A) FGENESH+ 2.6 Prediction of potential genes (Sea urchin model) Seq name: AKZP01053170-72 merged AKZP01053170 (L=3624-bp), AKZP01053171 (L=4845-bp), and AKZP01053172 (L=8983-bp) Length of sequence: 17452 Homology: SPRAG1L Length of homolog: 983 Number of predicted genes 1: in +chain 1, in -chain 0. Number of predicted exons 3: in +chain 3, in -chain 0. Positions of predicted genes and exons: Variant 1 from 1, Score:1926.453711 G Str Feature Start End Score ORF Len 1 + TSS 29 -1.63 1 + 1 CDSf 2757 - 2935 121.22 2757 - 2933 177 4 61 34 1 + 2 CDSi 5886 - 6384 162.66 5887 - 6384 498 296 386 28 1 + 3 CDSl 8928 - 10643 1671.74 8928 - 10643 1716 395 959 52 1 + PolA 12040 1.88 Predicted protein(s): >FGENESH:[mRNA] 1 3 exon (s) 2757 - 10643 2394 bp, chain + ATGGAGGGGCACATCAATGCCTTGGCTATGATGTGTAGGATCTGCGGCCAGATCATCACC TCATCCAAAAACAAGTCAAGCTCAGCAAAGTACAAGACACAGCTCCTTGCTGTGTACAAC CTCAATTTAGATGAGAAGCAGGGCGGCATCCATCCACCATCTGTGTGCAACAAATGCAGG CAACAGGTGCAACGTGCACATAGTTCAATGGAGCAAGGCAAGCAGTATCAGGGCAAACTT CCGCAGATCCAGAATTTCTCTGCTCATGATGCTGCTTGCTGGGTGTGCAGTGCTTATACT GCTCATGTGGCACAACTCCGCCCTCAGTTCGCAGCACACCAGTCCTCATCTAGCGACCAA CCAGACCAACCAGAATCCCAACCGTCAACCAGCGCACAAGACCCAGCATCTTCTCAGCCA AGCCTGTCAACAGCCACTAGGACCCTTTTTGGGGATACAGCTCCGGACCCCGGCATGGCA TCACAGGGAAAGAAACGTGTATGGAATGTCAAGGCCAGCTTGAATCATGTCAGGCGGGAT TATGCCCGTAAGCGGACCAAAGAGGCATCTGTCTTCATCAGCGACTTTTGCGAGAGGCAG AAAGAGGACAAGCTTGACCTCCTCTACTTCTTGCTTTGCGACAATCCAAACGAATGTGGT GACTCCAGGTATAAAGAGGTTTTGGCATCCTGGAGCAAGGAAAGCGTGGAGCTCACGGCT GAAGATTGCCTTGCGATGAGAGTCACAACGAAGACATCAAAAGCACATTATGATGCTCAA TACCGAAAGTTCAAGGCGAAGGGCACAAACATTCTCAAGCCACCGCACATTCTCACCGAA TTGGAAAAGGATTTTATGCCCGGTAGCGTTAGGTTTCGGCTGGAGGGAGGGACGGACATC ATCCATCACACCCCAGTCAAGGCAGGACAGTCTCATGTAGAGTATGGGGAGCTGTCCTTC GAGCCCCAGGACCTGAATAGGGAGGATCACCCAGGATTGGAGACCCCCTTCCCCAACATG AAAGGCGTGGCTTGGCCTTATGCACACGCTCTTGCCAAGACCCTGGAGGAGTTGGATGCA GAGATCGTCATGGGCTTGCAGCAGGCGGGACTTGAACCTGATGACGATCTCTGCATTCTT ACTACTATCAAAGACGGCGCTGACGGAATGGGTGACATCTCCGTGACCAAAGCGGCGAGG GATCGTCTCTTGCCAGACAAGGCCTTCCGGGCAGCTTTTGCAGTAATAAAGTGCGAGGTA AACAGGGACGGGGAGAAGGTTACAGTGTACGAGCCAGATGCTCCAGACTCCACTTTTATT ACACGGCCATTGATTGAGGCTATAGGGGACGAGAACAATAGAGCGTCGGCCACTGTCCTC CTTGACGGCATGGAACATGACCGACAGGTGCTACGAGGGAAGGAGATGTCTATAAACGTA GGTCCTGTGTGGCGAAGGCATAAATTAAAATTCTTCAATTCCATGATTGATGAAAAACTG GACCGAGCGAATGGGGGTCTCCAGGGCAGTGGTTCACGCTTTGTGTGCACTCTGTGCCAT GCAACAAAAGAATCTGCAAAAACTGATTTGGGCACCTTCAGCATATCTCGATCATATGAG GAAACAGCATCAACTGCAAAGTATGTCCAAGTTAATCCGGACAATCTGTCAGCAGCAGAA CTCACAGAAATATCAAGGGGGGTAAAATCAAATCCAATATTGCAGTCGGACCCGAAGGAC AAACTAATCGATGCCACCCATACAGATATTAACATGGGAAACTTTTTCAAGAAGTTGATC ATCTGTGAGGTTGCCAGGGTCCAAAGCTGGGACATCTCCAAAGAAATAAGGCCGATGTAC GAAGCTGCCGAGAAACGCCTCAATGACCACCTAACGGAAACAATCGGCTTAGTGCCAAAA TTAATGATGCCGGGGAACTTTGCCCGGGATTTGTTTTCGTCAGCAAAAGTTGATTCTTTT CTTGCACTCCTGCCAGAAGAAGACAGAAGAAACAACCTGGCCGAAGTTTTGGGCATCTTC AGGAATCTCCGAACTGTGTACCGGGCTCATCACCCTGAAGCAGAAGACGTCAGCACCTTC AAACAACGTGCAGTGGAGATGGGGCGTCTTCTGCTGACCAACTTTTCTTATGCTGGGTGG CCCAATTATCTTCACAAGATAATTGAGCATGTGCAGGAAATCATCGAGGATCCCGAGGGG CCTGGCACAATTGGCAGCTTAAGCGGAGAAGGAAATGAGGCAGCGAACAAGTTGTTCAGA GATCTGCGTGGCCACTTCGCCAGGAAGCATGATGAATCTCAGGCCCTCAGAGACATCATA TGGTTCCACTGGCTGCACACTAGCCCAAAGCTGAGGAGAATCAGCCATGTATAA >PMRAG1L 1 3 exon (s) 2757 - 10643 797 aa, chain + MEGHINALAMMCRICGQIITSSKNKSSSAKYKTQLLAVYNLNLDEKQGGIHPPSVCNKCR QQVQRAHSSMEQGKQYQGKLPQIQNFSAHDAACWVCSAYTAHVAQLRPQFAAHQSSSSDQ PDQPESQPSTSAQDPASSQPSLSTATRTLFGDTAPDPGMASQGKKRVWNVKASLNHVRRD YARKRTKEASVFISDFCERQKEDKLDLLYFLLCDNPNECGDSRYKEVLASWSKESVELTA EDCLAMRVTTKTSKAHYDAQYRKFKAKGTNILKPPHILTELEKDFMPGSVRFRLEGGTDI IHHTPVKAGQSHVEYGELSFEPQDLNREDHPGLETPFPNMKGVAWPYAHALAKTLEELDA EIVMGLQQAGLEPDDDLCILTTIKDGADGMGDISVTKAARDRLLPDKAFRAAFAVIKCEV NRDGEKVTVYEPDAPDSTFITRPLIEAIGDENNRASATVLLDGMEHDRQVLRGKEMSINV GPVWRRHKLKFFNSMIDEKLDRANGGLQGSGSRFVCTLCHATKESAKTDLGTFSISRSYE ETASTAKYVQVNPDNLSAAELTEISRGVKSNPILQSDPKDKLIDATHTDINMGNFFKKLI ICEVARVQSWDISKEIRPMYEAAEKRLNDHLTETIGLVPKLMMPGNFARDLFSSAKVDSF LALLPEEDRRNNLAEVLGIFRNLRTVYRAHHPEAEDVSTFKQRAVEMGRLLLTNFSYAGW PNYLHKIIEHVQEIIEDPEGPGTIGSLSGEGNEAANKLFRDLRGHFARKHDESQALRDII WFHWLHTSPKLRRISHV ============================================================ B) Query= PMRAG1L 1 3 exon (s) 2757 - 10643 797 aa, chain + Length=797 Score E Sequences producing significant alignments: (Bits) Value Query_7615 gi|71082680|gb|AAZ23546.1| recombination activatin... 581 0.0 ALIGNMENTS >lcl|Query_7615 gi|71082680|gb|AAZ23546.1| recombination activating protein 1-like [Strongylocentrotus purpuratus] Length=983 Score = 75.5 bits (184), Expect = 6e-18, Method: Compositional matrix adjust. Identities = 36/103 (35%), Positives = 54/103 (52%), Gaps = 2/103 (2%) Query 1 MEGHINALAMMCRICGQIITSSKNKSSSAKYKTQLLAVYNLNLDEKQGGIHPPSVCNKCR 60 +E H AL+ CR+CG + + K+ SS KY+ +L+VY ++ +HPP +C CR Sbjct 4 VELHRKALSQTCRVCGSYVKNKKSLSSKEKYEELILSVYGIDFKLDDEDVHPPRICVSCR 63 Query 61 QQVQRAHSSMEQGKQYQGKLPQIQNFSAHD--AACWVCSAYTA 101 + R+ S +G Y + NFSAH C +C AY A Sbjct 64 LWMTRSDSRNAEGPTYPTSGKTLANFSAHPELEPCSICEAYQA 106 Score = 581 bits (1497), Expect = 0.0, Method: Compositional matrix adjust. Identities = 321/684 (47%), Positives = 433/684 (63%), Gaps = 17/684 (2%) Query 128 PSTSAQDPASSQPSLS-TATR---TLFGDTAP------DPGMASQGKKRVWNVKASLNHV 177 P+ +A P ++ L+ TATR + D AP P + +K K SL++V Sbjct 278 PTATAPLPPTATALLTPTATRYRPIVTKDRAPFTRALFSPVLTVPARKSPARAKGSLHYV 337 Query 178 RRDYARKRTKEASVFISDFCERQKEDKLDLLYFLLCDNPNECGDSRYKEVLASWS--KES 235 RRD A+ R + A F++ + E++ DL +F L + D R K V+ W+ K+S Sbjct 338 RRDCAKNRARGALDFMTSHSAAKNENETDLWFFGLHNRLRNEEDERAKMVMELWTERKKS 397 Query 236 VELTAEDCLAMRVTTKTSKAHYDAQYRKFKAKGTNILKPPHILTELEKDFMPGSVRFRLE 295 +L+ +DCLAMRV T +K Y +Y K+KG +PP LT+ E +MPG+VRF L Sbjct 398 TDLSVDDCLAMRVGTLCTKGMYAEKYSFLKSKGDKTFRPPGQLTKRESCYMPGNVRFGLM 457 Query 296 GGTDIIHHTPVKAGQSHVEYGELSFEPQDLNREDHPGLETPFPNMKGVAWPYAHALAKTL 355 G ++HTP K+ + ++ +EP +N E PN GVAW Y A+AKTL Sbjct 458 EGGKCVYHTPEKSLEEFDDHS--MYEPIRINVRSK-LTEFALPNCIGVAWSYPEAVAKTL 514 Query 356 EELDAEIVMGLQQAGLEPDDDLCIL-TTIKDGADGMGDISVTKAARDRLLPDKAFRAAFA 414 EELD I G+ + GL PD I+ TT+KDGADGMG+I+V K D LPDKAFRA+F Sbjct 515 EELDENIREGMLKVGLNPDGPSIIIDTTLKDGADGMGEIAVHKMKSDTFLPDKAFRASFV 574 Query 415 VIKCEVNRD-GEKVTVYEPDAPDSTFITRPLIEAIGDENNRASATVLLDGMEHDRQVLRG 473 V+KCEV RD G + V+E P+S + RPL+EAIGDEN+ +++ VL+ ME +R +L+ Sbjct 575 VLKCEVKRDDGTRDLVFEEPKPNSVIVNRPLLEAIGDENSASTSAVLMRKMEKERLILQN 634 Query 474 KEMSINVGPVWRRHKLKFFNSMIDEKLDRANGGLQGSGSRFVCTLCHATKESAKTDLGTF 533 M+I+ G R H+ +NSMIDEKL R++GGLQGSGS F+CTLCHATK SAKT LG+F Sbjct 635 SIMTIHAGTYTRLHRFTIYNSMIDEKLARSSGGLQGSGSNFICTLCHATKTSAKTQLGSF 694 Query 534 SISRSYEETASTAKYVQVNPDNLSAAELTEISRGVKSNPILQSDPKDKLIDATHTDINMG 593 I R+ ET T Y+ NPDNL+ ELT + GVK P+L S+PK +L+DATH DI++G Sbjct 695 KIDRTLTETQQTLTYITTNPDNLTPDELTTEAGGVKRKPLLTSEPKQQLMDATHADIDLG 754 Query 594 NFFKKLIICEVARVQSWDISKEIRPMYEAAEKRLNDHLTETIGLVPKLMMPGNFARDLFS 653 FFKK+I+ E+A V W+ S+ ++ AE+RLN ++ E +G P LMMPGN+AR LF Sbjct 755 QFFKKIIVREMAGVHKWEASENVKQYIVDAERRLNINVRELLGTAPSLMMPGNYARALFK 814 Query 654 SAKVDSFLALLPEEDRRNNLAEVLGIFRNLRTVYRAHHPEAEDVSTFKQRAVEMGRLLLT 713 D FL L+ E+R+ L VL FR LR +YR HHP +V FK++AV++GR LL Sbjct 815 EKNEDVFLELIRNEERKELLRSVLQKFRALRKIYREHHPNKREVQGFKKKAVQIGRELLE 874 Query 714 NFSYAGWPNYLHKIIEHVQEIIEDPEGPGTIGSLSGEGNEAANKLFRDLRGHFARKHDES 773 +F Y WPNYLHKI EH QE + +GPG+IG LS EG+EAANKLFR LR +F+R+ D Sbjct 875 HFEYVCWPNYLHKIFEHTQEAMLSEDGPGSIGILSSEGSEAANKLFRKLRNNFSRRGDVL 934 Query 774 QALRDIIWFHWLHTSPKLRRISHV 797 LRDI+WFHWL+TSPKL R+ V Sbjct 935 DGLRDILWFHWLYTSPKLVRLRAV 958 ============================================================= C) FGENESH+ 2.6 Prediction of potential genes (Sea urchin model) Seq name: AKZP01064647 Length of sequence: 3734 Homology: RAG2L_LVar Length of homolog: 467 Number of predicted genes 1: in +chain 1, in -chain 0. Number of predicted exons 3: in +chain 3, in -chain 0. Positions of predicted genes and exons: Variant 1 from 1, Score:1022.151367 G Str Feature Start End Score ORF Len 1 + TSS 83 -3.54 1 + 1 CDSf 851 - 1151 266.38 851 - 1150 300 2 99 49 1 + 2 CDSi 1456 - 1698 177.53 1458 - 1697 240 101 184 49 1 + 3 CDSl 2354 - 3198 583.61 2356 - 3198 843 186 468 38 1 + PolA 3614 1.87 Predicted protein(s): >FGENESH:[mRNA] 1 3 exon (s) 851 - 3198 1389 bp, chain + ATGGCTGACCAATACGCAGACTTTGATTTCATCCCTCTCAAAGCTGCAAAAGACAATAAA AGAAAAGTAACGCGAAAGCGAACGCAACTGGAAATGAATCTGGGTGAAAATTACCCTGCG GAGGGTCACTGTTCCGTAATTTTGTCTTTGGAAAACAACTCCGATCGAGTGCTTACTTTT GGTGGTGCACGTAGAAAGGAAGAGAGAACATGGCAAGATGGAGCAGCCATTACCGAGTTC GTCATCACAGCTGATGATGAGGATGTATCCATTAGGTCTATTACAACTTGCAAGACGAAA GGAGGCATGCTTCCACCACTTCATGGAGCTGCCATCGTAAATCTTTGTACAAGGTTCATC ATGTGGGGCGGCCTCGATCTGTGCGAGTACAGATGTAGAGACGACTTGCTGGTGATTGAT GAACAACCACGCCAACGGAGAGTATCACCCTTATTCCAAATTACCTATGTAGAGACTCTA CATCACAAGACAATTTCGAGACAAGGGCAGGACACTCCCCACCAAACTGGACCAGTACCA TCAGGAAGATCAGGTCACACATTGACAAAATTGCCAGGTTCGAATAAAGCTCTTCTGTTT GGCGGGATATGTATGGGAAAGAGCAAGGAGTACTTTGGATCGCGCTTTTGCAAGTCTTGT AAGGATGGTAGGTTTTATATTCTTAATACTGAGACCTATGAGTGGCAACACCTGAAAGTG CCCCTGATTACACCCCGAGCATATCATTCAGCAACTGCCATCGAAAAAGATGCTGAATAC AACGTAGCTGTTATTGGTGGGGTGATCTTTGATGGAAACTTGCCAAGCCACCGGGAAGCT CTGAACGAAATTGTCATCCTCACCATGGACAAAGAAATGAAAAACTGTACACTACAAGAG TTGTCTCTAGCCTCCACAACGCCAAACACTAGGGACGTTTTTCTTTCGTCCCATGCTACA CTTCTGCATAATGATAGCATTATCGTCGTTGGTGGCATACAAATGCATGCAAAGGAGATT ACAGACAGAGCACCGACTGCTGTACCCACTGCGTACCGTTTAAGTTTATCTGCAAAAGAA TATGAAGCCCTCCCCAAAACAACTTTTGCACCTGCAATTTTTGGCACATATGGACATTCC CTGCATAAACTCCAGAGTGACAATACACTTCTTATACTTGGTGGCAGCTCGCGGCAAATT TCCTTGCTTACTGACAGGAGTTTTGAACCAGAACCCTGCGATTGTGTACCGTGTACCATA GTCTCATCTCCACAGCTCAAGGACCCAACATGGATTCAGTGCGATAAATGCAAAAAATGG TTCCACACTTACTGCATTAAACTTGCAGCAGTTCCAGAAGGGCAGTTCTATTGCTCAAAT TGCAAGTGA >PMRAG2L 1 3 exon (s) 851 - 3198 462 aa, chain + MADQYADFDFIPLKAAKDNKRKVTRKRTQLEMNLGENYPAEGHCSVILSLENNSDRVLTF GGARRKEERTWQDGAAITEFVITADDEDVSIRSITTCKTKGGMLPPLHGAAIVNLCTRFI MWGGLDLCEYRCRDDLLVIDEQPRQRRVSPLFQITYVETLHHKTISRQGQDTPHQTGPVP SGRSGHTLTKLPGSNKALLFGGICMGKSKEYFGSRFCKSCKDGRFYILNTETYEWQHLKV PLITPRAYHSATAIEKDAEYNVAVIGGVIFDGNLPSHREALNEIVILTMDKEMKNCTLQE LSLASTTPNTRDVFLSSHATLLHNDSIIVVGGIQMHAKEITDRAPTAVPTAYRLSLSAKE YEALPKTTFAPAIFGTYGHSLHKLQSDNTLLILGGSSRQISLLTDRSFEPEPCDCVPCTI VSSPQLKDPTWIQCDKCKKWFHTYCIKLAAVPEGQFYCSNCK ============================================================ D) Query= PMRAG2L 1 3 exon (s) 851 - 3198 462 aa, chain + Length=462 Score E Sequences producing significant alignments: (Bits) Value Query_51425 SPRAG2L NP_001028184.1 recombination activating p... 339 5e-115 ALIGNMENTS >lcl|Query_51425 SPRAG2L NP_001028184.1 recombination activating protein 2-like [Strongylocentrotus purpuratus] Length=499 Score = 339 bits (870), Expect = 5e-115, Method: Compositional matrix adjust. Identities = 186/470 (40%), Positives = 288/470 (61%), Gaps = 18/470 (4%) Query 7 DFDFIPLK-AAKDNKRKVTRKRTQLEMNLGENYPAEGHCSV---ILSLEN--NSDRVLTF 60 DF I L+ A+K+ KRK++RK+ Q ++ L E Y AEGH +V +L E R+ + Sbjct 6 DFGMILLQQASKEGKRKISRKKPQSDLKLNEYYLAEGHFAVMCPVLGAEEPEKKKRIFSS 65 Query 61 GGARRKEERTWQDGAAITEFVITAD-DEDVSIRSITTCKTKGGMLPPLHGAAIVNLCTRF 119 GGARR + +W D I E+V+ D ++DV++ S+ +CKT GG +P L AA + +RF Sbjct 66 GGARRGGDNSWGDAGRIIEYVVEMDKNDDVTLASVVSCKTTGGRMPALQSAAAIESDSRF 125 Query 120 IMWGGLDLCEYRCRDDLLVIDEQPRQRRV-SPLFQITYVETLHHKTISRQGQDTPHQTGP 178 +WGG DL EYRC+DDL++++E R+ +P+F I YV T + SR+G P Q G Sbjct 126 YVWGGFDLMEYRCKDDLIILEEGRRRGATGAPVFDIKYVPTTANMVASRRGNTVPVQKGT 185 Query 179 VPSGRSGHTLTKLPGSNKALLFGGICMGKSKEYFGSRFCKSCKDGRFYILNTETYEWQHL 238 VP R+GHTLT+L + +ALLFGG+ + ++ F + +C+DG FYIL+ +T+ W+ + Sbjct 186 VPHARTGHTLTRLGETKEALLFGGVMEQEERKSFSVEWELACRDGTFYILDLDTFIWRRV 245 Query 239 KVPLIT-PRAYHSATAIEKDAEYNVAVIGGVIFDGNLPSHREALNEIVILTMD-KEMKNC 296 VP T R YH+A +E + +A +GGV+ D N + R +NE+++LTM+ ++ Sbjct 246 PVPSATLARTYHTAECLETVRSFVIAFVGGVMHDKNTTT-RIPINEVLLLTMNSQDTDTA 304 Query 297 TLQELSLASTTPNTRDVFLSSHATLLHNDSIIVVGGIQM-HAKEITDRAPTAVPTAYRLS 355 L ++LAS P+T ++S HAT N +I+V GG Q+ H+ +I + A + L Sbjct 305 VLSTVTLASDGPSTPVPYISYHATAQVNYNILVSGGFQLQHSSDIPKTSRHASSRVFILD 364 Query 356 LSAKEYEALPKTTFAPAIFGTYGHSLHKLQSDNTLLILGGSSRQISLLTDRSFEPEPCDC 415 + K+Y+ LPKT FGT GH L L D ++ +GG+S+QIS+L+DR ++PE CD Sbjct 365 IVGKKYKLLPKTQNNNQ-FGTAGHVLLTLAPD-CIISVGGTSKQISMLSDRKYKPEKCDL 422 Query 416 VP-CTIVSSPQLKDPTWIQCD--KCKKWFHTYCIKLAAVPEGQFYCSNCK 462 +P CTI + + W+QC+ +C KW H YC+KL ++PE ++C +CK Sbjct 423 LPSCTIAEAEGTVEIQWVQCETPRCGKWVHVYCLKLNSIPE-IYFCPHCK 471