Phylogeny:POL LTR retroelements

From The Gypsy Database

[quality revision][quality revision]
 
Line 8: Line 8:
rect 383 3957 429 3973 [[Element:SIRE1-4|SIRE1-4]]
rect 383 3957 429 3973 [[Element:SIRE1-4|SIRE1-4]]
rect 383 3925 427 3941 [[Element:ToRTL1|ToRTL1]]
rect 383 3925 427 3941 [[Element:ToRTL1|ToRTL1]]
-
rect 383 3893 412 3909 [[Element:TSI-9|TSI-9]]
+
rect 383 3893 412 3909 [[Element:Araco|Araco]]
rect 383 4191 415 4207 [[Element:RTvr2|RTvr2]]
rect 383 4191 415 4207 [[Element:RTvr2|RTvr2]]
rect 383 4175 407 4191 [[Element:Tto1|Tto1]]
rect 383 4175 407 4191 [[Element:Tto1|Tto1]]
Line 248: Line 248:
rect 383 3272 417 3288 [[Element:Zeco1|Zeco1]]
rect 383 3272 417 3288 [[Element:Zeco1|Zeco1]]
rect 383 3288 417 3304 [[Element:Zeco2|Zeco2]]
rect 383 3288 417 3304 [[Element:Zeco2|Zeco2]]
-
rect 383 3909 414 3925 [[Element:Araco|Araco]]
+
rect 383 3909 414 3925 [[Element:TSI-9|TSI-9]]
rect 383 3129 428 3145 [[Element:CoDi5.4|CoDi5.4]]
rect 383 3129 428 3145 [[Element:CoDi5.4|CoDi5.4]]
rect 383 3256 415 3272 [[Element:Olco1|Olco1]]
rect 383 3256 415 3272 [[Element:Olco1|Olco1]]

Latest revision as of 14:04, 1 August 2020

Vitico1-2MelmothOpie-2SIRE1-4ToRTL1AracoRTvr2Tto1V12KoalaRetrofitHopscotchEndovir1-1BatataTnt-1Tork4Sto-4FourfOsserCoDi6.2CoDi6.3CoDi6.5CoDi6.4CoDi6.6CoDi6.7CoDi6.1CoDi7.1CoDi2.4CoDi4.5CoDi3.1CoDi4.1CoDi4.3CoDi4.4Tdh2pCalSinbadKobelYokozunaZebelTy2Ty1BMaxGabelSpirobelCer7SuzuHydra3-1MoosePurbelCubelTasMabelTribelBelCer10-1RooSaci-6NabelLPDVJSRVSMRV-HSERVRSVHTLV-2STcLV2PP1664SRV-1MPMVK-HERVHTLV-1MMTVBLVTat4-1PyERVHERV-K10RCHO-K1SA-OMVVZFERV-2IdefixTomHIV-1EIAVCer6Cinful-1MuLVFFVMdEVGALVZamPERV-MSLFeLVGrande1-4KoRVB1147A04.5RetroSor1Bagy-2MicropiaTv1Gypsy297Athila4-1YoyoTedMuERV-LMdg117.6Cyclops-2Tft2ScBIMV412BlastopiaMdg3CYMVKTSVCLNVBSVAVOgreRIRE2CalypsoBSMyVDrMVBSOLVHMS-BeagleBurdockBSGFVCSSVmarY1GrasshopperTaBVTVCVSushi-ichiDBVRTBVNomadAmn-niPyggyBsCVBVCer1RealAmn-sanTy3-1ComYMVAmn-ichiPyretDane-1CerebaSkippyTF2TF1SkipperMGLR3Ifg7Bagy-1GloinMonkeyCft-1MaggyReinaTntom1CgretTse3Beetle1GimliREM1CSVMVDiasporaLLDAVRuFDVTor4aGaladrielCer2TmaPeabodyCRMEVCVG-RhodoPVCVMiMVCERVCmYLCVRetrosat-2FMVCaMVDelPCSVSVBVHydra2-1MagSPMBRRVLegolasGypsyvirSpringerCer5Cer4GulliverSURLSbCMVCer3SnRVDRMOsvaldoBAEVMCFG1HERV-ERTVL-IaBoudiccaCsRN1UlyssesGmr1Tor2WootrGmr1REVCigr-1KabukiTor1CirceFIVSFV-1EFVWdSVBFVHFVDrFV-1ZFERVSIVAGMSIVMNDASSBSVXEN1Ty4VMVSIVMACCAEVHIV-2BIVTamyCoDi5.3CoDi5.1CoDi5.2PaoNinjaCoDi5.6CoDi5.5Zeco1Zeco2TSI-9CoDi5.4Olco1Cico1CopiaKocoMtangaHydra1-2Hydra1-1pCretro6pCretro31731TricopiaOryco1-1Vitico1-1PocoOryco1-2GalEa1Tse1Tkm1PyRE1G1XanthiasHumnumPol ltr retroelement.png

Method of phylogenenetic reconstruction

Phylogenetic reconstruction inferred based on the concatenated protein product encoded by the pol internal region common to Ty3/Gypsy, Retroviridae, Bel/Pao, Caulimoviridae and Ty1/Copia LTR retroelements families using MEGA 4.1 (Kumar et al. 2008) and the Neighbor joining (NJ) method of phylogenetic reconstruction (Saitou and Nei 1987) with 100 bootstrap replicates under the conditions uniform rates among sites and pairwise deletion of gaps.

 

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