Ppp2r5d (protein phosphatase 2, regulatory subunit B', delta) - Rat Genome Database
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Gene: Ppp2r5d (protein phosphatase 2, regulatory subunit B', delta) Rattus norvegicus
Analyze
Symbol: Ppp2r5d
Name: protein phosphatase 2, regulatory subunit B', delta
RGD ID: 1306666
Description: Predicted to have phosphoprotein phosphatase activity. Involved in negative regulation of peptidyl-threonine phosphorylation. Human ortholog(s) of this gene implicated in autosomal dominant non-syndromic intellectual disability 35. Orthologous to human PPP2R5D (protein phosphatase 2 regulatory subunit B'delta); PARTICIPATES IN dopamine signaling pathway; interleukin-2 signaling pathway; mRNA decay pathway; INTERACTS WITH 2,6-dinitrotoluene; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC363193; protein phosphatase 2, regulatory subunit B (B56), delta isoform; protein phosphatase 2, regulatory subunit B', delta isoform; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2914,270,364 - 14,300,396 (+)NCBI
Rnor_6.0 Ensembl916,586,803 - 16,609,631 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0916,580,995 - 16,610,425 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0915,487,588 - 15,516,365 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4910,054,005 - 10,078,501 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1910,052,322 - 10,075,842 (-)NCBI
Celera912,018,838 - 12,048,685 (+)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:18496528   PMID:19029245   PMID:24157919   PMID:29294329  


Genomics

Comparative Map Data
Ppp2r5d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2914,270,364 - 14,300,396 (+)NCBI
Rnor_6.0 Ensembl916,586,803 - 16,609,631 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0916,580,995 - 16,610,425 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0915,487,588 - 15,516,365 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4910,054,005 - 10,078,501 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1910,052,322 - 10,075,842 (-)NCBI
Celera912,018,838 - 12,048,685 (+)NCBICelera
Cytogenetic Map9q12NCBI
PPP2R5D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl642,984,553 - 43,012,342 (+)EnsemblGRCh38hg38GRCh38
GRCh38642,984,570 - 43,012,342 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37642,952,308 - 42,980,080 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36643,060,308 - 43,088,058 (+)NCBINCBI36hg18NCBI36
Build 34643,060,307 - 43,088,056NCBI
Celera644,504,572 - 44,532,321 (+)NCBI
Cytogenetic Map6p21.1NCBI
HuRef642,669,485 - 42,697,406 (+)NCBIHuRef
CHM1_1642,954,714 - 42,982,536 (+)NCBICHM1_1
Ppp2r5d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391746,993,917 - 47,015,952 (-)NCBIGRCm39mm39
GRCm39 Ensembl1746,993,917 - 47,016,037 (-)Ensembl
GRCm381746,682,991 - 46,705,026 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1746,682,991 - 46,705,111 (-)EnsemblGRCm38mm10GRCm38
MGSCv371746,819,940 - 46,841,951 (-)NCBIGRCm37mm9NCBIm37
MGSCv361746,146,183 - 46,168,138 (-)NCBImm8
Celera1750,118,859 - 50,140,684 (-)NCBICelera
Cytogenetic Map17CNCBI
cM Map1722.9NCBI
Ppp2r5d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554378,968,565 - 8,986,654 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554378,968,517 - 8,987,680 (+)NCBIChiLan1.0ChiLan1.0
PPP2R5D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1643,871,939 - 43,899,183 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl643,871,915 - 43,899,183 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0642,576,759 - 42,604,609 (+)NCBIMhudiblu_PPA_v0panPan3
PPP2R5D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1211,519,092 - 11,540,109 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11211,519,194 - 11,540,658 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ppp2r5d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647616,922,204 - 16,945,400 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PPP2R5D
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl738,055,589 - 38,079,867 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1738,055,589 - 38,078,429 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2743,503,956 - 43,526,797 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PPP2R5D
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11729,147,560 - 29,175,700 (-)NCBI
ChlSab1.1 Ensembl1729,145,918 - 29,174,997 (-)Ensembl
Ppp2r5d
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475416,487,275 - 16,507,539 (-)NCBI

Position Markers
UniSTS:143850  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0916,610,379 - 16,610,609NCBIRnor6.0
Rnor_6.01344,837,513 - 44,837,666NCBIRnor6.0
Rnor_5.01349,922,685 - 49,922,838UniSTSRnor5.0
Rnor_5.0915,516,994 - 15,517,224UniSTSRnor5.0
RGSC_v3.41340,828,931 - 40,829,084UniSTSRGSC3.4
RGSC_v3.4910,053,825 - 10,054,055UniSTSRGSC3.4
Celera1339,994,958 - 39,995,111UniSTS
Celera912,048,639 - 12,048,870UniSTS
Cytogenetic Map9q12UniSTS
Cytogenetic Map13q12UniSTS
RH127839  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0916,610,349 - 16,610,559NCBIRnor6.0
Rnor_6.01095,502,312 - 95,502,653NCBIRnor6.0
Rnor_5.01095,237,195 - 95,237,536UniSTSRnor5.0
Rnor_5.0915,516,964 - 15,517,174UniSTSRnor5.0
RGSC_v3.4910,053,875 - 10,054,085UniSTSRGSC3.4
RGSC_v3.41096,661,306 - 96,661,647UniSTSRGSC3.4
Celera912,048,609 - 12,048,820UniSTS
Celera1090,898,167 - 90,898,508UniSTS
RH 3.4 Map953.1UniSTS
Cytogenetic Map10q32.1UniSTS
Cytogenetic Map9q12UniSTS
RH129717  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0916,610,130 - 16,610,344NCBIRnor6.0
Rnor_5.0915,516,745 - 15,516,959UniSTSRnor5.0
RGSC_v3.4910,054,090 - 10,054,304UniSTSRGSC3.4
Celera912,048,390 - 12,048,604UniSTS
RH 3.4 Map955.0UniSTS
Cytogenetic Map9q12UniSTS
RH144000  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.09605,596 - 605,922NCBIRnor6.0
Rnor_6.0916,605,447 - 16,605,773NCBIRnor6.0
Rnor_5.09589,873 - 590,199UniSTSRnor5.0
Rnor_5.0915,512,062 - 15,512,388UniSTSRnor5.0
RGSC_v3.4910,058,661 - 10,058,987UniSTSRGSC3.4
Celera912,043,707 - 12,044,033UniSTS
Cytogenetic Map9q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9129467098Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9140383872Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9140383872Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9140383872Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9145029794Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9235572247355722Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9235572247355722Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9288097747375681Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9288097747880977Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9498609549986095Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9498609549986095Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9572425425692342Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)91221677157216771Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)91242546357425463Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)91242546357425463Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91555490147249201Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:275
Count of miRNA genes:161
Interacting mature miRNAs:197
Transcripts:ENSRNOT00000022862
Prediction methods:Microtar, 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 36 49 33 16 33 2 5 74 31 41 11 2
Low 7 8 8 3 8 6 6 4 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022862   ⟹   ENSRNOP00000022862
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl916,586,803 - 16,609,631 (+)Ensembl
RefSeq Acc Id: XM_001062510   ⟹   XP_001062510
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2914,270,371 - 14,300,396 (+)NCBI
Rnor_6.0916,581,003 - 16,610,425 (+)NCBI
Rnor_5.0915,487,588 - 15,516,365 (+)NCBI
RGSC_v3.4910,054,005 - 10,078,501 (-)RGD
Sequence:
RefSeq Acc Id: XM_001065844   ⟹   XP_001065844
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera912,018,846 - 12,048,685 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006226735   ⟹   XP_006226797
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera912,018,846 - 12,048,685 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006244570   ⟹   XP_006244632
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2914,270,375 - 14,300,396 (+)NCBI
Rnor_6.0916,581,003 - 16,610,425 (+)NCBI
Rnor_5.0915,487,588 - 15,516,365 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596731   ⟹   XP_017452220
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2914,270,364 - 14,300,396 (+)NCBI
Rnor_6.0916,580,995 - 16,610,425 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017603809   ⟹   XP_017459298
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera912,018,838 - 12,048,685 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_001062510 (Get FASTA)   NCBI Sequence Viewer  
  XP_006244632 (Get FASTA)   NCBI Sequence Viewer  
  XP_017452220 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH99800 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_001065844   ⟸   XM_001065844
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_001062510   ⟸   XM_001062510
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006226797   ⟸   XM_006226735
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006244632   ⟸   XM_006244570
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017459298   ⟸   XM_017603809
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017452220   ⟸   XM_017596731
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000022862   ⟸   ENSRNOT00000022862

Transcriptome

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

Promoters
RGD ID:13696512
Promoter ID:EPDNEW_R7032
Type:initiation region
Name:Ppp2r5d_1
Description:protein phosphatase 2, regulatory subunit B', delta
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_6.0916,586,796 - 16,586,856EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 16607401 16607402 T C snv WKY/N (MCW), MR/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306666 AgrOrtholog
Ensembl Genes ENSRNOG00000016849 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000022862 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022862 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7936565 IMAGE-MGC_LOAD
InterPro ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  PP2A_B56 UniProtKB/TrEMBL
MGC_CLONE MGC:124849 IMAGE-MGC_LOAD
NCBI Gene 363193 ENTREZGENE
PANTHER B56 UniProtKB/TrEMBL
Pfam B56 UniProtKB/TrEMBL
PhenoGen Ppp2r5d PhenoGen
PIRSF PP2A_B56 UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
UniProt F1MAA3_RAT UniProtKB/TrEMBL
  Q499R1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 Ppp2r5d  protein phosphatase 2, regulatory subunit B', delta  Ppp2r5d  protein phosphatase 2, regulatory subunit B', delta isoform  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-12-15 Ppp2r5d  protein phosphatase 2, regulatory subunit B', delta isoform  Ppp2r5d  protein phosphatase 2, regulatory subunit B (B56), delta isoform  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Ppp2r5d  protein phosphatase 2, regulatory subunit B (B56), delta isoform  Ppp2r5d_predicted  protein phosphatase 2, regulatory subunit B (B56), delta isoform (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Ppp2r5d_predicted  protein phosphatase 2, regulatory subunit B (B56), delta isoform (predicted)      Symbol and Name status set to approved 70820 APPROVED