Ppp1r9a (protein phosphatase 1, regulatory subunit 9A) - Rat Genome Database

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Gene: Ppp1r9a (protein phosphatase 1, regulatory subunit 9A) Rattus norvegicus
Analyze
Symbol: Ppp1r9a
Name: protein phosphatase 1, regulatory subunit 9A
RGD ID: 632280
Description: Enables several functions, including enzyme binding activity; protein C-terminus binding activity; and transmembrane transporter binding activity. Involved in several processes, including modulation of chemical synaptic transmission; regulation of actin filament organization; and regulation of synapse organization. Located in several cellular components, including dendritic spine neck; glutamatergic synapse; and growth cone lamellipodium. Is active in postsynaptic actin cytoskeleton. Used to study transient cerebral ischemia. Biomarker of hepatocellular carcinoma. Orthologous to human PPP1R9A (protein phosphatase 1 regulatory subunit 9A); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: actin-binding protein neurabin; Neb1; neurabin 1; neurabin-1; neurabin-I; neural tissue-specific F-actin-binding protein I; p180; PP1bp175; protein phosphatase 1 regulatory subunit 9A; protein phosphatase 1, regulatory (inhibitor) subunit 9A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2432,970,501 - 33,292,360 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl433,024,450 - 33,286,907 (+)Ensembl
Rnor_6.0429,976,485 - 30,247,371 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl429,978,739 - 30,241,911 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0429,856,082 - 30,154,334 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4429,654,468 - 29,928,476 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1429,695,157 - 29,966,996 (+)NCBI
Celera428,548,989 - 28,813,836 (+)NCBICelera
Cytogenetic Map4q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-(hydroxymethyl)cytosine  (ISO)
acrolein  (ISO)
acrylamide  (ISO)
aflatoxin B2  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
butanal  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (ISO)
folic acid  (ISO)
gentamycin  (EXP)
hydralazine  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
latrunculin B  (EXP)
menadione  (ISO)
methamphetamine  (EXP)
methapyrilene  (ISO)
methoxychlor  (EXP)
methylmercury chloride  (ISO)
N-acetyl-beta-D-glucosamine  (ISO)
N-acetyl-D-glucosamine  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
ozone  (ISO)
paclitaxel  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
phenobarbital  (EXP,ISO)
phenyl acetate  (ISO)
phenylmercury acetate  (ISO)
potassium chromate  (ISO)
quercetin  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
temozolomide  (ISO)
testosterone enanthate  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
valproic acid  (EXP,ISO)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Becanovic K, etal., Hum Mol Genet. 2010 Apr 15;19(8):1438-52. doi: 10.1093/hmg/ddq018. Epub 2010 Jan 20.
2. Brown AM, etal., Eur J Neurosci. 2005 Jul;22(1):247-56.
3. Burnett PE, etal., Proc Natl Acad Sci U S A. 1998 Jul 7;95(14):8351-6.
4. Carmody LC, etal., FASEB J. 2008 Jun;22(6):1660-71. doi: 10.1096/fj.07-092841. Epub 2008 Jan 23.
5. Chen Y, etal., J Neurosci. 2012 Feb 22;32(8):2683-95. doi: 10.1523/JNEUROSCI.4125-11.2011.
6. Colbran RJ, etal., J Neurochem. 1997 Sep;69(3):920-9.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Goel M, etal., Pflugers Arch. 2005 Oct;451(1):87-98. Epub 2005 Jul 16.
9. Hu XD, etal., J Neurochem. 2006 Sep;98(6):1841-51. Epub 2006 Aug 8.
10. Kakehashi A, etal., Toxicol Sci. 2011 Jan;119(1):61-72. doi: 10.1093/toxsci/kfq307. Epub 2010 Oct 8.
11. McAvoy T, etal., Biochemistry. 1999 Sep 28;38(39):12943-9.
12. MGD data from the GO Consortium
13. Nakanishi H, etal., J Cell Biol 1997 Nov 17;139(4):951-61.
14. Oliver CJ, etal., Mol Cell Biol 2002 Jul;22(13):4690-701.
15. Orioli D, etal., Mol Biol Cell. 2006 May;17(5):2391-400. Epub 2006 Mar 8.
16. Ragusa MJ, etal., Nat Struct Mol Biol. 2010 Apr;17(4):459-64. doi: 10.1038/nsmb.1786. Epub 2010 Mar 21.
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Ruscher K, etal., Brain. 2011 Mar;134(Pt 3):732-46. doi: 10.1093/brain/awq367. Epub 2011 Jan 28.
21. Satoh A, etal., J Biol Chem 1998 Feb 6;273(6):3470-5.
22. Stephens DJ and Banting G, J Biol Chem. 1999 Oct 15;274(42):30080-6.
23. Terry-Lorenzo RT, etal., J Biol Chem 2002 Aug 2;277(31):27716-24.
24. Terry-Lorenzo RT, etal., J Biol Chem 2002 Nov 29;277(48):46535-43. Epub 2002 Sep 21.
25. Wang C, etal., J Proteome Res. 2010 Jun 4;9(6):3225-34. doi: 10.1021/pr1001274.
26. Zito K, etal., Neuron. 2004 Oct 14;44(2):321-34.
Additional References at PubMed
PMID:10585469   PMID:15016827   PMID:15996550   PMID:16600521   PMID:17460080   PMID:17464283   PMID:17600833   PMID:17699587   PMID:20124353   PMID:21094159   PMID:24625528   PMID:29383693  
PMID:29476059  


Genomics

Comparative Map Data
Ppp1r9a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2432,970,501 - 33,292,360 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl433,024,450 - 33,286,907 (+)Ensembl
Rnor_6.0429,976,485 - 30,247,371 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl429,978,739 - 30,241,911 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0429,856,082 - 30,154,334 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4429,654,468 - 29,928,476 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1429,695,157 - 29,966,996 (+)NCBI
Celera428,548,989 - 28,813,836 (+)NCBICelera
Cytogenetic Map4q13NCBI
PPP1R9A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl794,907,202 - 95,296,415 (+)EnsemblGRCh38hg38GRCh38
GRCh38794,907,202 - 95,296,415 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37794,536,906 - 94,925,727 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36794,374,885 - 94,763,663 (+)NCBINCBI36hg18NCBI36
Build 34794,185,142 - 94,567,392NCBI
Celera789,235,114 - 89,624,424 (+)NCBI
Cytogenetic Map7q21.3NCBI
HuRef789,144,178 - 89,532,759 (+)NCBIHuRef
CHM1_1794,466,972 - 94,855,738 (+)NCBICHM1_1
CRA_TCAGchr7v2793,865,965 - 94,254,723 (+)NCBI
Ppp1r9a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3964,902,702 - 5,165,661 (+)NCBIGRCm39mm39
GRCm39 Ensembl64,902,917 - 5,165,661 (+)Ensembl
GRCm3864,902,872 - 5,165,661 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl64,902,917 - 5,165,661 (+)EnsemblGRCm38mm10GRCm38
MGSCv3764,853,320 - 5,115,661 (+)NCBIGRCm37mm9NCBIm37
MGSCv3664,853,320 - 5,115,661 (+)NCBImm8
Celera65,049,683 - 5,311,917 (+)NCBICelera
Cytogenetic Map6A1NCBI
cM Map61.86NCBI
Ppp1r9a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543211,608,382 - 11,886,044 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543211,607,269 - 11,891,568 (+)NCBIChiLan1.0ChiLan1.0
PPP1R9A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17100,453,090 - 100,839,325 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7100,455,357 - 100,833,220 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0786,863,919 - 87,251,634 (+)NCBIMhudiblu_PPA_v0panPan3
PPP1R9A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11420,251,791 - 20,563,315 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1420,251,738 - 20,557,208 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1419,810,502 - 20,122,327 (+)NCBI
ROS_Cfam_1.01420,073,523 - 20,385,742 (+)NCBI
UMICH_Zoey_3.11420,218,353 - 20,530,386 (+)NCBI
UNSW_CanFamBas_1.01419,953,584 - 20,265,515 (+)NCBI
UU_Cfam_GSD_1.01420,211,007 - 20,522,870 (+)NCBI
Ppp1r9a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511833,585,519 - 33,881,736 (+)NCBI
SpeTri2.0NW_0049365854,981,555 - 5,277,185 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PPP1R9A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl974,635,280 - 74,940,362 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1974,635,285 - 74,944,050 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2981,987,561 - 82,105,844 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PPP1R9A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12153,744,202 - 54,129,709 (-)NCBI
ChlSab1.1 Ensembl2153,747,857 - 54,127,005 (-)Ensembl
Vero_WHO_p1.0NW_02366604250,200,716 - 50,591,491 (+)NCBI
Ppp1r9a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248131,587,567 - 1,951,620 (+)NCBI

Position Markers
D4Got286  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2433,044,357 - 33,044,568 (+)MAPPERmRatBN7.2
Rnor_6.0429,998,647 - 29,998,857NCBIRnor6.0
Rnor_5.0429,904,944 - 29,905,154UniSTSRnor5.0
RGSC_v3.4429,676,774 - 29,676,984UniSTSRGSC3.4
Celera428,571,044 - 28,571,254UniSTS
Cytogenetic Map4q13UniSTS
RH143674  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2433,128,541 - 33,128,665 (+)MAPPERmRatBN7.2
Rnor_6.0430,082,664 - 30,082,787NCBIRnor6.0
Rnor_5.0429,988,963 - 29,989,086UniSTSRnor5.0
RGSC_v3.4429,764,016 - 29,764,139UniSTSRGSC3.4
Celera428,655,245 - 28,655,368UniSTS
Cytogenetic Map4q13UniSTS
BF393278  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2433,279,761 - 33,280,001 (+)MAPPERmRatBN7.2
Rnor_6.0430,234,766 - 30,235,005NCBIRnor6.0
Rnor_5.0430,141,729 - 30,141,968UniSTSRnor5.0
RGSC_v3.4429,921,314 - 29,921,553UniSTSRGSC3.4
Celera428,806,691 - 28,806,930UniSTS
RH 3.4 Map4218.84UniSTS
Cytogenetic Map4q13UniSTS
AW530668  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2433,260,061 - 33,260,212 (+)MAPPERmRatBN7.2
Rnor_6.0430,215,066 - 30,215,216NCBIRnor6.0
Rnor_5.0430,122,029 - 30,122,179UniSTSRnor5.0
RGSC_v3.4429,901,614 - 29,901,764UniSTSRGSC3.4
Celera428,786,991 - 28,787,141UniSTS
RH 3.4 Map4218.44UniSTS
Cytogenetic Map4q13UniSTS
U66888  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2433,162,835 - 33,163,499 (+)MAPPERmRatBN7.2
Rnor_6.0430,117,906 - 30,118,569NCBIRnor6.0
Rnor_5.0430,024,205 - 30,024,868UniSTSRnor5.0
RGSC_v3.4429,802,996 - 29,803,659UniSTSRGSC3.4
Celera428,689,537 - 28,690,200UniSTS
Cytogenetic Map4q13UniSTS
UniSTS:532171  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2433,204,705 - 33,204,819 (+)MAPPERmRatBN7.2
Rnor_6.0430,159,776 - 30,159,889NCBIRnor6.0
Rnor_5.0430,066,075 - 30,066,188UniSTSRnor5.0
Celera428,731,458 - 28,731,571UniSTS
Cytogenetic Map4q13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4994088544463908Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41002490139524530Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41008408955084089Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41008408955084089Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41008408955084089Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41008408955084089Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41008408955084089Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41008408955084089Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41467806559678065Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41793350862933508Rat
70222Eae2Experimental allergic encephalomyelitis QTL 24.3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)42133334339505420Rat
1354665Stl10Serum triglyceride level QTL 103.57blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42133334344463908Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42133334362278020Rat
8552803Bw144Body weight QTL 14416body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)42271068534430484Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
11530004Niddm71Non-insulin dependent diabetes mellitus QTL 710.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43258419952754138Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:59
Count of miRNA genes:53
Interacting mature miRNAs:58
Transcripts:ENSRNOT00000011756
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 4 6 4 4 1 1 74 21 30 7 1
Low 2 39 35 22 17 22 7 7 14 11 4 7
Below cutoff 1 15 14 2 14 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236064 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006236068 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108474 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108476 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108479 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108480 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005503322 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC124867 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U72994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000011756   ⟹   ENSRNOP00000011756
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl433,024,450 - 33,286,907 (+)Ensembl
Rnor_6.0 Ensembl429,978,739 - 30,241,911 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104466   ⟹   ENSRNOP00000078577
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl433,024,450 - 33,286,907 (+)Ensembl
RefSeq Acc Id: NM_053473   ⟹   NP_445925
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,297 - 33,286,907 (+)NCBI
Rnor_6.0429,976,587 - 30,241,911 (+)NCBI
Rnor_5.0429,856,082 - 30,154,334 (+)NCBI
RGSC_v3.4429,654,468 - 29,928,476 (+)RGD
Celera428,548,989 - 28,813,836 (+)RGD
Sequence:
RefSeq Acc Id: XM_006236057   ⟹   XP_006236119
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,165 - 33,292,360 (+)NCBI
Rnor_6.0429,976,485 - 30,247,371 (+)NCBI
Rnor_5.0429,856,082 - 30,154,334 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006236058   ⟹   XP_006236120
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,546 - 33,292,360 (+)NCBI
Rnor_6.0429,976,836 - 30,247,371 (+)NCBI
Rnor_5.0429,856,082 - 30,154,334 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592928   ⟹   XP_017448417
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,800 - 33,292,360 (+)NCBI
Rnor_6.0429,977,350 - 30,247,371 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039108474   ⟹   XP_038964402
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2432,970,501 - 33,292,360 (+)NCBI
RefSeq Acc Id: XM_039108475   ⟹   XP_038964403
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,546 - 33,292,360 (+)NCBI
RefSeq Acc Id: XM_039108476   ⟹   XP_038964404
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,546 - 33,292,360 (+)NCBI
RefSeq Acc Id: XM_039108477   ⟹   XP_038964405
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,546 - 33,292,360 (+)NCBI
RefSeq Acc Id: XM_039108478   ⟹   XP_038964406
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,546 - 33,292,360 (+)NCBI
RefSeq Acc Id: XM_039108479   ⟹   XP_038964407
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,546 - 33,292,360 (+)NCBI
RefSeq Acc Id: XM_039108480   ⟹   XP_038964408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,546 - 33,292,360 (+)NCBI
RefSeq Acc Id: XM_039108481   ⟹   XP_038964409
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,546 - 33,292,360 (+)NCBI
RefSeq Acc Id: XM_039108482   ⟹   XP_038964410
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,546 - 33,292,360 (+)NCBI
RefSeq Acc Id: XM_039108483   ⟹   XP_038964411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,546 - 33,269,864 (+)NCBI
RefSeq Acc Id: XM_039108485   ⟹   XP_038964413
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,029,298 - 33,292,360 (+)NCBI
RefSeq Acc Id: XR_005503322
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2433,022,546 - 33,270,127 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_445925   ⟸   NM_053473
- UniProtKB: O35867 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006236119   ⟸   XM_006236057
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006236120   ⟸   XM_006236058
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017448417   ⟸   XM_017592928
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000011756   ⟸   ENSRNOT00000011756
RefSeq Acc Id: XP_038964402   ⟸   XM_039108474
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038964403   ⟸   XM_039108475
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038964407   ⟸   XM_039108479
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038964408   ⟸   XM_039108480
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038964404   ⟸   XM_039108476
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038964405   ⟸   XM_039108477
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038964406   ⟸   XM_039108478
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038964409   ⟸   XM_039108481
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038964410   ⟸   XM_039108482
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038964411   ⟸   XM_039108483
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038964413   ⟸   XM_039108485
- Peptide Label: isoform X11
RefSeq Acc Id: ENSRNOP00000078577   ⟸   ENSRNOT00000104466
Protein Domains
PDZ   SAM

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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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)
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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/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:632280 AgrOrtholog
BIND 130598
  130599
Ensembl Genes ENSRNOG00000008869 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000011756 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000011756 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.150.50 UniProtKB/Swiss-Prot
  2.30.42.10 UniProtKB/Swiss-Prot
InterPro Neurabin-1 UniProtKB/Swiss-Prot
  Neurabin-1/2_PDZ UniProtKB/Swiss-Prot
  Neurabin-like UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
  PDZ_sf UniProtKB/Swiss-Prot
  SAM UniProtKB/Swiss-Prot
  SAM/pointed_sf UniProtKB/Swiss-Prot
KEGG Report rno:84685 UniProtKB/Swiss-Prot
NCBI Gene 84685 ENTREZGENE
PANTHER PTHR16154 UniProtKB/Swiss-Prot
  PTHR16154:SF22 UniProtKB/Swiss-Prot
Pfam PDZ UniProtKB/Swiss-Prot
  PDZ_5 UniProtKB/Swiss-Prot
  SAM_2 UniProtKB/Swiss-Prot
PhenoGen Ppp1r9a PhenoGen
PROSITE PDZ UniProtKB/Swiss-Prot
  SAM_DOMAIN UniProtKB/Swiss-Prot
SMART PDZ UniProtKB/Swiss-Prot
  SAM UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47769 UniProtKB/Swiss-Prot
  SSF50156 UniProtKB/Swiss-Prot
UniProt NEB1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-10-18 Ppp1r9a  protein phosphatase 1, regulatory subunit 9A  Ppp1r9a  protein phosphatase 1, regulatory (inhibitor) subunit 9A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-25 Ppp1r9a  protein phosphatase 1, regulatory (inhibitor) subunit 9A  Ppp1r9a  neurabin 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Ppp1r9a  neurabin 1  Neb1    Symbol and Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized in the PSD (post-synaptic density) 625568
gene_cellular_localization localized in the PSD (post-synaptic density) 625591
gene_cellular_localization localized in the PSD (post-synaptic density) 625592
gene_domains has one F-actin binding domain at the amino-terminal region, one PSD-95, DlgA, ZO-1-like domain in the middle and a domain which interacts with transmembrane proteins at the COOH-terminus 625568
gene_domains has one F-actin binding domain at the amino-terminal region, one PSD-95, DlgA, ZO-1-like domain in the middle and a domain which interacts with transmembrane proteins at the COOH-terminus 625591
gene_domains has one F-actin binding domain at the amino-terminal region, one PSD-95, DlgA, ZO-1-like domain in the middle and a domain which interacts with transmembrane proteins at the COOH-terminus 625592
gene_expression purified from rat brain neural tissues 625568
gene_expression purified from rat brain neural tissues 625591
gene_expression purified from rat brain neural tissues 625592
gene_function binds to protein phosphatase 1 625568
gene_function binds to protein phosphatase 1 625591
gene_function binds to protein phosphatase 1 625592
gene_function neural tissue-specific F-actin-binding protein 625568
gene_function neural tissue-specific F-actin-binding protein 625591
gene_function neural tissue-specific F-actin-binding protein 625592
gene_function binds to actin filaments 625568
gene_function binds to actin filaments 625591
gene_function binds to actin filaments 625592
gene_physical_interaction interacts with protein phosphatase type 1 alpha and type 1 gamma isoform 1 to regulate synaptic transmission 625568
gene_physical_interaction interacts with protein phosphatase type 1 alpha and type 1 gamma isoform 1 to regulate synaptic transmission 625591
gene_physical_interaction interacts with protein phosphatase type 1 alpha and type 1 gamma isoform 1 to regulate synaptic transmission 625592
gene_physical_interaction binds to protein phosphatase1 625568
gene_physical_interaction binds to protein phosphatase1 625591
gene_physical_interaction binds to protein phosphatase1 625592
gene_process involved in vesicular trafficking in developing and developed neurons and formation and maintenance of synaptic junctions 625568
gene_process involved in vesicular trafficking in developing and developed neurons and formation and maintenance of synaptic junctions 625591
gene_process involved in vesicular trafficking in developing and developed neurons and formation and maintenance of synaptic junctions 625592
gene_process regulates synaptic activity by binding to protein phosphatase type 1 alpha and gamma isoform 1 present in the PSD and can be phosphorylated by PKA 625568
gene_process regulates synaptic activity by binding to protein phosphatase type 1 alpha and gamma isoform 1 present in the PSD and can be phosphorylated by PKA 625591
gene_process regulates synaptic activity by binding to protein phosphatase type 1 alpha and gamma isoform 1 present in the PSD and can be phosphorylated by PKA 625592
gene_process interacts with protein phosphatase type 1 alpha and type 1 gamma isoform 1 to regulate synaptic transmission  
gene_product 180 kD protein 625568
gene_product 180 kD protein 625591
gene_product 180 kD protein 625592
gene_product neural tissue-specific F-actin-binding protein  
gene_protein 180 kD in size 625592