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Nipponbare MATRGGGGGGGGKEAKGKVMGPLFPRLHVNDAAKGGGPRAPPRNKMALYEQFTVPSHRFS 60

Nipponbare MATRGGGGGGGGKEAKGKVMGPLFPRLHVNDAAKGGGPRAPPRNKMALYEQFTVPSHRFS 60 Koshihikari MATRGGGGGGGGKEAKGKVMGPLFPRLHVNDAAKGGGPRAPPRNKMALYEQFTVPSHRFS 60 Arabidopsis -MKRG--------KDEEKILEPMFPRLHVNDADKGG-PRAPPRNKMALYEQLSIPSQRFG 50

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Nipponbare MATRGGGGGGGGKEAKGKVMGPLFPRLHVNDAAKGGGPRAPPRNKMALYEQFTVPSHRFS 60

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  1. Nipponbare MATRGGGGGGGGKEAKGKVMGPLFPRLHVNDAAKGGGPRAPPRNKMALYEQFTVPSHRFS 60 Koshihikari MATRGGGGGGGGKEAKGKVMGPLFPRLHVNDAAKGGGPRAPPRNKMALYEQFTVPSHRFS 60 Arabidopsis -MKRG--------KDEEKILEPMFPRLHVNDADKGG-PRAPPRNKMALYEQLSIPSQRFG 50 .** : : *:: *:********* *** **************:::**:**. Nipponbare GGGGGGGVGGSPAHSTSAASQSQSQSQVYGRDSSLFQPFNVPSNRPGHSTEKINSDKINK 120 Koshihikari GGGGGGGVGGSPAHSTSAASQSQSQSQVYGRDSSLFQPFNVPSNRPGHSTEKINSDKINK 120 Arabidopsis ----DHGTMNSRSNNTSTLVHPGPSSQPCGVER------NLSVQHLDSSAANQATEKFVS 100 . *. .* ::.**: :. ..** * : *:. :: . *: : ::*: . Nipponbare KISGSRKELGMLSSQTKGMDIYASRSTAEAPQRRAENTIKSSSGKRLADDDEFMVPSVFN 180 Koshihikari KISGSRKELGMLSSQTKGMDIYASRSTAEAPQRRAENTIKSSSGKRLADDDEFMVPSVFN 180 Arabidopsis QMSFMEN----------------VRSSAQHDQR-----------KMVREEEDFAVPVYIN 133 ::* .: **:*: ** * : ::::* ** :* Nipponbare SRFPQYSTQENAGVQ-DQSTPLVAANPHKSPSTVSKSSTKCYNTVSKKLERIHVSDVKSR 239 Koshihikari SRFPQYSTQENAGVQ-DQSTPLVAANPHKSPSTVSKSSTKCYNTVSKKLERIHVSDVKSR 239 Arabidopsis SRRSQSHGRTKSGIEKEKHTPMVAPSSHHS---------IRFQEVNQTGSKQNVCLATCS 184 ** .* : ::*:: :: **:**...*:* :: *.:. .: :*. ... Nipponbare TPLKDKEMEAAQTSKNVEVEKSSSFHASKDMFESRHAKVYPKMDKTGIINDSDEPHGGNS 299 Koshihikari TPLKDKEMEAAQTSKNVEVEKSSSFHASKDMFESRHAKVYPKMDKTGIINDSDEPHGGNS 299 Arabidopsis KPEVRDQVKANARSGGFVISLDVSVTEEIDLEKSASSHDRVNDYNASLRQES-------- 236 .* .:::* * .. :. . *. . *: :* :: : ::.: ::* Nipponbare GHQATSRNGGSMKFQNPPMRRNEISSNPSSENTDRHYNLPQGGIEETGTKRKRLLEQHDA 359 Koshihikari GHQATSRNGGSMKFQNPPMRRNEISSNPSSENTDRHYNLPQGGIEETGTKRKRLLEQHDA 359 Arabidopsis -RNRLYRDGGKTRLKDTDN------GAESHLATENHSQEGHGSPEDIDNDR-------EY 282 :: *:**. ::::. . * *:.* : :*. *: ...* : Nipponbare EKSDDVSRLLEQHDAENIDDVSDSSVECITGWEISPDKIVGAIGTKHFWKARRAIMNQQR 419 Koshihikari EKSDDVSRLLEQHDAENIDDVSDSSVECITGWEISPDKIVGAIGTKHFWKARRAIMNQQR 419 Arabidopsis SKSRACASLQQINEEASDDVSDDSMVDSISSIDVSPDDVVGILGQKRFWRARKAIANQQR 342 .** : * : :: . * .** *:.*:. ::***.:** :* *:**:**:** **** Nipponbare VFAVQVFELHKLVKVQKLIAASPHVLIESDPCLGNALLGSKNKLVEENLKAQPLLVATID 479 Koshihikari VFAVQVFELHKLVKVQKLIAASPHVLIESDPCLGNALLGSKNKLVEENLKAQPLLVATID 479 Arabidopsis VFAVQLFELHRLIKVQKLIAASPDLLLDEISFLG--KVSAKSYPVKKLLPSEFLVKPPLP 400 *****:****:*:**********.:*::. . ** :.:*. *:: * :: *: ..: Nipponbare DVEPSLQQPEVSKENTEDSPPSPHDTGLGSGQRDQAATNGVSKSNRRATPVASDNKQNNW 539 Koshihikari DVEPSLQQPEVSKENTEDSPPSPHDTGLGSGQRDQAATNGVSKSNRRATPVASDNKQNNW 539 Arabidopsis HVVVKQRGDSEKTDQHKMESSAENVVGRLSNQGHHQQSNYMPFANNPPASPAPNGYCFPP 460 .* . : . ..:: : ...: : .* *.* .: :* :. :*. .:. *.:. Nipponbare GVQLQPPQNQWLVPVMSPLEGLVYKPYSGPCPP--AGSILAPFYAN--CTPLSLPSTAGD 595 Koshihikari GVQLQPPQNQWLVPVMSPSEGLVYKPYSGPCPP--AGSILAPFYAN--CTPLSLPSTAGD 595 Arabidopsis QPPPSGNHQQWLIPVMSPSEGLIYKPHPGMAHTGHYGGYYGHYMPTPMVMPQYHPGMGFP 520 . ::***:***** ***:***:.* . . *. . : .. * *. . Nipponbare FMNSAYGVPMPHQPQHMGAPGPPSMPMNYFPPFSIPVMNPTAPAPVVEQGRHPSMPQPYG 655 Koshihikari FMNSAYGVPMPHQPQHMGAPGPPSMPMNYFPPFSIPVMNPTAPAPVVEQGRHPSMPQPYG 655 Arabidopsis PPGNGYFPPYGMMPTIMNPYCSSQQQQQQQPNEQMNQFGHPGNLQNTQQQQQRSDNEPAP 580 ...* * * *.. ... : * .: :. .. .:* :: * :* Nipponbare NFEQQSWISCNMSHPSGIWRFHASRDSEAQASSASSPFDRFQCSG-----SGPVSAFPTV 710 Koshihikari NFEQQSWISCNMSHPSGIWRFHASRDSEAQASSASSPFDRFQCSG-----SGPVSAFPTV 710 Arabidopsis QQQQQPTKSYPRARKS-RQGSTGSSPSGPQGISGSKSFRPFAAVDEDSNINNAPEQTMTT 639 : :**. * :: * .* * .*. *.*..* * . . ... . *. Nipponbare SAQNNQPQPSYSSRDNQ--TNVIKVVPHNSRTASESAARIFRSIQMERQRDD---- 760 Koshihikari SAQNNQPQPSYSSRDNQ--TNVIKVVPHNSRTASESAARIFRSIQMERQRDD---- 760 Arabidopsis TTTTTRTTVTQTTRDGGGVTRVIKVVPHNAKLASENAARIFQSIQEERKRYDSSKP 695 :: ..:. : ::**. *.********:: ***.*****:*** **:* * Supplementary Fig. S3 Alignment of deduced amino acid sequences of the rice Hd17 and Arabidopsis ELF3 proteins. The sequences were aligned using the ClustalW2 software (http://www.ebi.ac.uk/Tools/clustalw2/index.html). The sequences that are highly conserved between rice and Arabidopsis are shown by blue letters. The site of a nonsynonymous amino acid change between 'Nipponbare' and 'Koshihikari' (L558S) is shown by a red letter. Asterisks, colons, and dots indicate identical, highly conserved, and weakly conserved residues, respectively.

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