Ppm1a (protein phosphatase, Mg2+/Mn2+ dependent, 1A)

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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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	6	91,439,094 - 91,486,139 (+)	NCBI
Rnor_6.0 Ensembl	6	94,429,068 - 94,484,351 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	6	94,433,658 - 94,484,979 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	6	103,874,809 - 103,935,598 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	95,162,067 - 95,198,936 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	6	95,165,522 - 95,202,392 (+)	NCBI
Celera	6	89,903,080 - 89,939,925 (+)	NCBI		Celera
Cytogenetic Map	6	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

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

Biological Process

cellular response to transforming growth factor beta stimulus (IEA,ISO)

dephosphorylation (ISO)

N-terminal protein myristoylation (IEA,ISO,ISS)

negative regulation of BMP signaling pathway (IEA,ISO)

negative regulation of I-kappaB kinase/NF-kappaB signaling (IBA,IEA,ISO,ISS)

negative regulation of NIK/NF-kappaB signaling (IEA,ISO,ISS)

negative regulation of SMAD protein complex assembly (IEA,ISO)

negative regulation of transforming growth factor beta receptor signaling pathway (IEA,ISO)

peptidyl-threonine dephosphorylation (IEA,ISO)

positive regulation of canonical Wnt signaling pathway (IBA,IEA,ISO)

positive regulation of I-kappaB kinase/NF-kappaB signaling (ISO)

positive regulation of protein export from nucleus (IEA,ISO)

positive regulation of transcription, DNA-templated (IEA,ISO)

protein dephosphorylation (ISO,ISS)

Cellular Component

cytosol (IBA,IEA,ISO,ISS)

membrane (ISO,ISS)

neuron projection (IDA)

nucleus (IBA,IEA,ISO)

plasma membrane (IEA,ISO)

Molecular Function

calmodulin-dependent protein phosphatase activity (IEA,ISO)

ion channel binding (IDA)

magnesium ion binding (IEA)

manganese ion binding (IEA)

phosphoprotein phosphatase activity (ISO)

protein binding (IPI,ISO)

protein C-terminus binding (IPI)

protein serine phosphatase activity (IEA)

protein serine/threonine phosphatase activity (ISO)

protein threonine phosphatase activity (IEA)

R-SMAD binding (IEA,ISO,ISS)

Molecular Pathway Annotations Click to see Annotation Detail View

Bone morphogenetic proteins signaling pathway (ISO)

mitogen activated protein kinase signaling pathway (IEA)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	Li D, etal., J Neurosci. 2005 Feb 23;25(8):1914-23.
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.	Pipeline to import Pathway Interaction Database annotations from NCI into RGD
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.	Tamura S, etal., Proc Natl Acad Sci U S A 1989 Mar;86(6):1796-800.

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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	6	91,439,094 - 91,486,139 (+)	NCBI
Rnor_6.0 Ensembl	6	94,429,068 - 94,484,351 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	6	94,433,658 - 94,484,979 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	6	103,874,809 - 103,935,598 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	95,162,067 - 95,198,936 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	6	95,165,522 - 95,202,392 (+)	NCBI
Celera	6	89,903,080 - 89,939,925 (+)	NCBI		Celera
Cytogenetic Map	6	q24	NCBI

PPM1A
(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	60,245,752 - 60,299,087 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	14	60,245,750 - 60,299,087 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	14	60,712,468 - 60,765,805 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	14	60,712,470 - 60,765,805 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	14	59,782,223 - 59,829,826 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	14	59,782,222 - 59,829,823	NCBI
Celera	14	40,762,274 - 40,815,941 (+)	NCBI
Cytogenetic Map	14	q23.1	NCBI
HuRef	14	40,876,613 - 40,929,690 (+)	NCBI		HuRef
CHM1_1	14	60,651,750 - 60,705,118 (+)	NCBI		CHM1_1

Ppm1a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	72,804,231 - 72,846,593 (+)	NCBI	GRCm39		mm39
GRCm38	12	72,761,211 - 72,799,819 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	72,757,455 - 72,799,819 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	73,862,198 - 73,895,927 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	12	73,680,442 - 73,713,400 (+)	NCBI			mm8
Celera	12	73,877,430 - 73,911,618 (+)	NCBI		Celera
Cytogenetic Map	12	C3	NCBI

Ppm1a
(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	NW_004955466	9,315,227 - 9,331,213 (-)	NCBI	ChiLan1.0	ChiLan1.0

PPM1A
(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	59,117,020 - 59,169,524 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	14	59,117,020 - 59,162,928 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	14	40,853,227 - 40,906,044 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

PPM1A
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	8	35,336,140 - 35,377,551 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	8	35,336,055 - 35,384,249 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Ppm1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936495	4,542,576 - 4,560,603 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PPM1A
(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	189,170,585 - 189,291,350 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	189,248,974 - 189,296,147 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	210,387,426 - 210,406,136 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PPM1A
(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	37,474,371 - 37,522,956 (+)	NCBI
ChlSab1.1 Ensembl	24	37,506,914 - 37,516,414 (+)	Ensembl

Position Markers

D6Arb18

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	94,483,226 - 94,484,314	NCBI	Rnor6.0
Rnor_5.0	6	103,928,416 - 103,929,504	UniSTS	Rnor5.0
RGSC_v3.4	6	95,197,641 - 95,198,729	UniSTS	RGSC3.4
Celera	6	89,938,630 - 89,939,718	UniSTS
Cytogenetic Map	6	q24	UniSTS

RH144473

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	94,476,084 - 94,476,274	NCBI	Rnor6.0
Rnor_5.0	6	103,921,274 - 103,921,464	UniSTS	Rnor5.0
RGSC_v3.4	6	95,190,499 - 95,190,689	UniSTS	RGSC3.4
Celera	6	89,931,492 - 89,931,682	UniSTS
RH 3.4 Map	6	663.0	UniSTS
Cytogenetic Map	6	q24	UniSTS

RH140124

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	6	94,484,013 - 94,484,214	NCBI	Rnor6.0
Rnor_5.0	6	103,929,203 - 103,929,404	UniSTS	Rnor5.0
RGSC_v3.4	6	95,198,428 - 95,198,629	UniSTS	RGSC3.4
Celera	6	89,939,417 - 89,939,618	UniSTS
RH 3.4 Map	6	658.9	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
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
1331722	Thshl1	Thyroid stimulating hormone level QTL 1	11.7	0.0001	blood thyroid-stimulating hormone amount (VT:0005119)	serum thyroid stimulating hormone level (CMO:0001248)	6	93706176	111134673	Rat

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_017038	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039111786	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039111787	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC097333	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473947	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	J04503	(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:

ENSRNOT00000008238 ⟹ ENSRNOP00000008238

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	6	94,429,068 - 94,484,351 (+)	Ensembl

RefSeq Acc Id:

NM_017038 ⟹ NP_058734

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	6	91,443,266 - 91,480,252 (+)	NCBI
Rnor_6.0	6	94,433,661 - 94,484,521 (+)	NCBI
Rnor_5.0	6	103,874,809 - 103,935,598 (+)	NCBI
RGSC_v3.4	6	95,162,067 - 95,198,936 (+)	RGD
Celera	6	89,903,080 - 89,939,925 (+)	RGD

Sequence:

show sequence

TGCCCGGCCGCCGTCGCCACCGCCGCCCCGGCCGACCGAGGGACCCGCCCGCCCGCGGCTGCTC
CGGATCTAGAGGATCAAGTCATAATGGGAGCATTTTTAGACAAGCCAAAGATGGAAAAGCATAA
TGCCCAGGGCCAGGGGAACGGGTTGCGATACGGCCTAAGCAGCATGCAAGGTTGGCGAGTTGAA
ATGGAGGATGCACATACGGCTGTGATCGGTTTGCCAAGTGGACTTGAGACATGGTCATTCTTTG
CTGTATATGATGGGCATGCTGGTTCTCAGGTTGCCAAATACTGCTGTGAGCACTTGTTAGATCA
CATCACCAATAACCAGGATTTTAAAGGCTCTGCAGGAGCACCCTCTGTGGAAAACGTAAAGAAC
GGAATCAGAACAGGTTTTCTGGAGATTGATGAACACATGAGAGTTATGTCAGAGAAGAAACACG
GTGCAGATAGAAGTGGGTCAACAGCTGTGGGTGTCTTAATTTCTCCCCAACATACTTATTTCAT
TAACTGTGGGGACTCAAGAGGTTTACTTTGTAGAAATAGAAAAGTTCACTTCTTCACTCAAGAC
CATAAACCAAGTAATCCTCTGGAAAAAGAACGAATTCAGAATGCAGGGGGCTCTGTGATGATTC
AGCGTGTCAATGGCTCTCTGGCTGTATCAAGAGCTCTTGGGGATTTTGATTACAAATGTGTCCA
TGGAAAAGGTCCCACAGAGCAGCTTGTCTCGCCAGAGCCTGAAGTCCATGATATTGAAAGGTCT
GAAGAAGATGACCAGTTCATCATTCTTGCATGTGATGGCATCTGGGACGTCATGGGCAACGAAG
AGCTCTGTGACTTTGTGAGATCCAGACTTGAAGTCACTGATGACCTTGAGAAAGTTTGCAATGA
AGTAGTCGACACCTGTTTGTATAAGGGAAGTCGAGACAACATGAGTGTGATTTTGATCTGCTTT
CCAAACGCGCCTAAAGTCTCAGCAGAGGCGGTGAAGAAGGAGGCAGAGCTGGACAAGTACCTGG
AGAACAGAGTAGAAGAAATCATAAAGAAGCAGGGGGAAGGCGTCCCTGACTTAGTCCATGTGAT
GCGCACGTTAGCCAGTGAGAACATCCCCAGCCTCCCACCAGGGGGTGAACTGGCAAGCAAGCGG
AATGTAATTGAAGCCGTTTACAATAGACTGAACCCTTACAAAAACGACGACACTGATTCTGCGT
CAACTGATGATATGTGGTAAAGCTGCTCATCTAGCCATGGTTTCACCTTTGCCTGGAAGAGAGA
GAGAGATCAGCGCATCCTTGCTGAGCCTTTAACATCCATCACCGACTTAAGGAAGGGGTCCGAC
ATGGGTGAGGGACTACAGCTTCAGCGATGGAACAGCCAGCCCAGAATGGATTTTTTTTTTTATT
GTAAATTTGAGACTTATGTAAGCGTGATTTCAAACCGTAATTCATGTTGTAAATCAGACTCCAG
CAATTTTTGTTGTATGATTTTGGTTTTTTGTAAAGTGTAATTGTCCTTGTACAAAGTGCTCATA
TTTAATTATGAACTGCTTTAAAATCACTATCAATGATAAAGGAAATTTGGCTTGTTGTGTGGCA
CA

hide sequence

RefSeq Acc Id:

XM_017594034 ⟹ XP_017449523

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	6	94,433,658 - 94,484,979 (+)	NCBI

Sequence:

show sequence

CCGTGCCCGGCCGCCGTCGCCACCGCCGCCCCGGCCGACCGAGGGACCCGCCCGCCCGCGGCTG
CTCCGGATCTAGAGGATCAAGTCATAATGGGAGCATTTTTAGACAAGCCAAAGATGGAAAAGCA
TAATGCCCAGGGCCAGGGCAACGGGTTGCGATACGGCCTGAGCAGCATGCAAGGTTGGCGAGTT
GAAATGGAGGATGCACATACGGCTGTGATCGGTTTGCCAAGTGGACTCGAGACATGGTCATTCT
TTGCTGTATATGATGGGCATGCTGGTTCTCAGGTTGCCAAATACTGCTGTGAGCACTTGTTAGA
TCACATCACCAATAACCAGGATTTTAAAGGCTCTGCAGGAGCACCTTCTGTGGAAAACGTAAAG
AACGGAATCAGAACAGGTTTTCTGGAGATTGATGAACACATGAGAGTTATGTCAGAGAAGAAAC
ACGGTGCAGATAGAAGTGGGTCAACAGCTGTGGGTGTCTTAATTTCTCCCCAACATACTTATTT
CATTAACTGTGGGGACTCAAGAGGTTTACTTTGTAGAAATAGAAAAGTTCACTTCTTCACTCAA
GACCATAAACCAAGTAATCCTCTGGAAAAAGAACGAATTCAGAATGCAGGGGGCTCTGTGATGA
TTCAGCGTGTCAATGGCTCTCTGGCTGTATCAAGAGCTCTTGGGGATTTTGATTACAAATGTGT
CCATGGAAAAGGTCCCACAGAGCAGCTTGTCTCGCCAGAGCCTGAAGTCCATGATATTGAAAGG
TCTGAAGAAGATGACCAGTTCATCATTCTTGCATGTGATGGCATCTGGGACGTCATGGGCAACG
AAGAGCTCTGTGACTTTGTGAGATCCAGACTTGAAGTCACTGATGACCTTGAGAAAGTTTGCAA
TGAAGTAGTCGACACCTGTTTGTATAAGGGAAGTCGAGACAACATGAGTGTGATTTTGATCTGC
TTTCCAAACGCGCCTAAAGTCTCAGCAGAGGCGGTGAAGAAGGAGGCAGAGCTGGACAAGTACC
TGGAGAACAGAGTAGAAGAAATCATAAAGAAGCAGGGGGAAGGCGTCCCTGACTTAGTCCATGT
GATGCGCACGTTAGCCAGTGAGAACATCCCCAGCCTCCCACCAGGGGGTGAACTGGCAAGCAAG
CGGAATGTAATTGAAGCCGTTTACAATAGACTGAACCCTTACAAAAACGACGACACTGATTCTG
CGTCAACTGATGATATGTGGTAAAGCTGCTCATCTAGCCATGGTTTCACCTTTGCCTCCAAGGG
AGAGAGATCAGCGCATCCTTGCTGAGCCTTTAACATCCATCACCGACTTAAGGAAGGGGTCCGA
CATGGGTGAGGGACTACAGCTTCAGCGATGGAACAGCCAGCCCAGAATGGATTTTTTTTTTTTT
TTATTGTAAATTTGAGACTTATGTAAGCGTGATTTCAAACCGTAATTCATGTTGTAAATCAGAC
TCCAGCAATTTTTGTTGTATGATTTTGGTTTTTTGTAAAGTGTAATTGTCCTTGTACAAAGTGC
TCATATTTAATTATGAACTGCTTTAAAATCACTATCAATGATAAAGGAAATTTGGCTTGTTGTG
TGGCACAACAGACATAGTCATGCTGTATCTGGACTTGGGGTAGGGAAAGCAGCAGCAGCCACAT
AGCTAGATGCTCATGTGCACATGATTATGAAGACTTCCCAAAGCTATACATCAGGGTGTATGGA
GAACTGTCGTCTCTGTGTCCTGGCGAGGGCCTGGCCTGTTGGTGCAGCCACCCCTTCTCACCTG
TCTGTAGGATGTCCTCTCCTCGTAGCCAAGAGTGTCACAGCTGACCCTCTGTATTCATGAGAGC
ATCTACCAGTTTTGGGCTAACATGCCTTGATTCTCTGCACCTCTTTATGAGTTCTTACATTTAA
TTACTAATTGGCAAGCAGCAGCTTCCCACTCAGTGGGAGACTGCCACATTTCGTTCCTATCATG
ATTGGCTGGGCCTGCTGCTGTCCCTAGTAAGATATTCCGAATTCCATTTTATCAATAAAGCTTG
GTTTAACAAACAAGAGA

hide sequence

RefSeq Acc Id:

XM_039111786 ⟹ XP_038967714

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	6	91,439,094 - 91,486,139 (+)	NCBI

RefSeq Acc Id:

XM_039111787 ⟹ XP_038967715

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	6	91,465,994 - 91,486,139 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_058734	(Get FASTA)	NCBI Sequence Viewer
	XP_038967714	(Get FASTA)	NCBI Sequence Viewer
	XP_038967715	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA41917	(Get FASTA)	NCBI Sequence Viewer
	AAH97333	(Get FASTA)	NCBI Sequence Viewer
	EDM03598	(Get FASTA)	NCBI Sequence Viewer
	EDM03599	(Get FASTA)	NCBI Sequence Viewer
	EDM03600	(Get FASTA)	NCBI Sequence Viewer
	P20650	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_058734 ⟸ NM_017038

- UniProtKB:

P20650 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MGAFLDKPKMEKHNAQGQGNGLRYGLSSMQGWRVEMEDAHTAVIGLPSGLETWSFFAVYDGHAG
SQVAKYCCEHLLDHITNNQDFKGSAGAPSVENVKNGIRTGFLEIDEHMRVMSEKKHGADRSGST
AVGVLISPQHTYFINCGDSRGLLCRNRKVHFFTQDHKPSNPLEKERIQNAGGSVMIQRVNGSLA
VSRALGDFDYKCVHGKGPTEQLVSPEPEVHDIERSEEDDQFIILACDGIWDVMGNEELCDFVRS
RLEVTDDLEKVCNEVVDTCLYKGSRDNMSVILICFPNAPKVSAEAVKKEAELDKYLENRVEEII
KKQGEGVPDLVHVMRTLASENIPSLPPGGELASKRNVIEAVYNRLNPYKNDDTDSASTDDMW

hide sequence

RefSeq Acc Id:

XP_017449523 ⟸ XM_017594034

- Peptide Label:

isoform X1

- Sequence:

show sequence

MGAFLDKPKMEKHNAQGQGNGLRYGLSSMQGWRVEMEDAHTAVIGLPSGLETWSFFAVYDGHAG
SQVAKYCCEHLLDHITNNQDFKGSAGAPSVENVKNGIRTGFLEIDEHMRVMSEKKHGADRSGST
AVGVLISPQHTYFINCGDSRGLLCRNRKVHFFTQDHKPSNPLEKERIQNAGGSVMIQRVNGSLA
VSRALGDFDYKCVHGKGPTEQLVSPEPEVHDIERSEEDDQFIILACDGIWDVMGNEELCDFVRS
RLEVTDDLEKVCNEVVDTCLYKGSRDNMSVILICFPNAPKVSAEAVKKEAELDKYLENRVEEII
KKQGEGVPDLVHVMRTLASENIPSLPPGGELASKRNVIEAVYNRLNPYKNDDTDSASTDDMW

hide 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)

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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: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

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 Annotations - KEGG (archival)

Imported Annotations - PID (archival)