Pafah1b1 (platelet-activating factor acetylhydrolase 1b, regulatory subunit 1) - Rat Genome Database
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Gene: Pafah1b1 (platelet-activating factor acetylhydrolase 1b, regulatory subunit 1) Rattus norvegicus
Analyze
Symbol: Pafah1b1
Name: platelet-activating factor acetylhydrolase 1b, regulatory subunit 1
RGD ID: 620331
Description: Exhibits dynein intermediate chain binding activity. Involved in several processes, including establishment of centrosome localization; generation of neurons; and nuclear migration. Localizes to several cellular components, including central region of growth cone; kinesin complex; and neuronal cell body. Predicted to colocalize with cell leading edge. Biomarker of visual epilepsy. Human ortholog(s) of this gene implicated in lissencephaly. Orthologous to human PAFAH1B1 (platelet activating factor acetylhydrolase 1b regulatory subunit 1); PARTICIPATES IN altered Reelin signaling pathway; Reelin signaling pathway; ether lipid metabolic pathway; INTERACTS WITH 17beta-estradiol; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LIS-1; LIS1; lissencephaly-1 protein; PAF acetylhydrolase 45 kDa subunit; PAF-AH 45 kDa subunit; PAF-AH alpha; PAF-AH beta; PAFAH alpha; platelet-activating factor acetylhydrolase beta subunit (PAF-AH beta); platelet-activating factor acetylhydrolase IB subunit alpha; platelet-activating factor acetylhydrolase, isoform 1b, subunit 1; platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa
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
Rnor_6.01061,456,144 - 61,577,412 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1061,456,145 - 61,577,412 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01061,186,183 - 61,299,247 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41061,955,348 - 62,037,871 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11061,968,971 - 62,051,494 (-)NCBI
Celera1058,565,530 - 58,623,461 (-)NCBICelera
Cytogenetic Map10q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
aldehydo-D-glucose  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
Apafant  (EXP)
arsenous acid  (ISO)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
butanal  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
carbon nanotube  (ISO)
castor oil  (EXP)
chloropicrin  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dorsomorphin  (ISO)
elemental selenium  (ISO)
ethanol  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
glucose  (ISO)
isosorbide mononitrate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nefazodone  (EXP)
paracetamol  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (EXP)
phosphatidylcholine  (EXP)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium dichromate  (ISO)
quercetin  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium dichromate  (ISO)
succimer  (ISO)
terbutaline  (EXP)
tert-butyl hydroperoxide  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
acrosome assembly  (ISO)
actin cytoskeleton organization  (ISO)
adult locomotory behavior  (ISO)
ameboidal-type cell migration  (ISO)
auditory receptor cell development  (ISO)
brain development  (IEP)
brain morphogenesis  (IBA,ISO)
cell migration  (ISO)
cerebral cortex development  (ISO)
cerebral cortex neuron differentiation  (IMP)
chemical synaptic transmission  (ISO)
cochlea development  (ISO)
corpus callosum morphogenesis  (ISO)
cortical microtubule organization  (ISO)
establishment of centrosome localization  (IMP)
establishment of mitotic spindle orientation  (IBA,ISO)
establishment of planar polarity of embryonic epithelium  (ISO)
germ cell development  (IBA)
hippocampus development  (ISO)
layer formation in cerebral cortex  (ISO)
learning or memory  (ISO)
lipid catabolic process  (IEA)
maintenance of centrosome location  (ISO)
microtubule cytoskeleton organization  (ISO)
microtubule cytoskeleton organization involved in establishment of planar polarity  (ISO)
microtubule organizing center organization  (IBA,ISO)
microtubule sliding  (IEA)
microtubule-based process  (ISO)
negative regulation of JNK cascade  (ISO)
negative regulation of neuron projection development  (IMP)
neuroblast proliferation  (ISO)
neuromuscular process controlling balance  (ISO)
neuron migration  (IMP,ISO)
nuclear envelope disassembly  (ISO)
nuclear migration  (IBA,IMP)
osteoclast development  (ISO)
positive regulation of axon extension  (IMP)
positive regulation of cellular component organization  (ISO)
positive regulation of cytokine-mediated signaling pathway  (ISO)
positive regulation of dendritic spine morphogenesis  (ISO)
positive regulation of embryonic development  (ISO)
positive regulation of mitotic cell cycle  (IMP)
protein secretion  (ISO)
reelin-mediated signaling pathway  (ISO,ISS)
regulation of GTPase activity  (ISO)
regulation of microtubule cytoskeleton organization  (ISO)
regulation of microtubule motor activity  (IBA)
retrograde axonal transport  (IBA,ISO)
stem cell division  (IMP)
transmission of nerve impulse  (ISO)
vesicle transport along microtubule  (IBA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bai J, etal., Dev Neurosci. 2008;30(1-3):144-56.
2. Cardoso C, etal., Hum Mol Genet. 2000 Dec 12;9(20):3019-28.
3. Caspi M, etal., Hum Mol Genet. 2000 Sep 22;9(15):2205-13.
4. Faulkner NE, etal., Nat Cell Biol. 2000 Nov;2(11):784-91.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Grabham PW, etal., J Neurosci. 2007 May 23;27(21):5823-34.
8. Guarda PG and Vitale M, Minerva Chir. 1991 Sep 30;46(18):985-7.
9. Hebbar S, etal., J Cell Biol. 2008 Sep 22;182(6):1063-71. doi: 10.1083/jcb.200803071.
10. Lipska BK, etal., Hum Mol Genet. 2006 Apr 15;15(8):1245-58. Epub 2006 Mar 1.
11. Manya H, etal., J Biol Chem. 1998 Jul 17;273(29):18567-72.
12. Morris SM, etal., Curr Biol. 1998 May 7;8(10):603-6.
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. OMIM Disease Annotation Pipeline
15. Paylor R, etal., Learn Mem. 1999 Sep-Oct;6(5):521-37.
16. Pipeline to import KEGG annotations from KEGG into RGD
17. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
18. Pletnikov MV, etal., Neurosci Res. 2007 Jul;58(3):234-44. Epub 2007 Mar 16.
19. RGD automated data pipeline
20. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. RGD automated import pipeline for gene-chemical interactions
22. Shmueli O, etal., J Neurosci Res. 1999 Jul 15;57(2):176-84.
23. Smith DS, etal., Nat Cell Biol. 2000 Nov;2(11):767-75.
24. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
25. Taya S, etal., J Neurosci. 2007 Jan 3;27(1):15-26.
26. Tsai JW, etal., J Cell Biol. 2005 Sep 12;170(6):935-45. Epub 2005 Sep 6.
27. Tsai JW, etal., Nat Neurosci. 2007 Aug;10(8):970-9. Epub 2007 Jul 8.
28. Watanabe M, etal., Biochim Biophys Acta 1998 Jan 2;1401(1):73-9.
29. Xing Z, etal., Biochem Biophys Res Commun. 2011 Jun 3;409(2):193-9. doi: 10.1016/j.bbrc.2011.04.117. Epub 2011 May 1.
30. Zhang G, etal., PLoS One. 2007 Feb 28;2(2):e252.
Additional References at PubMed
PMID:9063735   PMID:9697693   PMID:10729324   PMID:11163258   PMID:11163259   PMID:11163260   PMID:11344260   PMID:11889140   PMID:11940666   PMID:12551946   PMID:12629176   PMID:12796778  
PMID:12950100   PMID:13129914   PMID:14507966   PMID:14578885   PMID:14691133   PMID:15331402   PMID:15489334   PMID:16107726   PMID:16481446   PMID:17314247   PMID:17433713   PMID:18469343  
PMID:19056867   PMID:21212011   PMID:21399614   PMID:21844209   PMID:21911489   PMID:22073305   PMID:22871113   PMID:23483716   PMID:23533177   PMID:23551859   PMID:28000671   PMID:28576829  
PMID:31505169  


Genomics

Comparative Map Data
Pafah1b1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01061,456,144 - 61,577,412 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1061,456,145 - 61,577,412 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01061,186,183 - 61,299,247 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41061,955,348 - 62,037,871 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11061,968,971 - 62,051,494 (-)NCBI
Celera1058,565,530 - 58,623,461 (-)NCBICelera
Cytogenetic Map10q24NCBI
PAFAH1B1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl172,593,210 - 2,685,615 (+)EnsemblGRCh38hg38GRCh38
GRCh38172,593,210 - 2,685,617 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37172,496,923 - 2,588,909 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36172,443,686 - 2,535,638 (+)NCBINCBI36hg18NCBI36
Build 34172,443,685 - 2,535,638NCBI
Celera172,513,612 - 2,605,584 (+)NCBI
Cytogenetic Map17p13.3NCBI
HuRef172,389,423 - 2,481,264 (+)NCBIHuRef
CHM1_1172,525,188 - 2,529,780 (+)NCBICHM1_1
CHM1_1172,505,702 - 2,597,647 (+)NCBICHM1_1
Pafah1b1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391174,564,775 - 74,615,210 (-)NCBIGRCm39mm39
GRCm381174,673,949 - 74,724,384 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1174,673,949 - 74,724,670 (-)EnsemblGRCm38mm10GRCm38
MGSCv371174,487,452 - 74,537,886 (-)NCBIGRCm37mm9NCBIm37
MGSCv361174,490,150 - 74,540,865 (-)NCBImm8
Celera1182,183,768 - 82,236,827 (-)NCBICelera
Cytogenetic Map11B5NCBI
cM Map1145.76NCBI
Pafah1b1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955481608,897 - 686,452 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955481608,897 - 686,454 (-)NCBIChiLan1.0ChiLan1.0
PAFAH1B1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1172,589,129 - 2,680,994 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl172,590,007 - 2,680,994 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0172,584,349 - 2,676,928 (+)NCBIMhudiblu_PPA_v0panPan3
PAFAH1B1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl946,648,052 - 46,771,400 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1946,648,057 - 46,731,259 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Pafah1b1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365388,612,142 - 8,693,698 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PAFAH1B1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1248,567,337 - 48,735,838 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11248,567,329 - 48,735,836 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21250,398,376 - 50,505,192 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PAFAH1B1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1162,270,126 - 2,293,705 (+)NCBI
ChlSab1.1 Ensembl162,270,085 - 2,296,825 (+)Ensembl
Pafah1b1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247865,223,890 - 5,306,033 (+)NCBI

Position Markers
RH130886  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01061,457,936 - 61,458,136NCBIRnor6.0
Rnor_5.01061,186,903 - 61,187,103UniSTSRnor5.0
RGSC_v3.41061,956,068 - 61,956,268UniSTSRGSC3.4
Celera1058,566,250 - 58,566,450UniSTS
Cytogenetic Map10q24UniSTS
RH134247  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01061,457,279 - 61,457,458NCBIRnor6.0
Rnor_5.01061,186,246 - 61,186,425UniSTSRnor5.0
RGSC_v3.41061,955,411 - 61,955,590UniSTSRGSC3.4
Celera1058,565,593 - 58,565,772UniSTS
Cytogenetic Map10q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1076442166221621Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10587753664401490Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10622909575983805Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101482789492423564Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101537547462469074Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101646873661468736Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11712154262121542Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11712154262121542Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101940281464402814Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)1020170031102897474Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102152390683549467Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)12152390690312401Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102152390690312401Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102170776664648311Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102290149793886300Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102386101566539843Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102723753064648311Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)1027237530101482600Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1027237530102427718Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102878928073789280Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)103009990975099909Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)103009990975099909Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)103098380575983805Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103191939778343192Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103317903078179030Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103334319278343192Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103513942480139424Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)103618592982675365Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103618592995845311Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103658437366539843Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103658456066015527Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)104051404485514044Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)104051404485514044Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1041260363106105607Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104318865981042642Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1043289657108540162Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104370495588704955Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104659302198939209Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104684834691848346Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104684834691848346Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104684834691848346Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)105063833795638337Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)105128920384596393Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)105128920384596393Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)105128920384596393Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)105128920384596393Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)105128920384596393Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105310471898104718Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1053621375112626471Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1053621375112626471Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105362581598939209Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105363748594807701Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)1055224855100224855Rat
2306787Ean3Experimental allergic neuritis QTL 33.1nervous system integrity trait (VT:0010566)body weight loss (CMO:0001399)105567897669385767Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1055678976112626471Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)1055679084102427604Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1056698730101698730Rat
2298495Eae23Experimental allergic encephalomyelitis QTL 2316.93nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)105718065363976874Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1060450007105450007Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1060875260105875260Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1060875260105875260Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1060875260105875260Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:967
Count of miRNA genes:330
Interacting mature miRNAs:441
Transcripts:ENSRNOT00000003696
Prediction methods:Microtar, Miranda
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07029958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07029959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07029960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07029961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07029962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07029963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07029964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01064813 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01064814 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01064815 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01064816 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01064817 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01064818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF016049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC072510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000003696   ⟹   ENSRNOP00000003696
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1061,457,216 - 61,577,412 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092711
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1061,459,741 - 61,460,462 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092712   ⟹   ENSRNOP00000075779
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1061,456,145 - 61,576,952 (-)Ensembl
RefSeq Acc Id: NM_031763   ⟹   NP_113951
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01061,457,216 - 61,577,412 (-)NCBI
Rnor_5.01061,186,183 - 61,299,247 (-)NCBI
RGSC_v3.41061,955,348 - 62,037,871 (-)RGD
Celera1058,565,530 - 58,623,461 (-)RGD
Sequence:
RefSeq Acc Id: XM_017597550   ⟹   XP_017453039
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01061,456,144 - 61,509,028 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_113951   ⟸   NM_031763
- UniProtKB: P63004 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017453039   ⟸   XM_017597550
- Peptide Label: isoform X1
- UniProtKB: P63004 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075779   ⟸   ENSRNOT00000092712
RefSeq Acc Id: ENSRNOP00000003696   ⟸   ENSRNOT00000003696
Protein Domains
LisH

Transcriptome

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

Promoters
RGD ID:13697414
Promoter ID:EPDNEW_R7936
Type:multiple initiation site
Name:Pafah1b1_2
Description:platelet-activating factor acetylhydrolase 1b, regulatory subunit1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R7937  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01061,576,932 - 61,576,992EPDNEW
RGD ID:13697413
Promoter ID:EPDNEW_R7937
Type:initiation region
Name:Pafah1b1_1
Description:platelet-activating factor acetylhydrolase 1b, regulatory subunit1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R7936  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01061,577,444 - 61,577,504EPDNEW

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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620331 AgrOrtholog
Ensembl Genes ENSRNOG00000002755 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000003696 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000075779 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003696 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000092712 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7104733 IMAGE-MGC_LOAD
InterPro Dynein_regulator_LIS1 UniProtKB/Swiss-Prot
  G-protein_beta_WD-40_rep UniProtKB/Swiss-Prot
  LIS1_N UniProtKB/Swiss-Prot
  LisH UniProtKB/Swiss-Prot
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot
  WD40_repeat UniProtKB/Swiss-Prot
  WD40_repeat_CS UniProtKB/Swiss-Prot
  WD40_repeat_dom UniProtKB/Swiss-Prot
  WD40_repeat_dom_sf UniProtKB/Swiss-Prot
KEGG Report rno:83572 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91446 IMAGE-MGC_LOAD
NCBI Gene 83572 ENTREZGENE
Pfam LisH UniProtKB/Swiss-Prot
  WD40 UniProtKB/Swiss-Prot
PhenoGen Pafah1b1 PhenoGen
PIRSF Dynein_regulator_Lis1 UniProtKB/Swiss-Prot
PRINTS GPROTEINBRPT UniProtKB/Swiss-Prot
PROSITE LISH UniProtKB/Swiss-Prot
  WD_REPEATS_1 UniProtKB/Swiss-Prot
  WD_REPEATS_2 UniProtKB/Swiss-Prot
  WD_REPEATS_REGION UniProtKB/Swiss-Prot
SMART LisH UniProtKB/Swiss-Prot
  WD40 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF109925 UniProtKB/Swiss-Prot
  SSF50978 UniProtKB/Swiss-Prot
UniGene Rn.5827 ENTREZGENE
UniProt LIS1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O35592 UniProtKB/Swiss-Prot
  P43035 UniProtKB/Swiss-Prot
  P81692 UniProtKB/Swiss-Prot
  Q9R2A6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-06 Pafah1b1  platelet-activating factor acetylhydrolase 1b, regulatory subunit 1  Pafah1b1  platelet-activating factor acetylhydrolase, isoform 1b, subunit 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-04-21 Pafah1b1  platelet-activating factor acetylhydrolase, isoform 1b, subunit 1  Pafah1b1  platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Pafah1b1  platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit 45kDa    platelet-activating factor acetylhydrolase beta subunit (PAF-AH beta)  Name updated 1299863 APPROVED
2002-08-07 Pafah1b1  platelet-activating factor acetylhydrolase beta subunit (PAF-AH beta)      Symbol and Name status set to provisional 70820 PROVISIONAL