cm74	Cardiac mass QTL 74	0.4	0.64	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	60606431	108154445	Rat
70176	Mcsm1	Mammary carcinoma susceptibility modifier QTL 1			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	62263348	107263348	Rat
12801471	Schws9	Schwannoma susceptibility QTL 9			nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	66129520	111129520	Rat
731173	Uae22	Urinary albumin excretion QTL 22	10.1		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	68781170	147991367	Rat
2290393	Uae37	Urinary albumin excretion QTL 37		0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	68781170	147991367	Rat
1641904	Alcrsp4	Alcohol response QTL 4			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	6	71206251	116206251	Rat
1300075	Glom7	Glomerulus QTL 7	5.6	0.0000002	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	6	75449871	120449871	Rat
1331789	Rf37	Renal function QTL 37	3.224		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	6	75623277	120276465	Rat
70196	BpQTLcluster7	Blood pressure QTL cluster 7	6.82		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	75623277	120623277	Rat
724536	Uae7	Urinary albumin excretion QTL 7	3.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	75623277	136143011	Rat
1331799	Bp211	Blood pressure QTL 211	3.66407		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	75623277	136426962	Rat
1581550	Pur8	Proteinuria QTL 8			total urine protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	6	75623393	136142742	Rat
1581563	Uae33	Urinary albumin excretion QTL 33			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	75623393	136142742	Rat
724524	Uae2	Urinary albumin excretion QTL 2	2.7	0.0005	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	76902247	114203334	Rat
2293837	Kiddil1	Kidney dilation QTL 1	3.7		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	84763275	108464097	Rat
2293842	Kiddil3	Kidney dilation QTL 3	4.3		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	84763275	108464097	Rat
737827	Hcar11	Hepatocarcinoma resistance QTL 11	4.4		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	6	86422697	115379601	Rat
1576302	Schws4	Schwannoma susceptibility QTL 4		0.0078	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	87418448	111129520	Rat
738034	Anxrr5	Anxiety related response QTL 5	5.9		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	6	88507712	133507712	Rat
724513	Uae14	Urinary albumin excretion QTL 14	6.5		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	88996335	139410483	Rat
10054138	Gmadr3	Adrenal mass QTL 3	3.68	0.00045	adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	6	89631358	134631358	Rat
10054123	Srcrt6	Stress Responsive Cort QTL 6	2.5	0.0043	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	89631358	134631358	Rat
1300076	Glom8	Glomerulus QTL 8	7	0.000000009	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)	6	91703409	136703409	Rat
2303624	Vencon5	Ventilatory control QTL 5	4.45		respiration trait (VT:0001943)	minute ventilation (VE) (CMO:0000132)	6	92879510	137879510	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	152
Count of miRNA genes:	102
Interacting mature miRNAs:	124
Transcripts:	ENSRNOT00000010753
Prediction methods:	Miranda, 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_017280	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017594059	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC128303	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC081817	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ211111	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219582	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222497	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ224319	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ227243	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233787	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000164	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000010753 ⟹ ENSRNOP00000010753

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	6	93,423,002 - 93,444,240 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000075868

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	6	93,437,383 - 93,441,873 (+)	Ensembl

RefSeq Acc Id:

NM_017280 ⟹ NP_058976

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	6	89,483,777 - 89,503,775 (+)	NCBI
Rnor_6.0	6	93,423,029 - 93,443,025 (+)	NCBI
Rnor_5.0	6	102,868,534 - 102,898,751 (+)	NCBI
RGSC_v3.4	6	93,092,191 - 93,112,167 (+)	RGD
Celera	6	87,965,854 - 87,985,832 (+)	RGD

Sequence:

show sequence

CCATGAGCTCCATTGGCACTGGGTATGACCTGTCAGCCTCTACATTCTCTCCTGATGGAAGAGT
TTTCCAAGTTGAATATGCTATGAAGGCTGTGGAAAACAGTAGTACAGCTATTGGGATCAGATGT
AAAGATGGTGTTGTGTTTGGGGTAGAAAAACTAGTCCTTTCTAAACTTTATGAAGAAGGCTCCA
ATAAACGTCTTTTCAATGTTGATCGACATGTTGGAATGGCAGTGGCAGGTTTGTTGGCAGATGC
TCGTTCCTTGGCAGACATAGCAAGAGAAGAAGCGTCCAACTTTAGGTCTAACTTTGGCTATAAC
ATTCCTCTAAAACATCTTGCAGACAGAGTGGCCATGTATGTACACGCGTATACACTCTACAGTG
CTGTTAGACCTTTTGGCTGCAGTTTCATGTTGGGGTCTTACAGTGTGAATGATGGTGCACAGCT
CTATATGATCGATCCATCAGGTGTTTCATATGGTTACTGGGGCTGTGCCATTGGCAAAGCCAGG
CAAGCTGCAAAGACAGAAATAGAAAAGCTTCAGATGAAGGAAATGACCTGCCGTGATGTAGTTA
AAGAAGTTGCAAAAATAATTTACATAGTACATGATGAAGTTAAGGATAAAGCTTTTGAACTAGA
GCTCAGCTGGGTTGGTGAATTAACTAAAGGAAGACATGAAATTGTTCCCAAAGACGTAAGAGAG
GAAGCAGAGAAATATGCCAAGGAATCTTTGAAGGAAGAAGATGAATCAGATGACGACAATATGT
AACATTTCACCATCCTCTGGTGTCCATTTCTGTGACAGTTGCATATGGCTAGCACCATGGATTA
TATATACCCACTGACCAATTTTCATTAAATTTTGTCTTATAAACATTGTTGGGTAATTGAGGAT
ATCTGCGTTATATTAAAATGTAGATTCATGTTTGATTAGAAATTCTAGGAACTGGGCCTGGAGA
GATGGCTCAGCAGTTAAGAGCTGCTCTTCCAGGGGACATAGGTTCAATTCCCAGCACCCGCATG
GCAGCTCACACCTGTTTGTAACTCTAGCTCCAGGTCTCTGACACCTAGACACAGAGGTACTTGC
AGGCAAAACACCAATGAATATAAAATAAAAATAAATGATATATATATTTACACATATAACAAGT
ATATACAAATATGTATATTATACAGACACATGTGTGTGTATATACATATAAATTCTTGGTGCTA
TTCTGGTGTGGTAGTATATGTCTTTAATCCTAGTACTCTGGAGGCAGAGGCAGGTGGATCTCTT
GAGTTCAAGGCTAGTATTTAAAAACAAAAACAAATGTAGTGCCCAGACTAAGGCTGAAAGATTG
AGCCCACAAGTCAATTTACAATTCCATTTTGTTTTAACTAGAATTAAAAGAATAATTTTAGATT
TTTTTTTTCTTTTTTTCAGAGCTGGGGACCGAACCCAGGGCCTTGCGCTTCCTAGGCAAGCGCT
CTACCACTAAGCTAAATCCCCAACCCCTTAGATTTATTTTTATTTTTTGCATGTTTATGTATAT
TACAGTGCCATGCCTGGTGCTCATGGAGGTCAAAAGAATGCTTTAATCTAGAACTAAAGTTATG
GAGGACTGTGAATCATGTATGTTCGAAACTGAACTTGGGTCCTGTGTAAGAGCAACACGTCCTC
TTAACCACTGAGCCATCTCTCCAGCCCTCTTTGACTAGAATGATCATATTCTACTGTGGTTCTT
GTATAATGTTTTGTTTAATGTAGGGATATCCTGTAACCACTATTGAGGACTAACCTGCCTTTTG
TGGAAAATGTGACATATTCTAATTTGACATCAATACAGACAACATTTATTTTCAGACTGCATAA
ATATCTTATGACTGGAAATTATCTTGATATTGGCACCTGAAACAAAAACTTAAAAGTTCCAAAC
TGGGCTTAAATATTTCATGTAATAAAATGTTTATAGTACTTATCTGAAAAAAAAAAAAAAAAAA
AAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_017594059 ⟹ XP_017449548

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	6	89,483,741 - 89,502,746 (+)	NCBI
Rnor_6.0	6	93,424,370 - 93,444,223 (+)	NCBI

Sequence:

show sequence

GTATGACCTGTCAGCCTCTACATTCTCTCCTGATGGAAGAGTTTTCCAAGTTGAATATGCTATG
AAGGCTGTGGAAAACAGTAGCTATTGGGATCAGATGTAAAGATGGTGTTGTGTTTGGGGTAGAA
AAACTAGTCCTTTCTAAACTTTATGAAGAAGGCTCCAATAAACGTCTTTTCAATGTTGATCGAC
ATGTTGGAATGGCAGTGGCAGGTTTGTTGGCAGATGCTCGTTCCTTGGCAGACATAGCAAGAGA
AGAAGCGTCCAACTTTAGGTCTAACTTTGGCTATAACATTCCTCTAAAACATCTTGCAGACAGA
GTGGCCATGTATGTACACGCGTATACACTCTACAGTGCTGTTAGACCTTTTGGCTGCAGTTTCA
TGTTGGGGTCTTACAGTGTGAATGATGGTGCACAGCTCTATATGATCGATCCATCAGGTGTTTC
ATATGGTTACTGGGGCTGTGCCATTGGCAAAGCCAGGCAAGCTGCAAAGACAGAAATAGAAAAG
CTTCAGATGAAGGAAATGACCTGCCGTGATGTAGTTAAAGAAGTTGCAAAAATAATTTACATAG
TACATGATGAAGTTAAGGATAAAGCTTTTGAACTAGAGCTCAGCTGGGTTGGTGAATTAACTAA
AGGAAGACATGAAATTGTTCCCAAAGACGTAAGAGAGGAAGCAGAGAAATATGCCAAGGAATCT
TTGAAGGAAGAAGATGAATCAGATGACGACAATATGTAACATTTCACCATCCTCTGGTGTCCAT
TTCTGTGACAGTTGCATATGGCTAGCACCATGGATTATATATACCCACTGACCAATTTTCATTA
AATTTTGTCTTATAAACATTGTTGGGTAATTGAGGATATCTGCGTTATATTAAAATGTAGATTC
ATGTTTGATTAGAAATTCTAGGAACTGGGCCTGGAGAGATGGCTCAGCAGTTAAGAGCTGCTCT
TCCAGGGGACATAGGTTCAATTCCCAGCACCCGCATGGCAGCTCACACCTGTTTGTAACTCTAG
CTCCAGGTCTCTGACACCTAGACACAGAGGTACTTGCAGGCAAAACACCAATGAATATAAAATA
AAAATAAATGATATATATATTTACACATATAACAAGTATATACAAATATGTATATTATACAGAC
ACATGTGTGTGTATATACATATAAATTCTTGGTGCTATTCTGGTGTGGTAGTATATGTCTTTAA
TCCTAGTACTCTGGAGGCAGAGGCAGGTGGATCTCTTGAGTTCAAGGCTAGTATTTAAAAACAA
AAACAAATGTAGTGCCCAGACTAAGGCTGAAAGATTGAGCCCACAAGTCAATTTACAATTCCAT
TTTGTTTTAACTAGAATTAAAAGAATAATTTTAGATTTTTTTTTTCTTTTTTTCAGAGCTGGGG
ACCGAACCCAGGGCCTTGCGCTTCCTAGGCAAGCGCTCTACCACTAAGCTAAATCCCCAACCCC
TTAGATTTATTTTTATTTTTTGCATGTTTATGTATATTACAGTGCCATGCCTGGTGCTCATGGA
GGTCAAAAGAATGCTTTAATCTAGAACTAAAGTTATGGAGGACTGTGAATCATGTATGTTCGAA
ACTGAACTTGGGTCCTGTGTAAGAGCAACACGTCCTCTTAACCACTGAGCCATCTCTCCAGCCC
TCTTTGACTAGAATGATCATATTCTACTGTGGTTCTTGTATAATGTTTTGTTTAATGTAGGGAT
ATCCTGTAACCACTATTGAGGACTAACCTGCCTTTTGTGGAAAATGTGACATATTCTAATTTGA
CATCAATACAGACAACATTTATTTTCAGACTGCATAAATATCTTATGACTGGAAATTATCTTGA
TATTGGCACCTGAAACAAAAACTTAAAAGTTCCAAACTGGGCTTAAATATTTCATGTAATAAAA
TGTTTATAGTACTTATCTGATAAGAAAGAGTTCTTTTGGTTTGTTTCTGTTACTTTTGGTTTAT
CTGAGGCAGAGTTAGTCTTCCTACATAAGCCCTGCCTGTCCTGGAACTTATTACATAGGCCAGG
CTGGCTTTGAACTCTCGAGATCCCCTTGCCTCTGCCTCCACCACACCTGGCCCTGTTTCTGTTG
TTAAAATGACCTAAAAAAAAGAAAATCAAATTTAGATTGTCAGTATCTCTGAAACAATTTCCTT
TGTAAGACAAGTGGCAAAATTAAAATTATGTATATTTTTTAAACATAAAGTAAACACATACTAC
AATGCAGATAAGATACCAGAAGAAACTCCAAATGAAAACGTCTTGAATGTGTAACTTTCTGTTT
TATTCGTCTGTTGAAATGTAATCTAGAGCTGACCTATATTTTACATTCTGGAACATCGCTGTAT
CCATATTGTATTCCTCGTACTTAGGCTGTTTCTAAGAGGAAGACAGTCCTATGTATTCCCCACA
AAGCCACCATAAGATCTCAAAACCACCAAAGTTCCTCCCCACTAAAGGCCCTTCAAGTGTTTAA
TATTTTTATCATAAATTATGTTTGTAACTAACCATGTGCAGTTCCACCACCCAGAACATGAGTT
GTTTTAAATCAGACAAGGCATGGTGCCACATACATTGTAATTCTAGTTCTCTAGAAGGTAAGAT
AGGAGAATTTAGAGGTCAACTTTGGATAAGGAGTGAGTGAGTTTCAGGCAAATCTGGAGAATCT
TACTTAACAAGAAGCTTCTTATAGGTATATCTGTGAGTTCTAGGACACCCTGGCCTATAAAGTT
AGTTCCAAGACAGGCAGGGCTACACAAAAGAAACTCTGTTTCAAAAAAACAAAAATACACGTCT
AATTCAACTTCAGTTGCCTAACAACTGTCAAAGCATGCAAGATTAAAGACAGAAAATAGAAACC
GATTCTTACCCTTTATAAAATACTCTGAAAACCCCATAGTGATGAAACTGCTAGTTGCTATCTT
GCTCCCTATAATCTGACTACTTTTCAAGAGTTACAGGGCAAAAGGCATTCATTCTCATAACCCA
AGATGTTTTACCGTCTATTTATATCCACTGTCTATTCAGCTTGAACTGTGTTACACAATAGGTA
ACTGTATTTATTGTGCTTTGTATATTTGAACATTAAAATGTTCTTTTTTGATCATTTACCCTTG
AA

hide sequence

Protein Sequences


Protein RefSeqs	NP_058976	(Get FASTA)	NCBI Sequence Viewer
	XP_017449548	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH81817	(Get FASTA)	NCBI Sequence Viewer
	EDM03560	(Get FASTA)	NCBI Sequence Viewer
	P18422	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_058976 ⟸ NM_017280

- UniProtKB:

P18422 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSN
KRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSA
VRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMTCRDVVK
EVAKIIYIVHDEVKDKAFELELSWVGELTKGRHEIVPKDVREEAEKYAKESLKEEDESDDDNM

hide sequence

RefSeq Acc Id:	XP_017449548 ⟸ XM_017594059
- Peptide Label:	isoform X1
- Sequence:	show sequence MAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVRPFGCSFMLG SYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMTCRDVVKEVAKIIYIVHD EVKDKAFELELSWVGELTKGRHEIVPKDVREEAEKYAKESLKEEDESDDDNM hide sequence

RefSeq Acc Id:

ENSRNOP00000010753 ⟸ ENSRNOT00000010753

Transcriptome

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

Promoters

RGD ID:

13694647

Promoter ID:

EPDNEW_R5170

Type:

initiation region

Name:

Psma3_1

Description:

proteasome subunit alpha 3

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	6	93,422,967 - 93,423,027	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:61844	AgrOrtholog
Ensembl Genes	ENSRNOG00000007851	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000010753	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000010753	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	3.60.20.10	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7110009	IMAGE-MGC_LOAD
InterPro	Ntn_hydrolases_N	UniProtKB/Swiss-Prot
	Proteasome_alpha-type	UniProtKB/Swiss-Prot
	Proteasome_alpha_3	UniProtKB/Swiss-Prot
	Proteasome_asu_N	UniProtKB/Swiss-Prot
	Proteasome_sua/b	UniProtKB/Swiss-Prot
KEGG Report	rno:29670	UniProtKB/Swiss-Prot
	rno:408248	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:93511	IMAGE-MGC_LOAD
NCBI Gene	29670	ENTREZGENE
PANTHER	PTHR11599:SF10	UniProtKB/Swiss-Prot
Pfam	Proteasome	UniProtKB/Swiss-Prot
	Proteasome_A_N	UniProtKB/Swiss-Prot
PhenoGen	Psma3	PhenoGen
PROSITE	PROTEASOME_ALPHA_1	UniProtKB/Swiss-Prot
	PROTEASOME_ALPHA_2	UniProtKB/Swiss-Prot
SMART	Proteasome_A_N	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF56235	UniProtKB/Swiss-Prot
TIGR	TC216589
UniProt	P18422	ENTREZGENE, UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2019-09-13	Psma3	proteasome 20S subunit alpha 3	Psma3	proteasome subunit alpha 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2015-08-19	Psma3	proteasome subunit alpha 3	Psma3	proteasome (prosome, macropain) subunit, alpha type 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-06-10	Psma3	proteasome (prosome, macropain) subunit, alpha type 3			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)

Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)