Ppm1a (protein phosphatase, Mg2+/Mn2+ dependent, 1A) - Rat Genome Database
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Gene: Ppm1a (protein phosphatase, Mg2+/Mn2+ dependent, 1A) Rattus norvegicus
Analyze
Symbol: Ppm1a
Name: protein phosphatase, Mg2+/Mn2+ dependent, 1A
RGD ID: 3373
Description: Exhibits ion channel binding activity and protein C-terminus binding activity. Predicted to be involved in several processes, including cellular protein modification process; positive regulation of protein export from nucleus; and regulation of signal transduction. Localizes to neuron projection. Orthologous to human PPM1A (protein phosphatase, Mg2+/Mn2+ dependent 1A); PARTICIPATES IN Bone morphogenetic proteins signaling pathway; mitogen activated protein kinase signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3H-1,2-dithiole-3-thione; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: IA; MGC114340; PP2C-alpha; Pp2c1; protein phosphatase 1A; protein phosphatase 1A, magnesium dependent, alpha isoform; protein phosphatase 2C isoform alpha; protein phosphatase IA; Protein phosphatase type 1A (formely 2C) Mg-dependent alpha isoform; Protein phosphatase type 1A (formely 2C), Mg-dependent, alpha isoform
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2691,439,094 - 91,486,139 (+)NCBI
Rnor_6.0 Ensembl694,429,068 - 94,484,351 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0694,433,658 - 94,484,979 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06103,874,809 - 103,935,598 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4695,162,067 - 95,198,936 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1695,165,522 - 95,202,392 (+)NCBI
Celera689,903,080 - 89,939,925 (+)NCBICelera
Cytogenetic Map6q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxyphenyl retinamide  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (ISO)
bisphenol A  (EXP)
bortezomib  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clozapine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethyl methanesulfonate  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
glafenine  (EXP)
glyphosate  (ISO)
haloperidol  (EXP)
L-methionine  (ISO)
leflunomide  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
nickel atom  (ISO)
oxaliplatin  (EXP)
ozone  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
propiconazole  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
testosterone enanthate  (ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (EXP,ISO)
trichostatin A  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytosol  (IBA,IEA,ISO,ISS)
membrane  (ISO,ISS)
neuron projection  (IDA)
nucleus  (IBA,IEA,ISO)
plasma membrane  (IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10644691   PMID:11559703   PMID:12477932   PMID:12761501   PMID:14654243   PMID:14664809   PMID:14674259   PMID:16751101   PMID:18930133   PMID:20801214   PMID:21151953   PMID:21829547  
PMID:22019086   PMID:22384250   PMID:22926646   PMID:23088624   PMID:25100727  


Genomics

Comparative Map Data
Ppm1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2691,439,094 - 91,486,139 (+)NCBI
Rnor_6.0 Ensembl694,429,068 - 94,484,351 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0694,433,658 - 94,484,979 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06103,874,809 - 103,935,598 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4695,162,067 - 95,198,936 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1695,165,522 - 95,202,392 (+)NCBI
Celera689,903,080 - 89,939,925 (+)NCBICelera
Cytogenetic Map6q24NCBI
PPM1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1460,245,752 - 60,299,087 (+)EnsemblGRCh38hg38GRCh38
GRCh381460,245,750 - 60,299,087 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371460,712,468 - 60,765,805 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh371460,712,470 - 60,765,805 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361459,782,223 - 59,829,826 (+)NCBINCBI36hg18NCBI36
Build 341459,782,222 - 59,829,823NCBI
Celera1440,762,274 - 40,815,941 (+)NCBI
Cytogenetic Map14q23.1NCBI
HuRef1440,876,613 - 40,929,690 (+)NCBIHuRef
CHM1_11460,651,750 - 60,705,118 (+)NCBICHM1_1
Ppm1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391272,804,231 - 72,846,593 (+)NCBIGRCm39mm39
GRCm381272,761,211 - 72,799,819 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1272,757,455 - 72,799,819 (+)EnsemblGRCm38mm10GRCm38
MGSCv371273,862,198 - 73,895,927 (+)NCBIGRCm37mm9NCBIm37
MGSCv361273,680,442 - 73,713,400 (+)NCBImm8
Celera1273,877,430 - 73,911,618 (+)NCBICelera
Cytogenetic Map12C3NCBI
Ppm1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554669,315,227 - 9,331,213 (-)NCBIChiLan1.0ChiLan1.0
PPM1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11459,117,020 - 59,169,524 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1459,117,020 - 59,162,928 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01440,853,227 - 40,906,044 (+)NCBIMhudiblu_PPA_v0panPan3
PPM1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl835,336,140 - 35,377,551 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1835,336,055 - 35,384,249 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ppm1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364954,542,576 - 4,560,603 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PPM1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1189,170,585 - 189,291,350 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11189,248,974 - 189,296,147 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21210,387,426 - 210,406,136 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PPM1A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12437,474,371 - 37,522,956 (+)NCBI
ChlSab1.1 Ensembl2437,506,914 - 37,516,414 (+)Ensembl

Position Markers
D6Arb18  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0694,483,226 - 94,484,314NCBIRnor6.0
Rnor_5.06103,928,416 - 103,929,504UniSTSRnor5.0
RGSC_v3.4695,197,641 - 95,198,729UniSTSRGSC3.4
Celera689,938,630 - 89,939,718UniSTS
Cytogenetic Map6q24UniSTS
RH144473  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0694,476,084 - 94,476,274NCBIRnor6.0
Rnor_5.06103,921,274 - 103,921,464UniSTSRnor5.0
RGSC_v3.4695,190,499 - 95,190,689UniSTSRGSC3.4
Celera689,931,492 - 89,931,682UniSTS
RH 3.4 Map6663.0UniSTS
Cytogenetic Map6q24UniSTS
RH140124  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0694,484,013 - 94,484,214NCBIRnor6.0
Rnor_5.06103,929,203 - 103,929,404UniSTSRnor5.0
RGSC_v3.4695,198,428 - 95,198,629UniSTSRGSC3.4
Celera689,939,417 - 89,939,618UniSTS
RH 3.4 Map6658.9UniSTS
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
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
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)693706176111134673Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:57
Count of miRNA genes:44
Interacting mature miRNAs:55
Transcripts:ENSRNOT00000008238
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: ENSRNOT00000008238   ⟹   ENSRNOP00000008238
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl694,429,068 - 94,484,351 (+)Ensembl
RefSeq Acc Id: NM_017038   ⟹   NP_058734
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2691,443,266 - 91,480,252 (+)NCBI
Rnor_6.0694,433,661 - 94,484,521 (+)NCBI
Rnor_5.06103,874,809 - 103,935,598 (+)NCBI
RGSC_v3.4695,162,067 - 95,198,936 (+)RGD
Celera689,903,080 - 89,939,925 (+)RGD
Sequence:
RefSeq Acc Id: XM_017594034   ⟹   XP_017449523
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0694,433,658 - 94,484,979 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039111786   ⟹   XP_038967714
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2691,439,094 - 91,486,139 (+)NCBI
RefSeq Acc Id: XM_039111787   ⟹   XP_038967715
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2691,465,994 - 91,486,139 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_058734   ⟸   NM_017038
- UniProtKB: P20650 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017449523   ⟸   XM_017594034
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000008238   ⟸   ENSRNOT00000008238
RefSeq Acc Id: XP_038967714   ⟸   XM_039111786
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038967715   ⟸   XM_039111787
- Peptide Label: isoform X2
Protein Domains
PP2C_C   PPM-type phosphatase

Transcriptome

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


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)
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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

Database Acc Id Source(s)
AGR Gene RGD:3373 AgrOrtholog
Ensembl Genes ENSRNOG00000005916 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008238 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008238 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.430 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro PP2C_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PP2C_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PP2C_C_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PPM-type_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PPM-type_phosphatase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24666 UniProtKB/Swiss-Prot
NCBI Gene 24666 ENTREZGENE
Pfam PP2C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PP2C_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ppm1a PhenoGen
PROSITE PPM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PPM_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PP2Cc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF81601 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81606 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0H2UHE5_RAT UniProtKB/TrEMBL
  P20650 ENTREZGENE, UniProtKB/Swiss-Prot
  Q4V8L2_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-05-03 Ppm1a  protein phosphatase, Mg2+/Mn2+ dependent, 1A  Ppm1a  protein phosphatase 1A, magnesium dependent, alpha isoform  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Ppm1a  Protein phosphatase type 1A (formely 2C), Mg-dependent, alpha isoform      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_regulation requires Mg2+ for activity 729446