Ppef2 (protein phosphatase with EF-hand domain 2) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Ppef2 (protein phosphatase with EF-hand domain 2) Rattus norvegicus
Analyze
Symbol: Ppef2
Name: protein phosphatase with EF-hand domain 2
RGD ID: 1307093
Description: Predicted to have heat shock protein binding activity; mitogen-activated protein kinase kinase kinase binding activity; and protein serine/threonine phosphatase activity. Predicted to be involved in negative regulation of MAPK cascade and negative regulation of peptidyl-threonine phosphorylation. Predicted to localize to cytosol and nucleus. Orthologous to human PPEF2 (protein phosphatase with EF-hand domain 2); INTERACTS WITH 1,2-dimethylhydrazine; 3,3',4,4',5-pentachlorobiphenyl; cadmium dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC305246; protein phosphatase, EF hand calcium-binding domain 2; serine/threonine-protein phosphatase with EF-hands 2
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
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01417,306,825 - 17,333,588 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1417,306,825 - 17,333,588 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01417,220,015 - 17,254,101 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41417,359,298 - 17,392,820 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11417,366,155 - 17,392,304 (+)NCBI
Celera1415,191,812 - 15,226,681 (+)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component
cytosol  (IBA)
nucleus  (IBA)

References

Additional References at PubMed
PMID:20674765  


Genomics

Comparative Map Data
Ppef2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01417,306,825 - 17,333,588 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1417,306,825 - 17,333,588 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01417,220,015 - 17,254,101 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41417,359,298 - 17,392,820 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11417,366,155 - 17,392,304 (+)NCBI
Celera1415,191,812 - 15,226,681 (+)NCBICelera
Cytogenetic Map14p22NCBI
PPEF2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl475,859,864 - 75,902,571 (-)EnsemblGRCh38hg38GRCh38
GRCh38475,859,867 - 75,902,452 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37476,781,025 - 76,823,681 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36477,000,049 - 77,042,705 (-)NCBINCBI36hg18NCBI36
Build 34477,138,206 - 77,180,860NCBI
Celera474,081,428 - 74,124,167 (-)NCBI
Cytogenetic Map4q21.1NCBI
HuRef472,533,638 - 72,576,290 (-)NCBIHuRef
CHM1_1476,757,660 - 76,800,341 (-)NCBICHM1_1
Ppef2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39592,374,538 - 92,404,759 (-)NCBIGRCm39mm39
GRCm38592,226,679 - 92,256,278 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl592,226,679 - 92,256,278 (-)EnsemblGRCm38mm10GRCm38
MGSCv37592,656,000 - 92,682,185 (-)NCBIGRCm37mm9NCBIm37
MGSCv36593,301,879 - 93,331,478 (-)NCBImm8
Celera590,370,721 - 90,397,012 (-)NCBICelera
Cytogenetic Map5E2NCBI
Ppef2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554741,758,988 - 1,770,427 (+)NCBIChiLan1.0ChiLan1.0
PPEF2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1454,141,778 - 54,184,351 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl454,141,778 - 54,184,351 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0448,308,761 - 48,345,861 (+)NCBIMhudiblu_PPA_v0panPan3
PPEF2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.132443,495 - 467,929 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ppef2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493659865,009 - 102,349 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PPEF2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl871,520,275 - 71,554,766 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1871,519,873 - 71,555,977 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2875,655,670 - 75,700,481 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PPEF2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl724,371,587 - 24,406,695 (-)Ensembl
ChlSab1.1724,371,242 - 24,407,311 (-)NCBI
Ppef2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248724,726,169 - 4,805,021 (-)NCBI

Position Markers
stSG607015  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01417,303,009 - 17,304,096NCBIRnor6.0
Rnor_6.0138,574,590 - 8,575,683NCBIRnor6.0
Rnor_5.01417,219,636 - 17,220,723UniSTSRnor5.0
Rnor_5.01313,839,936 - 13,841,029UniSTSRnor5.0
Cytogenetic Map14p22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14134403399Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14141333960Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14141333960Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14142766285Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14222782519230541Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14483323319909932Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14483323319909932Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14483323323004027Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14483323326466248Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14483323333040042Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin141053997755539977Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)141053997755539977Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141268042430155192Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141268061332593926Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141633698833163485Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:38
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000003122
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 2
Low 2 31 25 9 18 9 4 6 72 33 34 11 4
Below cutoff 1 12 18 18 1 18 4 5 2 7 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000077636   ⟹   ENSRNOP00000075449
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1417,306,825 - 17,333,588 (-)Ensembl
RefSeq Acc Id: NM_001107210   ⟹   NP_001100680
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01417,306,825 - 17,333,588 (-)NCBI
Rnor_5.01417,220,015 - 17,254,101 (+)NCBI
RGSC_v3.41417,359,298 - 17,392,820 (+)RGD
Celera1415,191,812 - 15,226,681 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100680 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL88608 (Get FASTA)   NCBI Sequence Viewer  
  EDL88609 (Get FASTA)   NCBI Sequence Viewer  
  EDL88610 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100680   ⟸   NM_001107210
- UniProtKB: D3ZN69 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075449   ⟸   ENSRNOT00000077636
Protein Domains
EF-hand

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)
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)
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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/Gcrc (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
WKY/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
WKY/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
WKY/NHsd (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
WN/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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 17243652 17243653 G A snv HTX/Kyo (KyushuU), ZFDM (KyushuU), ACI/EurMcwi (MCW), BDIX.Cg-Tal/NemOda (KyushuU), BDIX/NemOda (KyushuU), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SDLEF7/Barth (UDEL), Crl:SD (UDEL), ZF (KyushuU)
14 17248459 17248460 C T snv IS/Kyo (KyushuU), SBH/Ygl (MCW), COP/CrCrl (MCW & UW), LE/Stm (KyushuU), KFRS3B/Kyo (KyushuU), LEC/Tj (KyushuU), IS-Tlk/Kyo (KyushuU)
14 17250003 17250004 G A snv SBH/Ygl (MCW), IS/Kyo (KyushuU), COP/CrCrl (MCW & UW), KFRS3B/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU)
14 17253556 17253557 C G snv DOB/Oda (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 17310831 17310832 C T snv WKY/NHsd (RGD), SBH/Ygl (RGD), WKY/Gcrc (RGD), SBH/Ygl (MCW), COP/CrCrl (MCW & UW), WKY/NCrl (RGD), SHR/NHsd (RGD)
14 17312375 17312376 G A snv SBH/Ygl (MCW), COP/CrCrl (MCW & UW), LE/Stm (RGD), WKY/Gcrc (RGD), WKY/NCrl (RGD), SHRSP/Gcrc (RGD), SHR/NHsd (RGD), SBH/Ygl (RGD), GK/Ox (RGD)
14 17317019 17317020 C T snv FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), FHL/EurMcwi (RGD), WAG/Rij (RGD), MHS/Gib (RGD), ACI/EurMcwi (RGD), ACI/EurMcwi (MCW), FHH/EurMcwi (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 17382773 17382774 G A snv FHH/EurMcwi (MDC), LCR/2Mco (UMich), HCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich), WAG/Rij (ICL), MHS/Gib (ICL), FHL/EurMcwi (ICL), FHH/EurMcwi (ICL), ACI/EurMcwi (ICL), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), MR/N (KNAW), ACI/N (KNAW), DA/BklArbNsi (ICAHN)
14 17387217 17387218 C T snv SHR/OlaIpcv (ICL), WKY/NCrl (ICL), WKY/NHsd (ICL), SHR/NHsd (ICL), LE/Stm (KNAW), SHRSP/Gcrc (ICL), WKY/N (KNAW), GK/Ox (ICL), SHR/OlaIpcv (KNAW), SBH/Ygl (ICL), WKY/Gcrc (ICL), COP/CrCrl (MCW & UW), SHR/OlaIpcv (ICL), LE/Stm (ICL), SHRSP/Gcrc (MDC)
14 17388761 17388762 G A snv SHR/NHsd (ICL), SHRSP/Gcrc (MDC), SHR/OlaIpcv (KNAW), SHRSP/Gcrc (ICL), WKY/Gcrc (ICL), SHR/OlaIpcv (ICL), SBH/Ygl (ICL), WKY/NCrl (ICL), GK/Ox (ICL), WKY/NHsd (ICL), COP/CrCrl (MCW & UW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307093 AgrOrtholog
Ensembl Genes ENSRNOG00000052061 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000075449 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077636 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.60.21.10 UniProtKB/TrEMBL
InterPro EF-hand-like_dom UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/TrEMBL
  EF_hand_Ca-bd UniProtKB/TrEMBL
  IQ_CaM-bd_region UniProtKB/TrEMBL
  M-pesterase UniProtKB/TrEMBL
  Metallo-depent_PP-like UniProtKB/TrEMBL
  PPP5 UniProtKB/TrEMBL
  Ser/Thr-Pase_EF-hand_contain UniProtKB/TrEMBL
  Ser/Thr-sp_prot-phosphatase UniProtKB/TrEMBL
KEGG Report rno:305246 UniProtKB/TrEMBL
NCBI Gene 305246 ENTREZGENE
Pfam EF_hand_5 UniProtKB/TrEMBL
  Metallophos UniProtKB/TrEMBL
  PPP5 UniProtKB/TrEMBL
PhenoGen Ppef2 PhenoGen
PIRSF PPEF UniProtKB/TrEMBL
PRINTS STPHPHTASE UniProtKB/TrEMBL
PROSITE EF_HAND_1 UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/TrEMBL
  PS50096 UniProtKB/TrEMBL
  SER_THR_PHOSPHATASE UniProtKB/TrEMBL
SMART EFh UniProtKB/TrEMBL
  PP2Ac UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/TrEMBL
UniGene Rn.99038 ENTREZGENE
UniProt D3ZN69 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-01 Ppef2  protein phosphatase with EF-hand domain 2  Ppef2  protein phosphatase, EF hand calcium-binding domain 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Ppef2  protein phosphatase, EF hand calcium-binding domain 2   Ppef2_predicted  protein phosphatase, EF hand calcium-binding domain 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ppef2_predicted  protein phosphatase, EF hand calcium-binding domain 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED