Psmc4 (proteasome 26S subunit, ATPase 4) - Rat Genome Database

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Gene: Psmc4 (proteasome 26S subunit, ATPase 4) Rattus norvegicus
Analyze
Symbol: Psmc4
Name: proteasome 26S subunit, ATPase 4
RGD ID: 621102
Description: Predicted to enable proteasome-activating activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to act upstream of or within blastocyst development. Located in inclusion body and synapse. Part of cytosolic proteasome complex. Orthologous to human PSMC4 (proteasome 26S subunit, ATPase 4); PARTICIPATES IN ubiquitin/proteasome degradation pathway; INTERACTS WITH (+)-schisandrin B; 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 26S protease regulatory subunit 6B; 26S proteasome AAA-ATPase subunit RPT3; 26S proteasome regulatory subunit 6B; proteasome (prosome, macropain) 26S subunit, ATPase, 4; proteasome 26S ATPase subunit 4; proteasome 26S subunit ATPase 4; S6 ATPase; TAT-binding protein 7; TBP-7; Tbp7
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
mRatBN7.2183,349,127 - 83,357,497 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl183,348,592 - 83,357,494 (-)Ensembl
Rnor_6.0184,978,220 - 84,986,536 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl184,978,206 - 84,986,581 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0186,194,919 - 86,203,235 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4183,151,149 - 83,159,464 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1183,229,258 - 83,237,575 (-)NCBI
Celera177,748,725 - 77,757,041 (-)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
1H-pyrazole  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-amino-14,16-dimethyloctadecan-3-ol  (ISO)
2-methylcholine  (ISO)
2-nitrofluorene  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
aflatoxin B1  (EXP,ISO)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
azoxystrobin  (EXP)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
Brodifacoum  (EXP)
bromobenzene  (EXP)
caffeine  (ISO)
cannabidiol  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (EXP)
choline  (ISO)
clofibrate  (EXP)
cobalt dichloride  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (ISO)
dichlorine  (EXP)
dicrotophos  (ISO)
diethylstilbestrol  (EXP)
disodium selenite  (ISO)
disulfiram  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
elesclomol  (ISO)
epoxomicin  (ISO)
ethanol  (EXP)
fenthion  (ISO)
fenvalerate  (EXP)
finasteride  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
gentamycin  (EXP)
glyphosate  (EXP)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP)
hydrogen sulfide  (ISO)
imidacloprid  (EXP)
ivermectin  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (EXP)
maneb  (ISO)
melatonin  (ISO)
methapyrilene  (EXP)
methidathion  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodimethylamine  (EXP)
nefazodone  (EXP)
nicotine  (ISO)
nimesulide  (EXP)
oxidopamine  (EXP)
ozone  (EXP)
paracetamol  (ISO)
paraquat  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (EXP,ISO)
phlorizin  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
rotenone  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
tetrachloromethane  (EXP,ISO)
thiabendazole  (EXP)
trimellitic anhydride  (ISO)
valdecoxib  (EXP)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
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
# Reference Title Reference Citation
1. Activity-dependent dynamics and sequestration of proteasomes in dendritic spines. Bingol B and Schuman EM, Nature. 2006 Jun 29;441(7097):1144-8.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Structures of the rat proteasomal ATPases: determination of highly conserved structural motifs and rules for their spacing. Makino Y, etal., Biochem Biophys Res Commun 1996 Mar 27;220(3):1049-54.
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Misfolding of proteins with a polyglutamine expansion is facilitated by proteasomal chaperones. Rousseau E, etal., J Biol Chem. 2009 Jan 16;284(3):1917-29. doi: 10.1074/jbc.M806256200. Epub 2008 Nov 5.
11. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:9688553   PMID:10945464   PMID:15489334   PMID:16857966   PMID:17323924   PMID:19946888   PMID:21630459   PMID:22871113   PMID:31904090  


Genomics

Comparative Map Data
Psmc4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2183,349,127 - 83,357,497 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl183,348,592 - 83,357,494 (-)Ensembl
Rnor_6.0184,978,220 - 84,986,536 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl184,978,206 - 84,986,581 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0186,194,919 - 86,203,235 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4183,151,149 - 83,159,464 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1183,229,258 - 83,237,575 (-)NCBI
Celera177,748,725 - 77,757,041 (-)NCBICelera
Cytogenetic Map1q21NCBI
PSMC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381939,971,165 - 39,981,764 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1939,971,165 - 39,981,764 (+)EnsemblGRCh38hg38GRCh38
GRCh371940,477,072 - 40,487,671 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361945,168,913 - 45,179,193 (+)NCBINCBI36hg18NCBI36
Build 341945,168,912 - 45,179,191NCBI
Celera1937,275,447 - 37,285,724 (+)NCBI
Cytogenetic Map19q13.2NCBI
HuRef1936,913,453 - 36,924,135 (+)NCBIHuRef
CHM1_11940,476,958 - 40,487,716 (+)NCBICHM1_1
T2T-CHM13v2.01942,791,375 - 42,801,971 (+)NCBI
Psmc4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39727,741,127 - 27,749,517 (-)NCBIGRCm39mm39
GRCm39 Ensembl727,741,132 - 27,749,526 (-)Ensembl
GRCm38728,041,702 - 28,050,092 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl728,041,707 - 28,050,101 (-)EnsemblGRCm38mm10GRCm38
MGSCv37728,826,721 - 28,835,111 (-)NCBIGRCm37mm9NCBIm37
MGSCv36727,750,477 - 27,758,803 (-)NCBImm8
Celera722,608,215 - 22,616,605 (-)NCBICelera
Cytogenetic Map7A3NCBI
cM Map716.11NCBI
Psmc4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555781,113,445 - 1,120,370 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555781,113,445 - 1,120,050 (-)NCBIChiLan1.0ChiLan1.0
PSMC4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11945,533,141 - 45,543,245 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1945,533,141 - 45,543,245 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01937,018,112 - 37,028,490 (+)NCBIMhudiblu_PPA_v0panPan3
PSMC4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11113,548,351 - 113,557,725 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1113,548,373 - 113,557,630 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1112,952,245 - 112,961,621 (-)NCBI
ROS_Cfam_1.01114,148,644 - 114,157,982 (-)NCBI
ROS_Cfam_1.0 Ensembl1114,148,650 - 114,157,892 (-)Ensembl
UMICH_Zoey_3.11113,707,548 - 113,716,884 (-)NCBI
UNSW_CanFamBas_1.01113,340,335 - 113,349,711 (-)NCBI
UU_Cfam_GSD_1.01114,334,441 - 114,343,783 (-)NCBI
Psmc4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934914,094,546 - 14,100,215 (+)NCBI
SpeTri2.0NW_0049366612,522,665 - 2,528,279 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PSMC4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl648,406,376 - 48,416,216 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1648,406,237 - 48,414,470 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PSMC4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1634,486,303 - 34,495,392 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl634,486,338 - 34,495,251 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607312,578,624 - 12,587,383 (+)NCBIVero_WHO_p1.0
Psmc4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624925119,777 - 130,723 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_004624925119,837 - 127,678 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
STS-T26522  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2183,349,154 - 83,349,325 (+)MAPPERmRatBN7.2
Rnor_6.0184,978,239 - 84,978,409NCBIRnor6.0
Rnor_5.0186,194,938 - 86,195,108UniSTSRnor5.0
RGSC_v3.4183,151,167 - 83,151,337UniSTSRGSC3.4
Celera177,748,744 - 77,748,914UniSTS
Cytogenetic Map1q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)165789093115540829Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)166023617118608521Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)17219768090508767Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)177494165122494165Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)177857876122857876Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)177876254106047988Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)178350581123350581Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)178430536123430536Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)17843075491209302Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)178479925123479925Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)180592172125592172Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)182174743118944897Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:34
Count of miRNA genes:30
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000025819
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025819   ⟹   ENSRNOP00000025819
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl183,348,592 - 83,357,494 (-)Ensembl
Rnor_6.0 Ensembl184,978,206 - 84,986,581 (-)Ensembl
RefSeq Acc Id: NM_057122   ⟹   NP_476463
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2183,349,127 - 83,357,497 (-)NCBI
Rnor_6.0184,978,220 - 84,986,536 (-)NCBI
Rnor_5.0186,194,919 - 86,203,235 (-)NCBI
RGSC_v3.4183,151,149 - 83,159,464 (-)RGD
Celera177,748,725 - 77,757,041 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_476463   ⟸   NM_057122
- UniProtKB: Q63570 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000025819   ⟸   ENSRNOT00000025819

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63570-F1-model_v2 AlphaFold Q63570 1-418 view protein structure

Transcriptome

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

Promoters
RGD ID:13689860
Promoter ID:EPDNEW_R385
Type:multiple initiation site
Name:Psmc4_1
Description:proteasome 26S subunit, ATPase 4
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_6.0184,986,562 - 84,986,622EPDNEW

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621102 AgrOrtholog
BioCyc Gene G2FUF-60267 BioCyc
Ensembl Genes ENSRNOG00000018994 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000025819 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000025819 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.50.140 UniProtKB/Swiss-Prot
  3.40.50.300 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6889167 IMAGE-MGC_LOAD
InterPro 26S_Psome_P45-like UniProtKB/Swiss-Prot
  AAA+_ATPase UniProtKB/Swiss-Prot
  AAA_lid_3 UniProtKB/Swiss-Prot
  ATPase_AAA_core UniProtKB/Swiss-Prot
  ATPase_AAA_CS UniProtKB/Swiss-Prot
  NA-bd_OB-fold UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot
  Prot_ATP_ID_OB UniProtKB/Swiss-Prot
  PSMC4 UniProtKB/Swiss-Prot
KEGG Report rno:117262 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72664 IMAGE-MGC_LOAD
NCBI Gene 117262 ENTREZGENE
PANTHER PTHR23073:SF120 UniProtKB/Swiss-Prot
Pfam AAA UniProtKB/Swiss-Prot
  AAA_lid_3 UniProtKB/Swiss-Prot
  Prot_ATP_ID_OB UniProtKB/Swiss-Prot
PhenoGen Psmc4 PhenoGen
PROSITE AAA UniProtKB/Swiss-Prot
SMART AAA UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot
TIGRFAMs 26Sp45 UniProtKB/Swiss-Prot
UniProt PRS6B_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-08-19 Psmc4  proteasome 26S subunit, ATPase 4  Psmc4  proteasome (prosome, macropain) 26S subunit, ATPase, 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Psmc4  proteasome (prosome, macropain) 26S subunit, ATPase, 4      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Psmc4  proteasome (prosome, macropain) 26S subunit, ATPase, 4      Symbol and Name status set to provisional 70820 PROVISIONAL