tra1 - dictyBase/community-annotations GitHub Wiki

tra1 from genomic sequence contains a 2 nt gap in the 3rd exon that has been introduced to create the best possible open reading frame; ESTs show there is a 1 nt deletion in the chromosomal sequence, leading to a frame shift; the resulting protein sequence is missing one asparagine residue at position 3856.

MSTNPPQPPPSSTIASNPPQPIATPMSTTNPSQPTITSSSAASSSSSSSSGNPVNFESYA
RRCFELNNNNEQTQLLALVTEIRDNIELVHTVEYPTFLNFLFPVFYNILRQGAVQFNDGP
EQKIRNTILDILNKLPNNELLRPHILVLLQLSMYLLEVDNEENALVCLRIIIELHKNYRN
ALESEIQPFLNIVLKLYTDLPSTIEKTFSSSSSASLSTTTTAISPTTTTTTTPATATTPA
TTTATGNTITTPPPATPPSTTATAISPTSSTTTTTTATTAAAATIATTTATTTITPPLPP
YMIKSIESFKILTECPIVVILLFQLYNSYMSSNVPKFIPLIIETLSLQAPANSTVTHHSQ
YVDFIAAQVKTLYLLAYVLKWHIEQIKQYSDRFPRSVIQLLQNCPAHSSAIRKELLVTLR
HILSSDFKSKFIVYLDLLLDEKIILGTSRTSYESLRSMAYGSLADFIHNMRNELNINQIS
KVVAIYSRHLHDQTNPVSIQIMSVKLIISLMDVIQRKQDPPEYKSRSIIYKVIESFINKF
SSLKRSIPKLLADQQKEKEKELKDPQSLKDKLDGLSSANTTTSSTGEIIILDPVKDTRTL
IKTMTSSLRNIFWSLSACPINKPGTGITTGAGATTTTTTNTNNTIIPPVRIALPSIEESL
LFIKLFKSTVKCFPIYGGCNPSPQEEKEMIENFTASFMMLDQRTFQEVSTFILPFLYQRS
LNNPSLLLIPQGFLSVTQMNPTGVQINRVFLEVLTPFLYEKIRNLQPTDKPDICMIKLIK
LIFNAIQPNNNSGVGGSGGSNSSGGGGGGGSNSSNNSTNSNTTTNIDSTCVQQVLSSMIL
ILLKLITESKQIDSIQYLLLLKTIFKSCTRPDQSKEITLLFPIILETLNDLLLSSSHSTM
IPAVQQLLIELSLSIPVQIATLLPSLHLLVKPLMLALDSSSSELLSTTFRILELIVDNAT
GDFLLFTFRDNKSEFLQILSKHLRPAPYFYGPHAIRILGKMAGKSRSFSVLSPILSIDST
SNSRSIPSSNKNNNNNNYYYNGSCSNSENYSKVFKLLLPCETGDDKTKSIPLDKSIQSIK
NILLYQLDDSYLQSNAYSLLKYYISLYLSSQDFLINQQSLLNELLNNLKQSNNNNNNNSS
TVNLNIIELDNENENENDNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNIKTFKT
KEEYLNEIKNFKDLVYCLFLSITNDHLKEKFDSLKFLNNFIYHFVLYLSTFKFNYSIISM
KELDPKIFLEALVDVMSMSSHNIINQSNIEDLQTISTSKFNKAHITSLLDMIFNCSNQIF
SENSNSKKNNELMTSSTDVKDGEKVEMETEDSLKKDEMSAAATSEIKKETNVVVENEQDK
DTVLISPIFKYLVKLFIKCCYDKDFSVKGAGLIGIEYIIENVKLSWIQPFQHLILKSLLF
VCEDLSYSGYQPTIDYASEIIINLIKLCVPNLNIVPDSMEIDQSTTTASTTETAATTTTT
ETATPMVTESTAIVTEPTATTPTATPTSTPTSTSTPTPTPIPTATTSSTTTAPTTTTTTT
TNLSSSSTINQKPHCKLNQLKLKDRELLKLILEILMERITSWSGHTRSLAQRMLTMISVE
ITKIPMSQLIEDLKMTVQKLLPKTPLKSLSISLQTGVIDGLTFCLSQKPSPLIEIGADTV
RVLQECLNVAGDESSPTQQSQIKSSSAKSISATNNLRVCGVEMVATAMTCPDFLQFECLE
FKNRIIRMFFKVVTARNKEMAMAAKRGLANSIQQQRLHRDLLQTCLRPVLSNITDPKSLS
VPFLQGLSRLLELLSNCFNAALGEKLFEYLKKFEEAGKLSYLANKYRDSEEVKICASIID
IFHLLPPAAKLLDSTIILTIRLEQSLCKEVTSPYREPLIRFLAKYPQRTIEIFMGQLPQF
NLIFRLILKHQPLSKPIVEELANTYSIWLEAHLKSPSADIRFHTLSMVSIIRKQLPNWLP
ENRKVLDILIEYWRPLSHMIQSASNPLDISNQTLRETKIIVKCFLQYCKAHSEETDLYFY
MLSVLTLRASMDFNFLRDYYQHDLAPSSTIEQKKKIIQTFLIFFKDQTIPSDNKVQAIQN
LITPILTNYFHQTDRNSSSGGGIIEDSLFIQLTKQTLETEVKASYDDTLLIELLQLETLL
VKNLSSVLVDCRKELIKFAWNHLKNEDLTCKQSAYILACGFIEAYETPHKIVLQVYVPLL
RAYQPESKHLVKQALDILMPCFKTRLPGGDPKNSTWVKWTKKIIVEEGHTTAQLVHIIQL
IVRHPQLFYPSRSQFVPHIILLLPKIALGSNLTAENKKLSIDIADTIIIWEKMRMSNLQQ
SIKTSSSSLPTTTTTTTSSNKPTDSSSLPPNTPIAEGSITTPSQGGVATPNVSDSTPTPG
IHHGATNIDDEYRPPLSAIEHISLFLIRMASNWYHINEKCSELLRQTLVIWPETNIKFSV
FEKPMNTDQPQMISTCLSMLNLIAEYQVNTFIPNNVVALQQSLLQALNSDNAKISSLLGS
LFKKILAAFPLPTNNTTTTTPVSSTTTTEQSSDSSSLPPPPPVQVTKPIPNEMVSFYTFI
GTQFEMILGAFDKNYNLSILSNIKVFSDHSESFIDPYISLIVKVLIRLTRNYLSQDSDGG
TGSLANKPLSSSGSTSQTGGASQTATSASNVVLKKSNSEIISGLCKTYGFLKTKTTKLNS
DQRNAFIQSLLVLIERSNDVELLSEIIKVVDYLISISPSPSPSTTPVVTETTIPSTTTTT
TTAATTTTTTTPSTTTTAATTTTAPTTTETTTTAATTTITPFLTIKEKINFLIKLGRVDQ
LSNAELSLSYYKLVLSFYSESNSSSKQELSQLEPCFMMGLRNTVDQGMRKSLFNILHKSI
GTTPYQRLNYIIGVQQWDILGTTYWIKHALDLLLAILPNDKFVKISNFCSKLPTSLKFAN
RNGNDINQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQHHQQEQPMEIDENLV
VEQSSSVNKGNEEFKKSLKLHTQWLESLKNEESLKFSEFNENLRELIFIDSHLVNDLWCH
LFSDMWSDLTKEEQFKLSKSLTLLLSKDYTKKVPLVSKPIIPPTSIPISKPIITTTTSTS
SSTSTTTPITTIPLINNSQLITIVTLTQQQTNPIIVPSLREPNVIKTWMETLGMCKPIPK
VPIEVISFLGENYNCWYYAIRMIEQQLIDRQKLLDSTDINWDYLSYLYGAIGEKDLLYGI
YRKRYQCDETKLGLLLEQFYMFQSSQEVFLSAMNKYSAVGCKPTPRSENLLWEDHWLECA
KRLNQWNFVHEFSKEKNMYDLTIESAWKIPQWNSVKENMKKMMSQGDTSIRKILQGYFLT
NEKRYHEVDPAIVTSNQLILDKWVSLPERSFRSHTNSLVEMQQVVELQESVHILKEISNI
TLSQQPADLSRSFLTSNYIKSIFNIWRERLPNKDEDLLIWFELMAWRQQVFNIIGTPSMN
GGIGANPVTPTNTTTTITNPDGTTTTTTTPLPPPQQPINQIEFASPRYMVLEMAWTMNKY
SHIVRKHNIIEVCLNSLSKMFDLQIELHDIFLNLKEQIKCYLQLPTHYDTGISIINSTNL
DFFTPMQKGEFLQLKGEFLNRLGRYDEANQSFASSVSQYENSAKNWISWAHFCDNQFTNH
SSSSITPSSTPTTYDIKTQWAESAISCYIQGIKCDPKYGSRYVPRIFWLLYLNGSGEVPQ
QIQTQQQQQQAAAQGGLPPQPRKLTPAQSVFQSFLNSWTILPQWIWLNYMPQLISGAANL
LNFPGYGFLCWQMIGKICYLFPNSSYYHFRKLVLEMKSNASKFTTSPPTTTTTATTTTTA
TTTITTATTTSTPTQNTTPTQNTTTPIKEESSTTTATTTPAVPSTSTPTSTSAPAPISTS
TNTPPNATTTTPQANTTSPPPPSSTFSPLKMTETLSLGLHQYHSCLINEIDMMLGSFSIL
SGSIPAVYQFNGSLNQILLEAFKLNKIEDSIYNSIRSLYKHYFVNEIKYQNSKEFLEAYK
SEFKVDFIEFNLDDIVSDTIKKESDQETNVVEGTTNVSKELETTSEKQQQQQQQLPTISI
LLLIEKLIKWIDRKPDNSLITVVNTDQSTNYYGIDTMICLESICPQLVNFKPSILEIPGQ
YNTNRDPNIENNVKVEKVGMFAKLIKHSNGMVCPRITLYGGNGKAYQFLIESSPSLINGI
TNSNNNNVARVYERKNQLLGSINSMLIKNRETRRRGLTLNSYPTVVPIKNSLTMIQNIGN
DSIKQLAEVWYTHSNQSNLFKPMLKYKEMLLNSNLHTELLSKKDQDGDLEFTNITEDNNI
SSSSSSSSSSGSNSGENSPIIDSSKLVVFREMSKEIGDELMINYIQSTLLPTNYQDQYEF
KLNFSNQFGLHSLLQYILFSDIGDIDPSKIYLTKSTGSVYYNDWSLKLTNRKLGFDLLQD
NPYNQQQLLRLSPNIRNYLGPLYLEGSYLSSMISTCICLSDLKDQLVNSINLFIFDEYMC
MNNVEPLQQSEQNKDRNIHYEFIDKTTATVHQMLENRIDSLTPSSQPDKTCFISPIVKKV
NQLIQNSLSSNISQLDQLSCPWL

pfey October 2009

Alignment of correct protein from ESTs on top and protein from genomic sequence with 2 nt gap because of frame shift, missing the Asp residue at position 3856 is bottom strand.

Correct: 301  TTTITTATTTSTPTQNTTPTQNTTTPIKEESSTTTATTTPAVPSTSTPTSTSAPAPISTS 360
              TTTITTATTTSTPTQ TTPTQNTTTPIKEESSTTTATTTPAVPSTSTPTSTSAPAPISTS 
Genomic: 3841 TTTITTATTTSTPTQ-TTPTQNTTTPIKEESSTTTATTTPAVPSTSTPTSTSAPAPISTS 3899

Correct: 361  TNTPPNATTTTPQANTTSPPPPSSTFSPLKMTETLSLGLHQYHSCLINEIDMMLGSFSIL 420
              TNTPPNATTTTPQANTTSPPPPSSTFSPLKMTETLSLGLHQYHSCLINEIDMMLGSFSIL 
Genomic: 3900 TNTPPNATTTTPQANTTSPPPPSSTFSPLKMTETLSLGLHQYHSCLINEIDMMLGSFSIL 3959

Alignment of genomic sequence on top and EST sequence at bottom; note the 1 nt deletion in genomic sequence.

Genomic: 396 cagcaacaacaacaacaacagcaacaacaacaataacaacagctactacaacctcaacac 455
             |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 
EST:     301 cagcaacaacaacaacaacagcaacaacaacaataacaacagctactacaacctcaacac 360

Genomic: 456 caactc-aaatacaacaccaactcaaaatacaactacacctattaaagaagaatcatcta 514
             |||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| 
EST:     361 caactcaaaatacaacaccaactcaaaatacaactacacctattaaagaagaatcatcta 420

pfey August 2022

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