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
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Symbol: Pafah1b1
Name: platelet-activating factor acetylhydrolase 1b, regulatory subunit 1
RGD ID: 620331
Description: Enables dynein intermediate chain binding activity. Involved in several processes, including establishment of centrosome localization; generation of neurons; and negative regulation of neuron projection development. Located in several cellular components, including central region of growth cone; neuronal cell body; and nuclear envelope. Part of 1-alkyl-2-acetylglycerophosphocholine esterase complex and kinesin complex. Biomarker of visual epilepsy. Human ortholog(s) of this gene implicated in lissencephaly and lissencephaly 1. 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21059,533,042 - 59,591,808 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1059,534,117 - 59,591,808 (-)Ensembl
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 alpha  (ISO)
aldehydo-D-glucose  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
Apafant  (EXP)
aristolochic acid  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzatropine  (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)
Cuprizon  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
deguelin  (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)
ivermectin  (ISO)
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)
phenylephrine  (EXP)
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)
triptonide  (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 membrane 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)
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
mRatBN7.21059,533,042 - 59,591,808 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1059,534,117 - 59,591,808 (-)Ensembl
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
GRCh37172,496,948 - 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_1172,505,702 - 2,597,647 (+)NCBICHM1_1
Pafah1b1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391174,564,775 - 74,615,210 (-)NCBIGRCm39mm39
GRCm39 Ensembl1174,564,775 - 74,615,496 (-)Ensembl
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
CanFam3.1946,648,057 - 46,731,259 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl946,648,052 - 46,771,400 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha945,800,900 - 45,884,016 (+)NCBI
ROS_Cfam_1.0947,482,963 - 47,566,431 (+)NCBI
ROS_Cfam_1.0 Ensembl947,482,963 - 47,607,125 (+)Ensembl
UMICH_Zoey_3.1946,250,595 - 46,333,659 (+)NCBI
UNSW_CanFamBas_1.0946,544,618 - 46,627,828 (+)NCBI
UU_Cfam_GSD_1.0946,599,366 - 46,680,302 (+)NCBI
Pafah1b1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560245,734,221 - 45,815,751 (+)NCBI
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1162,270,126 - 2,293,705 (+)NCBIChlSab1.1chlSab2
ChlSab1.1162,270,126 - 2,293,705 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl162,270,085 - 2,296,825 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605919,649,125 - 19,755,407 (-)NCBIVero_WHO_p1.0
Pafah1b1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247865,223,890 - 5,306,033 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH130886  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21059,534,835 - 59,535,036 (+)MAPPERmRatBN7.2
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
mRatBN7.21059,534,178 - 59,534,358 (+)MAPPERmRatBN7.2
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
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)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
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)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
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)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)104287676679813922Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)104944455181709989Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104944455181709989Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)104944455181709989Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
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)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
2306787Ean3Experimental allergic neuritis QTL 33.1nervous system integrity trait (VT:0010566)body weight loss (CMO:0001399)105379738566979128Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2298495Eae23Experimental allergic encephalomyelitis QTL 2316.93nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)105527369660677262Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat

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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003696   ⟹   ENSRNOP00000003696
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1059,534,117 - 59,591,808 (-)Ensembl
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
mRatBN7.21059,534,116 - 59,591,808 (-)NCBI
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_039086943   ⟹   XP_038942871
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21059,533,042 - 59,579,958 (-)NCBI
RefSeq Acc Id: XM_039086944   ⟹   XP_038942872
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21059,533,042 - 59,591,338 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_113951   ⟸   NM_031763
- UniProtKB: P63004 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075779   ⟸   ENSRNOT00000092712
RefSeq Acc Id: ENSRNOP00000003696   ⟸   ENSRNOT00000003696
RefSeq Acc Id: XP_038942872   ⟸   XM_039086944
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038942871   ⟸   XM_039086943
- Peptide Label: isoform X1
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 (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
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)
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-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
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)
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
BXH2/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (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: 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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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/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
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)
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
F344/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
FHH/EurMcwi (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
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
FXLE16/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
FXLE18/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
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/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)
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
HXB31/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
HXB4/IpcvMcwi (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: 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)
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
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)
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
LEXF11/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
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)
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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
LEXF3/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
LEXF4/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
LH/MavRrrc (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
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)
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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
LL/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
LN/MavRrrc (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
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)
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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
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)
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)
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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)
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 (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)
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 (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
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 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003696 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000092712 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_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
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