Psma3 (proteasome 20S subunit alpha 3) - Rat Genome Database

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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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2689,483,741 - 89,503,775 (+)NCBI
Rnor_6.0 Ensembl693,423,002 - 93,444,240 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0693,423,029 - 93,444,223 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06102,868,534 - 102,898,751 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4693,092,191 - 93,112,167 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1693,095,646 - 93,115,622 (+)NCBI
Celera687,965,854 - 87,985,832 (+)NCBICelera
Cytogenetic Map6q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
JMP syndrome  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2689,483,741 - 89,503,775 (+)NCBI
Rnor_6.0 Ensembl693,423,002 - 93,444,240 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0693,423,029 - 93,444,223 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06102,868,534 - 102,898,751 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4693,092,191 - 93,112,167 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1693,095,646 - 93,115,622 (+)NCBI
Celera687,965,854 - 87,985,832 (+)NCBICelera
Cytogenetic Map6q24NCBI
PSMA3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1458,244,843 - 58,272,012 (+)EnsemblGRCh38hg38GRCh38
GRCh381458,244,843 - 58,272,004 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371458,711,561 - 58,738,722 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361457,781,346 - 57,808,479 (+)NCBINCBI36hg18NCBI36
Build 341457,781,345 - 57,808,479NCBI
Celera1438,761,540 - 38,788,685 (+)NCBI
Cytogenetic Map14q23.1NCBI
HuRef1438,877,058 - 38,904,216 (+)NCBIHuRef
CHM1_11458,650,049 - 58,677,295 (+)NCBICHM1_1
Psma3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391271,016,057 - 71,042,651 (+)NCBIGRCm39mm39
GRCm39 Ensembl1271,021,395 - 71,043,121 (+)Ensembl
GRCm381270,969,283 - 70,995,877 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1270,974,621 - 70,996,347 (+)EnsemblGRCm38mm10GRCm38
MGSCv371272,075,610 - 72,095,924 (+)NCBIGRCm37mm9NCBIm37
MGSCv361271,893,298 - 71,913,526 (+)NCBImm8
Celera1272,078,082 - 72,098,500 (+)NCBICelera
Cytogenetic Map12C2NCBI
Psma3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546611,979,482 - 11,997,952 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546611,979,482 - 11,997,952 (+)NCBIChiLan1.0ChiLan1.0
PSMA3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11457,105,891 - 57,133,181 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1457,105,891 - 57,133,181 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01438,836,869 - 38,864,152 (+)NCBIMhudiblu_PPA_v0panPan3
PSMA3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1833,616,735 - 33,642,434 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl833,616,480 - 33,642,404 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha833,378,219 - 33,403,729 (+)NCBI
ROS_Cfam_1.0833,858,343 - 33,884,028 (+)NCBI
UMICH_Zoey_3.1833,471,278 - 33,496,743 (+)NCBI
UNSW_CanFamBas_1.0833,538,435 - 33,564,256 (+)NCBI
UU_Cfam_GSD_1.0833,913,572 - 33,939,074 (+)NCBI
Psma3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864071,519,504 - 71,541,053 (-)NCBI
SpeTri2.0NW_0049364952,650,668 - 2,672,192 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PSMA3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1187,343,507 - 187,372,215 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11187,342,231 - 187,371,149 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21208,246,764 - 208,274,223 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PSMA3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12435,438,084 - 35,465,320 (+)NCBI
ChlSab1.1 Ensembl2435,437,308 - 35,465,203 (+)Ensembl
Psma3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248843,324,390 - 3,346,128 (+)NCBI

Position Markers
RH127444  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0693,442,743 - 93,442,958NCBIRnor6.0
Rnor_5.06102,898,469 - 102,898,684UniSTSRnor5.0
RGSC_v3.4693,111,885 - 93,112,100UniSTSRGSC3.4
Celera687,985,550 - 87,985,765UniSTS
RH 3.4 Map6639.3UniSTS
Cytogenetic Map6q24UniSTS
RH138090  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0693,424,697 - 93,424,843NCBIRnor6.0
Rnor_5.06102,870,438 - 102,870,584UniSTSRnor5.0
RGSC_v3.4693,093,859 - 93,094,005UniSTSRGSC3.4
Celera687,967,522 - 87,967,668UniSTS
RH 3.4 Map6640.3UniSTS
Cytogenetic Map10q25UniSTS
Cytogenetic Map6q24UniSTS
RH130667  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0693,443,835 - 93,444,035NCBIRnor6.0
Rnor_5.06102,899,561 - 102,899,761UniSTSRnor5.0
RGSC_v3.4693,112,977 - 93,113,177UniSTSRGSC3.4
Celera687,986,642 - 87,986,842UniSTS
RH 3.4 Map6639.5UniSTS
Cytogenetic Map6q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat
4889848Pur25Proteinuria QTL 25140.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)65980306594001333Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)660606431108154445Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)660606431108154445Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)662263348107263348Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)666129520111129520Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)671206251116206251Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)675449871120449871Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)675623277120276465Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)675623277120623277Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)676902247114203334Rat
2293837Kiddil1Kidney dilation QTL 13.7kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)684763275108464097Rat
2293842Kiddil3Kidney dilation QTL 34.3kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)684763275108464097Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)686422697115379601Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)687418448111129520Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)688507712133507712Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)689631358134631358Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)689631358134631358Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat

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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010753   ⟹   ENSRNOP00000010753
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl693,423,002 - 93,444,240 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000075868
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl693,437,383 - 93,441,873 (+)Ensembl
RefSeq Acc Id: NM_017280   ⟹   NP_058976
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2689,483,777 - 89,503,775 (+)NCBI
Rnor_6.0693,423,029 - 93,443,025 (+)NCBI
Rnor_5.06102,868,534 - 102,898,751 (+)NCBI
RGSC_v3.4693,092,191 - 93,112,167 (+)RGD
Celera687,965,854 - 87,985,832 (+)RGD
Sequence:
RefSeq Acc Id: XM_017594059   ⟹   XP_017449548
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2689,483,741 - 89,502,746 (+)NCBI
Rnor_6.0693,424,370 - 93,444,223 (+)NCBI
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:
RefSeq Acc Id: XP_017449548   ⟸   XM_017594059
- Peptide Label: isoform X1
- 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 AssemblyChrPosition (strand)Source
Rnor_6.0693,422,967 - 93,423,027EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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

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