Phactr2 (phosphatase and actin regulator 2) - Rat Genome Database

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Gene: Phactr2 (phosphatase and actin regulator 2) Rattus norvegicus
Analyze
Symbol: Phactr2
Name: phosphatase and actin regulator 2
RGD ID: 1303141
Description: Predicted to enable actin binding activity. Predicted to be involved in actin cytoskeleton organization. Human ortholog(s) of this gene implicated in Parkinson's disease and multiple sclerosis. Orthologous to human PHACTR2 (phosphatase and actin regulator 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
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
mRatBN7.217,591,254 - 7,860,431 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl17,355,154 - 7,480,825 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.017,352,050 - 7,633,991 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.018,990,542 - 9,040,039 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.417,988,527 - 8,102,667 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.117,988,526 - 8,102,667 (-)NCBI
Celera16,086,830 - 6,198,133 (-)NCBICelera
Cytogenetic Map1p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References


Genomics

Comparative Map Data
Phactr2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.217,591,254 - 7,860,431 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl17,355,154 - 7,480,825 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.017,352,050 - 7,633,991 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.018,990,542 - 9,040,039 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.417,988,527 - 8,102,667 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.117,988,526 - 8,102,667 (-)NCBI
Celera16,086,830 - 6,198,133 (-)NCBICelera
Cytogenetic Map1p13NCBI
PHACTR2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6143,536,845 - 143,831,185 (+)EnsemblGRCh38hg38GRCh38
GRCh386143,536,878 - 143,831,185 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376143,929,317 - 144,152,322 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366143,971,010 - 144,194,015 (+)NCBINCBI36hg18NCBI36
Build 346143,971,092 - 144,188,885NCBI
Celera6144,669,714 - 144,892,732 (+)NCBI
Cytogenetic Map6q24.2NCBI
HuRef6141,493,526 - 141,716,094 (+)NCBIHuRef
CHM1_16144,192,176 - 144,415,204 (+)NCBICHM1_1
Phactr2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391013,083,461 - 13,350,266 (-)NCBIGRCm39mm39
GRCm39 Ensembl1013,083,461 - 13,350,156 (-)Ensembl
GRCm381013,207,717 - 13,474,525 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1013,207,717 - 13,474,412 (-)EnsemblGRCm38mm10GRCm38
MGSCv371012,933,201 - 13,043,966 (-)NCBIGRCm37mm9NCBIm37
MGSCv361012,903,593 - 13,014,358 (-)NCBImm8
Celera1013,112,086 - 13,221,736 (-)NCBICelera
Cytogenetic Map10A2NCBI
Phactr2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543616,619,552 - 16,694,053 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543616,607,279 - 16,690,412 (-)NCBIChiLan1.0ChiLan1.0
PHACTR2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16146,104,638 - 146,323,645 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6146,174,399 - 146,323,625 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06141,312,850 - 141,602,868 (+)NCBIMhudiblu_PPA_v0panPan3
PHACTR2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1135,158,678 - 35,348,875 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl135,088,248 - 35,342,584 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha136,056,282 - 36,244,938 (+)NCBI
ROS_Cfam_1.0135,340,396 - 35,530,115 (+)NCBI
UMICH_Zoey_3.1135,201,547 - 35,390,556 (+)NCBI
UNSW_CanFamBas_1.0135,084,683 - 35,275,814 (+)NCBI
UU_Cfam_GSD_1.0135,396,810 - 35,586,054 (+)NCBI
Phactr2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946130,096,980 - 130,292,200 (+)NCBI
SpeTri2.0NW_0049366252,336,455 - 2,474,032 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHACTR2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl121,441,492 - 21,723,790 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1121,438,744 - 21,723,255 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2123,765,368 - 23,938,799 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PHACTR2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11329,401,562 - 29,702,719 (-)NCBI
ChlSab1.1 Ensembl1329,401,382 - 29,560,452 (-)Ensembl
Vero_WHO_p1.0NW_0236660401,527,693 - 1,840,292 (-)NCBI
Phactr2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475310,456,910 - 10,742,311 (-)NCBI

Position Markers
BI294821  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.217,637,909 - 7,638,059 (+)MAPPERmRatBN7.2
Rnor_6.017,395,116 - 7,395,265NCBIRnor6.0
Rnor_5.019,030,107 - 9,030,256UniSTSRnor5.0
RGSC_v3.418,029,102 - 8,029,251UniSTSRGSC3.4
Celera16,126,805 - 6,126,954UniSTS
RH 3.4 Map1107.8UniSTS
Cytogenetic Map1p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298546Neuinf4Neuroinflammation QTL 45.1nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1128468970Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)125439343579402Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)125439343579402Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1164407321Rat
1300170Rf6Renal function QTL 63.14renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)1383915911314658Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1186804543724576Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)125439343579402Rat
1354647Despr8Despair related QTL 80.0000341locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1124368159Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1134993530Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1134993530Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)1134993530Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1565577285706974Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1457869349578693Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:68
Count of miRNA genes:62
Interacting mature miRNAs:64
Transcripts:ENSRNOT00000048754
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 40 16 6 12 6 2 2 33 31 35 11 2
Low 3 3 41 35 7 35 6 9 41 4 6 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000048754   ⟹   ENSRNOP00000045608
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl17,355,154 - 7,480,825 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088558   ⟹   ENSRNOP00000074696
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl17,364,079 - 7,443,863 (-)Ensembl
RefSeq Acc Id: NM_214458   ⟹   NP_999623
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.217,597,927 - 7,710,740 (-)NCBI
Rnor_6.017,355,294 - 7,480,789 (-)NCBI
Rnor_5.018,990,542 - 9,040,039 (-)NCBI
RGSC_v3.417,988,527 - 8,102,667 (-)RGD
Celera16,086,830 - 6,198,133 (-)RGD
Sequence:
RefSeq Acc Id: XM_017589097   ⟹   XP_017444586
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.217,591,254 - 7,860,431 (-)NCBI
Rnor_6.017,352,050 - 7,633,991 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017589098   ⟹   XP_017444587
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.217,591,254 - 7,860,431 (-)NCBI
Rnor_6.017,352,050 - 7,633,991 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017589099   ⟹   XP_017444588
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.217,591,254 - 7,710,960 (-)NCBI
Rnor_6.017,352,050 - 7,481,719 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017589100   ⟹   XP_017444589
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.217,591,254 - 7,860,427 (-)NCBI
Rnor_6.017,352,050 - 7,633,989 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017589101   ⟹   XP_017444590
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.217,591,254 - 7,860,424 (-)NCBI
Rnor_6.017,352,050 - 7,633,988 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017589102   ⟹   XP_017444591
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.217,591,254 - 7,860,426 (-)NCBI
Rnor_6.017,352,050 - 7,633,989 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017589103   ⟹   XP_017444592
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.217,591,254 - 7,860,427 (-)NCBI
Rnor_6.017,352,050 - 7,633,990 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039110957   ⟹   XP_038966885
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.217,591,254 - 7,777,524 (-)NCBI
RefSeq Acc Id: XM_039110962   ⟹   XP_038966890
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.217,591,254 - 7,710,963 (-)NCBI
RefSeq Acc Id: XM_039110963   ⟹   XP_038966891
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.217,591,254 - 7,648,081 (-)NCBI
RefSeq Acc Id: XM_039110966   ⟹   XP_038966894
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.217,591,254 - 7,860,425 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_999623   ⟸   NM_214458
- Sequence:
RefSeq Acc Id: XP_017444587   ⟸   XM_017589098
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017444586   ⟸   XM_017589097
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017444592   ⟸   XM_017589103
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017444591   ⟸   XM_017589102
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017444589   ⟸   XM_017589100
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017444590   ⟸   XM_017589101
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017444588   ⟸   XM_017589099
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000045608   ⟸   ENSRNOT00000048754
RefSeq Acc Id: ENSRNOP00000074696   ⟸   ENSRNOT00000088558
RefSeq Acc Id: XP_038966894   ⟸   XM_039110966
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038966885   ⟸   XM_039110957
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038966890   ⟸   XM_039110962
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038966891   ⟸   XM_039110963
- Peptide Label: isoform X10

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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303141 AgrOrtholog
Ensembl Genes ENSRNOG00000015473 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045608 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074696 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048754 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000088558 UniProtKB/TrEMBL
InterPro Phactr2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RPEL_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:308291 UniProtKB/Swiss-Prot
NCBI Gene 308291 ENTREZGENE
PANTHER PTHR12751:SF5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam RPEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Phactr2 PhenoGen
PROSITE RPEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART RPEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K8Q4_RAT UniProtKB/TrEMBL
  G3V9F4_RAT UniProtKB/TrEMBL
  P62025 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-11-17 Phactr2  phosphatase and actin regulator 2      Symbol and Name status set to approved 1299863 APPROVED
2005-02-14 Phactr2  phosphatase and actin regulator 2      Symbol and Name status set to provisional 70820 PROVISIONAL