Subject: Re: Drosophila CytP450's & FlyBase
Dear Michael,
6t2p has three in frame stops that make it a pseudogene compared to its
close cousins 6t1 and 6t3 shown below
6t1 AC012831 comp(42975-44564) no introns
MIAVFSLIAAALAVGSLVLLPVVLRGGCLLVVTIVWLWQILHFWHWRRLGVPFVPAAPFV
GNVWNLLRGACCFGDQFRELYESKEAAGRAFVGIDVLHNHALLLRDPALIKRIMVEDFAQ
FSSRFETTDPTCDTMGSQNLFFSKYETWRETHKIFAPFFAAGKVRNMYGLLENIGQKLEE
HMEQKLSGRDSMELEVKQLCALFTTDIIASLAFGIEAHSLQNPEAEFRRMCIEVNDPRPK
RLLHLFTMFFFPRLSHRVGTHLYSEEYERFMRKSMDYVLSQRAESGENRHDLIDIFLQLK
RTEPAESIIHRPDFFAAQAAFLLLAGFDTSSSTITFALYELAKNTTIQDRLRTELRAALQ
SSQDRQLSCDTVTGLVYLRQVVDEVLRLYPPTAFLDRCCNSRTGYDLSPWNGGSPFKLRA
GTPVYISVLGIHRDAQYWPNPEVFDPERFSAEQRQQHHPMTYLPFGAGPRGCIGTLLGQL
EIKVGLLHILNHFRVEVCERTLPEMRFDPKAFVLTAHNGTYLRFVKNSL
6t2p AC014742 1042-2504
VETAACCFGDQFRELYERKEAAGRAIVGINVLHSHALLLRDPALIRRILVEDFPEFSSSF
KSTDAIRDTMGSGNLLFTKYKTWWETHKIFAIRLGGRRIRSLLYGLLERI*QNLEAHMAQ
KLNGAESVELEVKQLCALFTTDIFAKFALQSLQNPEAEFRPMCIEVNDPKPKRLSHHLFT
HRPDFYVAQAAFLLLAGFDTSSSFALYELAKNPTIEHRLQAELRVDLQSSHNHQLSYDTL
TGLVYLRQVLEDLPFGAGPRGCIGTLLGQLGIKVGLLHTLKHFRVELCERTLPEMRFDP*
ASVLTAHNGTFLRFVRNSL*
6t3 AC015208 comp(17123-18689)
MLLIWLLLLTIVTLNFWLRHKYDYFRSRGIPHLPPSSWSPMGNLGQLLFLRISFGDLFRQ
LYADPRNGQAKIVGFFIFQTPALMVRDPELIRQVLIKNFNNFLNRFESADAGDPMGALTL
PLAKYHHWKESRQCMSQLFTSGRMRDVMYSQMLDVASDLEQYLNRKLGDRLERVLPLGRM
CQLYTTDVTGNLFYSLNVGGLRRGRSELITKTKELFNTNPRKVLDFMSVFFLPKWTGVLK
PKVFTEDYARYMRHLVDDHHEPTKGDLINQLQHFQLSRSSNHYSQHPDFVASQAGIILLA
GFETSSALMGFTLYELAKAPDIQERLRSELREAFISTATLSYDTLMTLPYLKMVCLEALR
LYPAAAFVNRECTSSASEGFSLQPHVDFIVPPGMPAYISILGLHRDERFWPEPCVFDPER
FGPERSRHIHPMTYIPFGAGPHGCIGSRLGVLQLKLGIVHILKQYWVETCERTVSEIRFN
PKSFMLESENEIYLRFCRSSL
6a15p is short and has stops and frameshifts.  Compare to 6a16 below
6a15p this is a pseudogene on AC020451 2595-3373 with in frame stops and
frame shifts
AFTVTNSKLAKKLKMKILRDDLTDFFLSVVKPALSGMTLWTSPPSGGRSSRQGGSKFDLS
HNWTLEQMAAQAIVFFLAGFETSSSTMSSCKYELALQPEI*NQIRDEIERVLEGNAITYD
ALAKINYPEQVLSETLRKHPIQLIKFLLETQESFRVRNTELIVEKGTSLLIPVHSVHYDP
HLYPHPKLFDSSRLKAYKSNSRHPFAYLPFGTFGPRSCIGLRFGKMQAKIGIVSLCQRFK
FGDSDLTDIPL
6a16 AC004721 comp(2956-5070)
MDFTLLLLTSLLSFLLGYLRYRFTYWELRGIPQLRPHFLFGHFFRLQSVHYSELLQETYD
AFRGSAKVAGTYVFLRPMAVVLDLDLVKAVLIRDFNNFVDRRSFHGDPLTANLFNLQGEE
WRNLRTKLSPTFTSGKMKYMFGTVSTVAQQLGGTFDELVGSQGAVLELHDLMARYTTDVI
GSCAFGTECSSLREPQAEFRQVGRRIFRNSNRSIRWRIFKMTYLSSLAKLGLPVRILHPD
ITKFFNRIVRETVELRERENIRRNDFMDLLLDLRRKGLTMEQMAAQAFVFFVAGFETSSS
NMSYALFELAKNQDVQQKLRMEINDSIGKHGKLTYEAMMEMPYLDQTITETLRKYPALSS
LTRLASEDYEIPSPDGGDPVVLEKGTSVHIPVLAIHYDPEVYPEPHEFRPERFAPDACRE
RHPTAFLGFGDGPRNCIGLRFGRMQVKVGLITLLRRFRFSLPPGSPTQLKVTKRNLILLP
SDGVRLQVDPVESRLM
307a2p is a short N-terminal fragment of a P450.  It is missing nearly all
of the seq. compare to 307a1.
307a1 AC014810 comp(54284-52654) also AC007840
MLAALIYTILAILLSVLATSYICIIYGVKRRVLQPVKTKNSTEINHNAYQKYTQAPGPRP
WPIIGNLHLLDRYRDSPFAGFTALAQQYGDIYSLTFGHTRCLVVNNLELIREVLNQNGKV
MSGRPDFIRYHKLFGGERSNSLALCDWSQLQQKRRNLARHCCEEMEHWNRELGNQLVPGE
PINIKPLILKACANMFSQYMCSLRFDYDDVDFQQIVQYFDEIFWEINQGHPLDFLPWLYP
FYQRHLNKIINWSSTIRGFIMERIIRHRELSVDLDEPDRDFTDALLKSLLEDKDVSRNTI
IFMLEDFIGGHSAVGNLVMLVLAYIAKNVDIGRRIQEEIDAIIEEENRSINLLDMNAMPY
TMATIFEVLRYSSSPIVPHVATEDTVISGYGVTKGTIVFINNYVLNTSEKFWVNPKEFNP
LRFLEPDNEKLQLKRNIPHFLPFSIGKRTCIGQNLVRGFGFLVVVNVMQRYNISSHNPST
IKISPESLALPADCFPLVLTPREKIGPL
307a2p AC019383 comp(3284-3706) AL078186
MLTSVFYVLFAIAITIILISYVFLLLKCKQKAFVVIGLLYQEKKYQCFDQAPGPHPWPII
GNINLLGRFQYNPFYGFGTLTKKYGDIYSLSLGHTRCIVVNNVDLIKEVLNKNGKYFGGR
PDFFRYHKLFGGDRNNCKFIXXLRF
9f3p is missing an exon or two at the active site.  This includes the heme
binding cys that is essential for activity.
9f2 AC017132 AC017240 AC009741 AC017170 AC007594 PLUS ESTs
MLWEFFALFAIAAALFYRWASANNDFFKDRGIAYEKPVLYFGNMAGMFLRKRAMFDIVCD
LYTKGGSKKFFGIFEQRQPLLMVRDPDLIKQITIKDFDHFINHRNVFATSSDDDPHDMSN
LFGSSLFSMRDARWKDMRSTLSPAFTGSKMRQMFQLMNQVAKEAVDCLKQDDSRVQENEL
DMKDYCTRFTNDVIASTAFGLQVNSFKDRENTFYQMGKKLTTFTFLQNMKFILLFALKSL
NKILKVEIFDRKSTQYFVRLVLDAMKYRQEHNIVRPDMINMLMEARGIIQTEKTKASAVR
EWSDRDIVAQCFVFFFAGFETSAVLMCFTAHELMENQDVQQRLYEEVQQVDQDLEGKELT
YEAIMGMKYLDQVVNEVLRKWPAAIAVDRECNK   DITFDVDGQKVEVKKGDVIWLPTCGFH
RDPKYFENPMKFDPERFSDENKESIQPFTYFPFGLGQRNCIGSRFALL   EAKAVIYYLLKD
YRFAPAKKSCIPLELITSGFQLSPKGGFWIKLVQRN
9f3p AC017132 AC017240 AC009741 AC017170 AC007594 PLUS ESTs
MLWEFLALFAIATALFYRWASANNDFFKDRGIAYEKPVLYLGNMAGMFLRKRAMLDIVCD
LYTKGGSGKFFGIFAQRQPLLMVRDPDLIKQITIKDFDHFINHRNEFDTSSDDDPHDMSN
LFSSSLFSMRDARWKDMRSTLSPAFTGSKMRQMFQLMNQVAKEAVDCLKQDDSRVQENEL
DMKDYCTRFTNDVIASTAFGLQVNSFKDRENTFYQMGKKLTTFTFLQSMKFMLFFALKGL
NKILKVELFDRKSTQYFVRLVLDAMKYRQEHNIVRPDMINMLMEARGIIQTEKTKASAVR
EWSDRDIVAQCFVFFFAGFETSAVLMCFTAHELMENQDVQQRLYEEVQQVDQDLEGKELK
YLDQVVSEVLRKWPPAIAFDRECNK  (see seq above for missing piece)
EAKAVIYYLLKDYRFAPAKKSCIPLELISSGFQLS
PKGGFWIKLVQRN
By my definition of not producing a functioning P450 protein these are all
pseudogenes.  The def. of a psuedogene is a bit slippery.  Some may say that
these proteins are made into mRNA since some have ESTs and maybe into a
protein, but it won't work as a P450.
David
----------
>Subject: Re: Drosophila CytP450's & FlyBase
>Date: Sat, Apr 15, 2000,  8:29  AM
>
> David
>
> Three CytP450 gene symbols end in 'p'. Two of these have no CT.
> Are these pseudogenes ?
>
>  '87B-C','Cyp9f3p','39772'
>  '44D','Cyp6a15p','34554'
>  '39C1-3','Cyp6t2p','none'
>  'unmapped','Cyp307a2p','none'
>
> Michael