D rosophila Virilis Dot Chromosome - GEP …...2 I. Overview Contig 39a-72 (chromosome 5) contains one previously unannotated putative gene, Ephrin. Only the last three of the five

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Drosophila Virilis Dot Chromosome

Annotated By: Anushree Sharma

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I. Overview

Contig 39a-72 (chromosome 5) contains one previously unannotated putative gene, Ephrin. Only the last three of the five exons of the gene are discernible in the sequence at bases 4165 – 4475, 4539 – 5177, and 7301 – 7581. The ephrin exon annotated last year on contig XAAA73 is most likely the second exon of the gene since the first exon is a UTR as indicated by ensembl data. My second contig, contig 43f-106 (chromosome 3), contains four putative genes – ATP synthase beta, eIF-5A, calcium dependent calmodulin kinase II (CaMKII), and plexA. ATP synthase beta consists of three coding exons at bases 18261-18198, 17522-17271, and 17199-16058; eIF-5A has only one exon extending from 19614-20093 in reverse orientation to the other genes. CaMKII has a 5’ UTR exon and 12 coding exons at bases 1-164, 243-302;739-793, 1156-1156, 1635-1726, 1963-2085, 2155-2281, 8732-8810, 8877-8971, 9049-9162, and 10551-10690. Gene plexA has a 5’UTR exon, a 3’ UTR exon, and 8 coding exons at bases 22168-23451, 24470-25715, 27589-29925, 30009-30204, 30560-30946, 31012-31142, 31142-31361, and 31830-31997. All genes except eIF-5A are syntenic to D. melanogaster fourth chromosome, with some variation in exon and intron lengths. Gene eIF-5A is actually homologous to 2R gene eIF-5A of D. melanogaster and may have arisen as the result of a duplication.

Fig 1: Chromosome 3 Genes.

Fig 2: Chromosome 5 Genes. My gene annotation focused mainly on bases 1-7200 bases.

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II. Genes

In annotating the Drosophila virils dot chromosome, I analyzed segments of two contigs, 39a-72 and 43f-106. Contig 39a-72 overlapped with XAAA72 and XAAA73 from last year’s sequence and only the first 7 kbs of the sequence were novel. Contig 43f-106 overlapped with contig XAAA106 from last year and the first ~ 27kbs of the sequence remained unannotated. For each contig, I began by running a blastx against swissprot database to identify putative genes with significantly low e-values. I cross-checked the blast matches with Genscan predictions on the UCSC browser, but focused on non D. virilis mRNA or Refseq evidence to identify putative genes (Fig 3 and Fig 4). I then extracted the regions that showed matches to known genes in the blastx results and aligned them to exons of the corresponding D. melanogaster proteins. I used the boundary matches from the alignment to identify start and stop codons as well as splice donor and acceptor sites of the exons in the D. virilis DNA sequence on UCSC browser.

Fig 3: Chromosome 5 Genscan Prediction – Genscan predicted the two genes (ephrin and onecut) as a single gene with 7 exon regions.

Fig 4: Chromosome 3 Genscan predictions – Genscan predicted five genes for contig 43f-106, one of which had previously been annotated. Chromosome 5 : 1) Ephrin The Ephrin gene Isoform A has 5 exons which encode a product with ephrin receptor binding at the membrane. According to NCBI databe, there are 10 recorded alleles : 8 in vitro constructs,1 classical mutant, and 1 wild-type. Mutations have been isolated which affect the eye and are visible. Genscan predicted the ephrin gene at ~ 5 kb to be part of a downstream gene at ~ 15 kb. Blastx results, however, indicated that the gene at ~15 kb

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matched the D. melanogaster onecut gene with an e-value of e-42, while the predicted gene at the 5kb region matched ephrin. Furthermore, the mRNA evidence from Drosph AF216287 indicated close matches at the 5 kb region to D. melanogaster ephrin IsoformA and mRNA BT005199 gave matches to D. simulins ephrin Isoform B (Fig 5). To gather further evidence for the identity of the gene, I obtained the primary sequence of D. melanogaster Ephrin protein from ensembl database and ran a blast2seq against my query region. Sequence alignment to the D. melanogaster protein exons 3, 4, and 5 produced significant matches to the extracted sequence of contig 39a-72 around the 5kb region. Chromosome 5

Fig 5: mRNA evidence for Ephrin Gene. The Ephrin blast2seq results obtained were as follows: Exon 1 – No significant matches were found as the exon is a 5’ UTR according to ensembl database. Since the clones are randomly generated, it is also very probable that my contig starts in the middle of the Ephrin gene and does not contain the UTR region. Exon 2 – No significant matches were found probably because my contig does not contain the exon 2 region. Exon 3 – Match identified!

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Using the match boundaries, I searched the UCSC browser for splice donor and acceptor sites to identify exon boundaries. Though Genscan gave close predictions for intron/exon boundaries of most of the genes that I annotated in my contigs, Genscan was significantly incorrect in predicting the Ephrin gene exons. Whereas Twinscan predicted 3 exons for the gene, Genscan predicted the three exons as a single exon and linked this gene to the downstream onecut gene exons.

Fig 6: AG at base 4163 indicates splice acceptor site at the start of Ephrin exon 3.

Fig 7: GT at base 4476 indicates splice donor site at the end of exon 3.

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Exon 4 – Match identified!

It is interesting to note that though the exon 4 start matches Genscan prediction closely, the end of exon 4 identified through the sequence alignment diverged from the Genscan prediction (Fig 8 and Fig 9)

Fig 8: AG at base 4537 indicates splice acceptor site at the start of Ephrin exon 4.

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Fig 9: GT at base 5178 indicates splice acceptor site at the end of Ephrin exon 4. Exon 5 – Match Identified!

To confirm the presence of a stop codon at the end of exon 5 DNA sequence, I extracted region 7306-7700 and translated it using the NCBI translate tool. Frame 3 gave the following results.

I similary extracted the other predicted exon sequences and translated them to obtain the protein sequence. Since my contig did not have significant match to exon 1 or 2, the protein sequence I obtained is only partial and spans the last three exons.

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Accession # Q8ST77 Exon Start Sequence End Sequence 3 4165 tttgtagATTTCGG 4475 TTTCATTTgtgagt 4 4539 aattagCGACGT 5177 GCAATGGTAaggaca 5 7301 aattacagATGATCA 7581 TACCGGTGAatggt Cds: (4165 – 4475; 4539 – 5177; 7301 – 7581) Chromosome 3 :

Though I followed the same procedure for the following genes as for the Ephrin gene, each gene provided novel challenges and interesting insight. 1) ATPB

This protein belongs to the ATPase alpha/beta chains family. The beta chain is the catalytic subunit that produces ATP from ADP in the presence of a proton gradient across the inner mitochondrial memberane. The ATPB gene was in the reverse orientation to other genes in chromosome 3 and I had to be particularly careful when determining the intron/exon boundaries as I had to read from right to left. In identifying the protein sequence using Translate tool, my initial sequence produced stop codons in every frame. I, however, noticed that the stops were just early on and the rest of the translated sequence was fine. I examined exon 1 and realized that there were infact two tandem GT’s at the end (Fig 10). Changing the exon boundary from 18196 to 18198 gave me the correct sequence.

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Fig 10: Tandem GT’s from base 18199-18196. Exon 1: 18261-18198

Exon 2 : 17524-17273

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Exon 3 (17199-16058)

Accession # Q05825 Exon Start Sequence End Sequence 1 18261 caaaaATGTTCG 18198 CAATTGTgtaagt 2 17524 aattgtagCCGTAA 17273 TCATTGgtgagc 3 17199 tttaagGCGAAC 16058 GCCTAAAatgc Cds: (18261-18198; 17522-17271; 17199-16058) 2) EIF-5A Though its precise role is not known, this gene is the eukaryotic translation initiation factor A that is involved in protein biosynthesis and functions by promoting the formation of the first peptide bond. This gene was particularly interesting since it is found on 2R chromosome of D. melanogaster instead of the fourth (Fig 11). Furthermore, an analysis of the exons showed that the gene had a single exon that matched exactly with the three-exon regions of D. melanogaster. This initially suggested that the gene might be a psuedogene. To investigate the matter, I ran a blat against the more closely related

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species D. mojavensis to see if it had the eIF-5A gene and if so, on what chromosome and with how many exons. The blat results indicated that D. mojavensis has two exons for the gene on the 2R chromosome. These results, coupled with the mRNA evidence for the UCSC Browser suggest that the D. virilis eIF-5A gene may have arisen as a result of a duplication of the 2R gene by reverse transcriptase. Since duplicated genes are more free to undergo mutations, it is possible that D. virilis eIF-5A gene on 2R lost its function so that only the fourth chromosome duplication served as the functional gene.

Fig 11 a: Gene eIF-5A on chromosome 2R of D. melanogaster. The gene has three coding exons and one 5’ UTR.

Fig 11b: Gene eIF-5A has mRNA evidence from D. melanogaster and Non- D. mojavensis species. Accession # Q9GU68 Exon Start Sequence End Sequence 1 20093 tcaaaATGTCGG 19614 TTTGGATAAAtaagct Cds: (20093-19614) 3) CaMKII This gene encodes a product with protein serine/threonine kinase activity involved in synaptic transmission. According to NCBI database, there are 6 recorded alleles: 3 in vitro constructs (none available from the public stock centers), 2 classical mutants (none available from the public stock centers) and 1 wild-type. Mutations have been isolated which are recessive lethal. Only isoform B has exon 9 as a coding region, while isoforms A and C do not. The CaMKII gene of D. virilis resembles isoforms A and C most closely in that it too does not have a coding exon 9. My contig begins in the middle of exon 2 and thus, I assumed that the coding sequence includes the first base of my contig.

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Exon 1 – No significant match found since this region is a UTR. Exon 2 – perfect match

Exon 3 –

Exon 4 –

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Exon 5 – perfect match

Exon 6 -

Exon 7

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Exon 8

Exon 9 – no significant match found. Exon 10 –

Exon 11 –

Exon 12 –

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Exon 13 -

Accession # Q24045 Exon Start Sequence End Sequence 1 UTR 2 1 GATCC 164 AGCAAGAGgtaagaa 3 243 ctttcahATTTT 302 AATATTGgtatgat 4 739 ctttcagTTTCGA 793 GATCTgtaag 5 1156 tthcahTgTAAC 1478 ATGGGCATgtggtaa 6 1635 tacaggagTCATACT 1726 CTACGATgtaagaa 7 1963 tttagTATCCT 2085 ATTTGTgtaagt 8 2155 aatagCAACG 2281 TCTCCAgtaaa 9 No matches found. 10 8732 aaaagCAGCT 8810 ATATACgtgagt 11 8877 gctacagTAAAT 8971 GAAAATGgtaat 12 9049 tttagTACTT 9162 CGACAagtaag 13 10551 acaagGACACG 10690 GAAGTAGgcggt Cds: (1-164;243-302;739-793;1156-1156;1635-1726; 1963-2085;2155-2281; 8732-8810; 8877-8971; 9049-9162; 10551-10690) 4) PlexA This gene encodes a product with semaphorin receptor activity involved in motor axon guidance which is putatively a component of the membrane. According to the NCBI database, it is expressed in the embryo (embryonic central nervous system , myoblast and

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neuron ) and its amino acid sequence contains a proteinase inhibitor, a plexin , a cell surface receptor IPT/TIG , a plexin/semaphorin/integrin and a rho GTPase activation domain. There are 4 recorded alleles : 2 in vitro constructs, 1 classical mutant, and 1 wild-type. Exon 1 UTR Exon 2

Exon 3 and 4

Exon 5

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Exon 6

Exon 7

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Exon 8

Exon 9

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Exon 10 UTR Accession # O96681 Exon Start Sequence End Sequence 1 UTR 2 22168 atgaatATGCTC 23451 GCCTTGTgtctt 3 24470 ttgtagTTGTGA 25715 TTCACGgtaag 4 27589 ttacagTTGTGA 29925 GATCTGGgtatg 5 30009 attagAATGG 30204 CACAAgtaag 6 30560 tttagATATG 30946 TTTGCGgttcg 7 31012 tctagTTTCT 31142 AATTGGgtagg 8 31216 attgcagGCAAA 31361 CTAGGgtaag 9 31830 ttcagCTGCA 31997 TGAATAAgcct 10 UTR Cds: (22168-23451;24470-25715;27589-29925;30009-30204;30560-30946;31012-31142;31142-31361;31830-31997) III. Repeats Chromosome 5 To examine the repetitive elements of the two contigs, I ran RepeatMasker with and without “nolow” command on both fragments to determine the percent of low complexity and simple repeats. I then ran similar RepeatMasker programs on the D. melanogaster sequence extracted from UCSB browser. The percent of simple repeats, complex repeats and total repeats in chromosome 5 of D. virilis closely matched the respective percentage for D. melanogaster (See Table 1). As shown in Table 2, the percentage of complex region, which includes retrotransposable elements, in chromosome 3 was significantly lower (2%) for D. virilis than for D. melanogaster (24.4%). Using the table, the calculated frequency repetitious elements of chromosome 5 is 1 in 6.79 compared to 1 in 6 for D melanogaster. The repitious elements in chromosome 3 occur once for 14 bases compared to once in about 4 bases for D. melanogaster. Table 1: Chromosome 5

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Total

Repeats (Novel Repeats)

Percent Simple Repeats + Low Complexity (bp)

Percent Complex Region (bp)

Percent

D. Virilis 7520 14.73 % 2830 5.54 % 4690 9.19 % D. melanogaster

1183 16.90 % 331 4.73 % 852 12.17 %

Table 2: Chromosome 3 Total

Repeats (Novel Repeats)

Percent Simple Repeats + Low Complexity (bp)

Percent Complex Region (bp)

Percent

D. Virilis 2673 7.02 % 1695 4.46 % 762 2.0 % D. melanogaster Region 1 (1 –25000)

7186 27.46 % 782 2.98 % 6404 24.48 %

D. melanogaster Region 2 (23000 –28000)

6144 20.83 % 1464 5.14 % 4680 15.69 %

I also analyzed the interspecies repeats according to the method suggested by Dr. Buhler. Blast search against the nt database produced repeat matches to a Penelope at ~16 kb for chromosome 5 (refer to data below). I also found repeat matches at ~12 kb and ~ 19kb but the e-values for the blastn search againt nt database was much greater than the 1e-5 significance level. Similar search for chromosome 3 identified bases 49266 – 49368 and 49430 – 49500 as Penelope regions. This region is within 100 bases of area masked by RepeatMasker as evident in the UCSB browser. This suggests that RepeatMasker might have missed this region. The search also produced matches to a D. virilis clone that matches D. virilis antennapedia (e value 9e-07) and Lpg-1, -2, -3 gene. This 26872 – 27087 base region is not within 100 bases of a masked region nor is it near a gene as part of a UTR. This evidence suggests that the region is a potential novel repeat.

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Chromosome 5 16 kb region - Penelope (15825 – 16149)

Chromosome 3 49 kb region – Penelope (49266 – 49368 and 49430 - 49500)

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27 kb – novel repeat (26872 – 27087)

The results of the interspecies repeat finding and RepeatMasker are summarized in the following tables. Chromosome 3 Repeat Type Start End Novel repeat 26872 27087 Penelope 49266 49368 DNAREP1_DM 4019 4072 Penelope 4073 4093 Penelope 9637 10044 Penelope 26313 26704 Chromosome 5 Repeat Type Start End Penelope 15825 16149

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I ran blast on both my contigs against D. melanogaster, D. pseudoobscura, and D. yakuba to identify cross-species repeats. The blast produced the following results. Due to limited time, however, I was unable to analyze each blast result to see if it matches a noncoding feature and if it is part of a syntenic region spanning two or more adjacent genes. Chromosome 5 Blast against D. melanogaster

Blast against D. pseudoobscura

Blast against D. yakuba

Chromosome 3 Blast against D. melanogaster

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Blast against D. pseudoobscura

Blast against D. yakuba

I also ran the blast search against the dmel-intergenic database to find non-coding conserved regions in both my contigs. Both blast results, however, produced medium sized fragments with lower than 90% identity as well as several sequences of less than 100 bases with above 90% (frequently 100%) identity. None of the fragments were long enough to split and find specific identity individually.

Fig 12: Blastn results for cng’s in chromosome 3.

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Fig 13: Blastn results for cng’s in chromosome 5. IV. Clustal W CLUSTAL W (1.82) multiple sequence alignment for ATP syn Beta _ATPBetaD.Virilis_ -------MFALR------------------------------------------AAAKAD 11 [Anopheles]_ -------MARSY------------------------------------------AAKAAA 11 [Mouse]_ -------MLSLVGRVASASASGALRGLSPSAALPQAQLLLRAAPAGVHPARDYAAQASAA 53 [Canisfamiliaris]_ ----VGRVAATSASG-------ALRGLGPSP-LPQVKVLLRASPAALQSARDYATQTSPS 48 [HomoSapien]_ MLGFVGRVAAAPASG-------ALRRLTPSASLPPAQLLLRAAPTAVHPVRDYAAQTSPS 53 : : . _ATPBetaD.Virilis_ KNLMPFLG-QLSVIGAVVDVQFDDNLPPILNALEVDNRSPRLVLEVAQHLGENTVRTIAM 70 [Anopheles]_ KAAAGAQGKVVAVIGAVVDVQFDEQLPPILNALEVQGRSARLVLEVAQHLGENTVRTIAM 71 [Mouse]_ PKAGTATGRIVAVIGAVVDVQFDEGLPPILNALEVQGRDSRLVLEVAQHLGESTVRTIAM 113 [Canisfamiliaris]_ PKAGAATGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAM 108 [HomoSapien]_ PKAGAATGRIVAVIGAVVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAM 113 * ::***********: **********:.*..************.******* _ATPBetaD.Virilis_ DGTEGLVRGQKVLDTGSPIRIPVGAETLGRIMNVIGEPIDERGPIPSAKTSPIHAEAPEF 130 [Anopheles]_ DGTEGLVRGQRVLDTGSPIRIPVGAETLGRIINVIGEPIDERGPIDTNLSAPIHAEAPEF 131 [Mouse]_ DGTEGLVRGQKVLDSGAPIKIPVGPETLGRIMNVIGEPIDERGPIKTKQFAPIHAEAPEF 173 [Canisfamiliaris]_ DGTEGLVRGQKVLDSGAPIKIPVGPETLGRIMNVIGEPIDERGPIKTKQFAAIHAEAPEF 168 [HomoSapien]_ DGTEGLVRGQKVLDSGAPIKIPVGPETLGRIMNVIGEPIDERGPIKTKQFAPIHAEAPEF 173 **********:***:*:**:****.******:************* : :.******** _ATPBetaD.Virilis_ VDMSVEQEILVTGIKVVDLLAPYCKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 190 [Anopheles]_ IEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 191 [Mouse]_ IEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 233 [Canisfamiliaris]_ VEM--------------------------------------------------------- 171 [HomoSapien]_ MEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSVF 233 ::* _ATPBetaD.Virilis_ AGVGERTREGNDLYNEMIESGVISLKDKTSKVALVYGQMNEPPGARARVALTGLTVAEYF 250 [Anopheles]_ AGVGERTREVNDLYNEMIEGGVISLKDKSSKVALVYGQMNEPPGARSRVALTGLTVAEYF 251 [Mouse]_ AGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYF 293 [Canisfamiliaris]_ ------------------------------------------------------------ [HomoSapien]_ AGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYF 293 _ATPBetaD.Virilis_ RDEEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGS 310 [Anopheles]_ RDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGSMQERITTTKKGS 311 [Mouse]_ RDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGS 353 [Canisfamiliaris]_ ------------------------------------------------------------ [HomoSapien]_ RDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKKGS 353 _ATPBetaD.Virilis_ ITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNII 370

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[Anopheles]_ ITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNII 371 [Mouse]_ ITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIV 413 [Canisfamiliaris]_ ------------------------------------------------------------ [HomoSapien]_ ITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIV 413 _ATPBetaD.Virilis_ GQEHYNVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAEV 430 [Anopheles]_ GAEHYNIARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAEV 431 [Mouse]_ GNEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEV 473 [Canisfamiliaris]_ ------------------------------------------------------------ [HomoSapien]_ GSEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEV 473 _ATPBetaD.Virilis_ FTGHAGKLVPLEQTIKGFSQILAGEYDHLPEIAFYMVGPIEEVVEKADRLAKEAA- 485 [Anopheles]_ FTGHAGKLVPLEETIKGFTKILNGELDHLPEVAFYMVGPIEEVVEKAERLAKEAA- 486 [Mouse]_ FTGHMGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHGS 529 [Canisfamiliaris]_ -------------------------------------------------------- [HomoSapien]_ FTGHMGKLVPLKETIKGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHSS 529 The ATPB sequence is highly conserved from Homo sapiens to mouse to D. virilis. Interestingly, the ATP beta protein of the dog is only a small protein, but retains its functionality. V. Synteny Chromosome 5 The synteny is well preserved from D. melanogaster to D.virilis in chromosome 5. Contig XAAA73 from last year identified gene Thd1, Pur-alpha, and first exon of Ephrin in this order, while contig XAAA72 had identified CG1909 and onecut genes. My contig XAAA39A-73 fills the gap between the last year’s contigs and contains the putative gene Ephrin. As represented in the UCSB browser windows, my contig matches the gene order and orientation in D. melanogaster exactly. In both species, the Ephrin, CG1909, and Eph genes are oriented in the forward direction, while the onecut gene is oriented in the reverse direction. The intron and exon lengths, however, vary slightly between the two species. D. virilis Chromosome 5

D. melanogaster

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Specifically, the intron/exon region of the Ephrin gene varies slightly between the two species. As seen in Fig 14, the distance between exon 4 and 5 in D. virilis is significantly greater than in D. melanogaster. This, however, is not surprising since the introns (being the non-coding regions) are more vulnerable to mutations and insertions by transposable elements. What is interesting about the arrangement of the exons is that exon 3 in virilis is shorter compared to exon 3 of melanogaster. A possible explanation for this observation maybe that the virilis protein retains its function despite the loss of some of the coding sequence from D. melanogaster. The gene frequency for D. virilis is calculated to be 1 in about 9000 bases compared to 1 in 12500 bases for D. melanogaster. Thus, D. virilis seems to have a more gene-dense region.

Fig 14: Synteny for Ephrin gene exons.

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Fig 15: This figure from ensemble further verifies the conserved synteny in chromosome 5. The figure also shows the simple repeats and masked regions. Furthermore, the figure confirms that Ephrin gene has four coding exons. Chromosome 3 All annotated genes, except the eIF-5A gene, are syntenic with D. melanogaster. Whereas the CaMKII, ATPB, PlexA, and even the Toy genes are ordered and oriented similar to the D. mekanogaster genes on the fourth chromosome, the fourth chromosome virilis eIF-5A gene has a homolog on the 2R chromosome of D. melanogaster. As mentioned previously, eIF-5A may have arisen on D. virilis fourth chromosome as the result of a duplication of the 2R gene by reverse transcriptase. Since duplicated genes are more free to undergo mutations, it is possible that D. virilis eIF-5A gene on 2R lost its function so that only the fourth chromosome duplication served as the functional gene. D. virilis Browser : Indicates position and orientation of chromosome 3 genes.

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D. melanogaster Browser: Indicates position and orientation of melanogaster genes.

Fig 16: Synteny view for Chromosome 3 genes. Another point to note is that the CaMKII gene in D. melanogaster is much longer than that for virilis. This is probably due to the fact that my contig started in the middle of CaMKII gene and does not include the complete exon 1 sequence. Also to consider is the fact that the distance between CaMKII and ATPB genes is greater in virilis than in melanogaster. Again, this is not surprising since noncoding regions are less likely to remain conserved than coding regions. The gene frequency for D. virilis in 1 gene in about 8250 bases compared to 1 gene in 9250 bases for D. melanogaster. For chromosome 3, as for chromosome 5, D. virilis has a slightly more gene-dense region.

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Fig 17: This figure from ensemble further verifies the conserved synteny in chromosome 3. The figure also shows the simple repeats and masked regions. VI. Appendex Protein Sequence

1) Ephrin 2)

>virt|VIRT14480|VIRT_14480 Translation of nucleotide sequence generated on ExPASy on 01-May-2005 by bio4342pb06.wulan.wustl.edu FRIDNTDHIIDVNKGNLAFEFDQVHIICPVYEPGAFENETEKYIIYNVSKVEYETCRITN ADPRVIAICDKPQKLMFFTITFRPFTPQPGGLEFLPGNDYYFISTSSKDDLYRRIGGRCS TNNMKVVFKVCCAAEDKNKTTETTLLGSVPAESGNGVDNAGLNVDQNLNANANHGHGHNG VNTISTNTGFIPGGSAVGSGSGGSGGGVQLKPINGMMGTSINTNIDQFNRIPIQPNVMGN NIGAAGGGASGSSGTGGIMLSPGHGSINMLPPGRGGVHMTYPGHHHIQTGIRINNVPTQP NNQHPHHKGNMNVNSNDDHHNYDKHPNEVVKNEELTYNSGSGQATRSHIWIWTWLAGGAA TQGLTSMHAYGINLTLLLAIIVITFQYLFWAPAAYTMRRRPEPLGINYR 2) ATPB >virt|VIRT17024|VIRT_17024 Translation of nucleotide sequence generated on ExPASy on 25-Apr-2005 by bio4342pb06.wustl.edu MFALRAAAKADKNLMPFLGQLSVIGAVVDVQFDDNLPPILNALEVDNRSPRLVLEVAQHL GENTVRTIAMDGTEGLVRGQKVLDTGSPIRIPVGAETLGRIMNVIGEPIDERGPIPSAKT SPIHAEAPEFVDMSVEQEILVTGIKVVDLLAPYCKGGKIGLFGGAGVGKTVLIMELINNV AKAHGGYSVFAGVGERTREGNDLYNEMIESGVISLKDKTSKVALVYGQMNEPPGARARVA LTGLTVAEYFRDEEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQ ERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDS TSRIMDPNIIGQEHYNVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRF LSQPFQVAEVFTGHAGKLVPLEQTIKGFSQILAGEYDHLPEIAFYMVGPIEEVVEKADRL AKEAA 3) EIF-5A

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>virt|VIRT15262|VIRT_15262 Translation of nucleotide sequence generated on ExPASy on 01-May-2005 by bio4342pb06.wulan.wustl.edu MQCSALRKNGYVMLKGRPCKIVDMSTSKTGKHGHAKVHLVGIDIFTQKKYEDICPSTHNM DVPHVKREDFQLTDISDDGYLCLMNDNGDLREDLKIPDSALGTSLRADHVAGKELLCTVM KACGEECVIAVKNNTALDK 4) CaMKII >virt|VIRT12082|VIRT_12082 Translation of nucleotide sequence generated on ExPASy on 27-Apr-2005 by bio4342pb06.wulan.wustl.edu ILLLLFLPLGKTSLFTIIYVFYRGAFSIVKRCVQKSTGFEFAAKIINTKKLTARDFQKLE REARICRKLHHPNIVRLHDSIQEENYHYLVFDLVTGGELFEDIVAREFYSEADASHCIQQ ILESVNHCHQNGVVHRDLKPENLLLASKAKGAAVKLADFGLAIEVQGDHQAWFGFAGTPG YLSPEVLKKEPYGKSVDIWAFILYILLVGYPPFWDEDQHRLYSQIKAGAYDYPSPEWDTV TPEAKNLINQMLTVNPNKRITAAEALKHPWICQRERVASVVHRQETVDCLKKFNARRKLK GAILTTMLATRNFSTARRQEIIKITEQLIEAINSGDFDGYTKICDPHLTAFEPEALGNLV EGIDFHKFYFENVLGKNCKAINTTILNPHVHLLGEEAACIAYVRLTQYIDRHAHTHQSEE TRVWHRRDNKWQNVHFHRSASGKISGATTFDFMPQK 5) PlexA >virt|VIRT23574|VIRT_23574 Translation of nucleotide sequence generated on ExPASy on 03-May-2005 by bio4342pb06.wulan.wustl.edu MLCILCLLSITILGNLPSRSAHGQILHLYKKSNEQLNSGFTYAQPSVLDVRADRIGRSAE ALRVNITETDPNVLTRNAGNFSTNIITNVAKFDTRLNHLLVDTVTGRVFVGGVNRLYQLS PDLELHETVKTGPQNDSVECTILDCPLNAVRKPTDNYNKVLLIDRATSRLIACGSLFQGT CTVRNLQNVSIVEHEVPDAVVANDANSSTVAFIAPGPPQHPVTNVMYVGVTYTNNSPYRS EIPAVASRSLEKTKMFQIASSAVTTGTRTFINSYARETYLVNYVYGFSSERFSYFLTTQL KHSHHSSPKEYITKLVRICQEDSNYYSYTEIPVECISEAQGGTKFNLVQAGFLGKPSSDL AQSLGISIQDDVLFAVFSKGESNTPTNNSALCIYSLKSIRRKFMQNIKFCFNGNGMRGLD FISPSMPCKLQTIGEDFCGLDVNSPLGGEQPITAVPVAMFNTRVTSVAATSTSGYTVVFI GTVDGYIKKVVVESATVANEYASLAVDLGSAINQDMQFDNQNLYVYAMSERKVSKVKVYD CADFRTCGECLGAKDPYCGWCSLENKCSPRSNCQDDANDPLYWVSYKTGKCTTITSVVPH QLQRTTARTLELIIDHLPQLKENLICAFTTEDKALFTNATKKRNGVNCTTPRTDMLPQIE QGKHHFTAKLSVRTRNGPDLVSTDFTFFDCSTHSSCTRCVSSEFPCDWCVEAHRCTHDTA ENCRNDILVTGVSRIGPSYRSGPGFCPTINATGDGSEVLVAAGTSKSIKVKVHIIGQFIV QTRFVCQFNIEGRVTSLNAQLLGDTIYCDSMEFQYTSRSPNLTATFAVIWGGSKPLDNPH NIHVVIYRCRVMADSCGICLALAEKYNCGWCSSTNTCEVVEQCNKNNEGKTDWLNRSEIC PNPEIHSFGPKTGPWEGGTNITIKGINLGKNYNDIYSGVRIAGINCMPFQQFYIDTKQIV CTVDSPGEQMYRNGRIVVQIGDYRGESKEDYEFVDPKISNFYPRFGPSSGGTQIRIIGKH LNAGSRIQAFINDHLPCKIISTDSSQAICQTSPSPGIIEGRLKMSFDNGPREFNDYNFKY VLDPTVEQVSSGPSGQIKVPKGIPAGGIRIIVTGTQFTSIQAPSIYVFYKGQMYASQCRV QSDNEMECPSPTIEADSQILDPENPTLLEYGFLMDNVLKVQNLSKKHNNHFELYPNPEYF TFEERVKYFKSEYLTINGRNLDRACKETDVEVKIGNGYCNITSLSRQQLTCRPPTEAVAA SNSPNGPEVIVRIGSSLEYRIGILSYESSNLIMDWGDNVVFVVIAGCVIFFLIFCALLVA YRKKTAESHRELRNMQEQMDILELRVAAECKEAFAELQTEMTDLTGDLTSGGIPFLDYRS YAMKILFPNHEDHVVLQWERPELLRKEKGLRLFAQLIMNKTFLLLFIRTLESNRYFSMRE RVNVASLIMVTLQSKLEYCTDILKTLLGDLIEKCIEGKSHPKLLLRRTESVAEKMLSAWF TFLLYKFLKECAGEPLYMLFRAVKGQVDKGPVDACTHEARYSLSEEKLIRQSIDFRPMTV NASIIQQPIFCNNLDMLPSHTENVSVKVLDCDTIGQVKEKCLETIYRNIPSSQRPRKDDL DLEWRTGATGRVILYDEDATSKTENDWKKLNTLQHYNVPDGAGLSLVPKQSSIYNFSILS DKNEKSHKYETLNISKYTSSSPTFSRAGSPLNNDMHENGMKYWHLVKHHDSDIQKEGERV NKLVSEIYLTRLLATKGTLQKFVDDLFETIFSTAHRGSALPLAIKYMFDFLDDQALLHGI TDPEVVHTWKSNSLPLRFWVNLIKNPNFVFDIHKSNIVDSCLSVVAQTFMDSCSTSDHRL GKDSPSSKLLYAKDIPEYRKWVDRYYRDIRDMSSISDQDMNAMLAEESRLHTTEFNTNCA LHELYTYAVKYNEQLTVTLEEDEFSQKQRLAFKLEQVHNIMSAE

32

Nucleotide Sequence

1) Ephrin >/usr/tmp/aaaa14612 [Unknown form], 1231 bases, FCD checksum. ATTTCGGATTGATAACACCGATCATATTATTGACGTGAATAAGGGCAATC TGGCATTCGAATTCGACCAGGTGCACATTATATGTCCAGTTTATGAGCCC GGCGCATTCGAGAACGAAACGGAGAAGTACATAATATACAACGTGTCTAA AGTGGAGTACGAAACATGTCGCATAACGAACGCAGATCCGCGAGTAATAG CTATATGTGATAAGCCTCAGAAATTAATGTTTTTTACGATAACTTTCCGG CCATTTACACCGCAGCCAGGTGGTTTAGAGTTCCTACCTGGAAATGACTA CTATTTCATTTCGACGTCATCGAAGGACGATTTGTACCGTCGCATTGGCG GTCGTTGTTCCACAAATAATATGAAAGTTGTGTTTAAAGTGTGCTGTGCA GCCGAAGATAAGAACAAGACAACGGAAACAACGCTTCTGGGCAGTGTCCC AGCCGAAAGTGGCAATGGCGTCGACAATGCGGGGCTTAATGTAGATCAAA ATCTAAATGCGAATGCTAACCATGGACATGGTCATAATGGTGTCAATACC ATTAGCACTAATACTGGATTCATACCGGGTGGATCAGCAGTTGGCAGCGG AAGCGGCGGCAGCGGAGGCGGTGTTCAACTAAAGCCCATAAACGGAATGA TGGGCACGTCGATCAACACGAACATTGATCAATTCAATCGCATACCCATT CAACCAAACGTAATGGGCAACAATATTGGAGCAGCTGGAGGTGGTGCTAG CGGTAGCTCTGGTACTGGCGGCATAATGCTGTCACCTGGCCATGGGAGCA TAAATATGCTGCCACCGGGTCGGGGCGGCGTTCATATGACCTATCCCGGC CATCATCACATACAGACTGGCATTCGAATTAATAATGTGCCAACGCAACC AAATAATCAGCATCCGCACCACAAGGGCAATATGAATGTGAATAGCAATG ATGATCACCACAATTATGACAAGCATCCCAATGAGGTAGTCAAAAACGAA GAGCTCACCTACAACAGTGGATCAGGGCAAGCAACTCGCAGCCATATCTG GATTTGGACCTGGCTGGCAGGCGGAGCAGCCACCCAGGGTCTAACTTCTA TGCATGCCTATGGTATTAATTTAACACTCTTGCTGGCCATCATAGTAATC ACATTTCAATACCTGTTTTGGGCACCTGCCGCATATACGATGCGTCGCCG CCCCGAACCTCTTGGCATTAATTACCGGTGA 2) ATPB TTAGGCTGCTTCCTTGGCTAGACGGTCGGCCTTCTCAACAACTTCTTCGA TTGGGCCAACCATGTAGAACGCAATCTCTGGCAGATGATCGTATTCACCA GCCAAAATCTGTGAGAAGCCCTTAATTGTTTGCTCCAATGGGACTAGTTT ACCGGCATGTCCAGTGAAGACCTCAGCGACTTGGAATGGCTGTGACAAGA AACGCTGGATCTTACGTGCGCGTGCGACAGTCAGTTTGTCCTCCTCGGAC AACTCATCCATACCCAAAATGGCAATGATATCTTGGAGAGATTTGTAATC TTGCAAGATTTTTTGCACACCGCGAGCGACATTGTAGTGTTCCTGGCCAA TGATGTTGGGATCCATGATACGTGAAGTGGAATCCAAAGGATCGACAGCC GGGTAGATACCCAATTCGGCAATGGCACGCGACAAGACAGTGGTGGCGTC CAAATGGGCGAAAGTTGTGGCTGGAGCAGGATCGGTCAAATCGTCAGCTG GCACATAAATAGCCTGGACCGAAGTGATGGAGCCCTTCTTGGTTGTGGTA ATACGCTCTTGCATAGTACCCATGTCAGTTGCCAAAGTCGGCTGGTAACC GACAGCCGATGGAATACGACCCAAAAGAGCGGACACTTCGGAACCGGCCT GAGTAAAACGGAATATGTTGTCAATGAAAAGCAGCACATCCTGTCCCTCC TCGTCACGGAAATATTCGGCAACGGTGAGACCAGTCAAGGCTACACGAGC ACGTGCGCCTGGAGGTTCATTCATTTGACCGTAGACGAGAGCCACCTTCG AGGTCTTATCCTTCAGCGAAATAACACCAGATTCAATCATCTCGTTGTAC AGATCATTGCCCTCACGAGTACGTTCGCCAACGCCGGCGAACACAGAGTA ACCACCATGTGCCTTGGCCACATTGTTAATTAGCTCCATAATTAGCACAG TTTTGCCGACACCGGCACCGCCAAACAGACCGATTTTACCACCCTTACAA TAGGGTGCCAGAAGATCGACGACTTTAATTCCGGTAACCAGAATTTCCTG TTCGACGGACATGTCCACGAATTCGGGAGCTTCAGCATGAATAGGCGAGG TCTTCGCAGACGGAATGGGACCACGCTCATCAATTGGTTCGC 3) EIF-5A

33

>droVir2_dna range=chr3:19614-20093 5'pad=0 3'pad=0 revComp=TRUE strand=? repeatMasking=none ATGTCGGATTCTGAACAGCATGAATTCGGCGGCGACTCGGGTGCATCTGC AACTTACCCGATGCAATGTTCAGCGCTGCGCAAAAATGGCTATGTGATGC TTAAGGGACGCCCTTGCAAGATAGTGGATATGTCTACCTCCAAGACAGGC AAGCATGGCCACGCCAAAGTCCATCTTGTTGGCATCGACATATTTACACA GAAAAAGTACGAGGATATCTGTCCCTCCACCCACAATATGGATGTGCCGC ATGTGAAACGAGAGGACTTCCAGCTCACCGATATTAGTGATGATGGCTAC CTATGTCTGATGAACGACAACGGCGACTTACGCGAAGATCTCAAGATTCC CGACAGTGCATTGGGTACATCTTTGCGCGCCGATCACGTTGCCGGAAAGG AGCTTTTGTGCACCGTGATGAAAGCCTGTGGAGAGGAGTGCGTTATTGCC GTCAAAAACAATACTGCTTTGGATAAATAA

3) CaMKII 4)

>/usr/tmp/aaaa14586 [Unknown form], 1372 bases, BAD checksum. GATCCTTCTTCTACTATTCTTGCCCTTAGGAAAAACCAGTTTATTTACAA TAATTTATGTTTTTTACAGGGGTGCCTTTTCAATAGTAAAAAGATGTGTC CAAAAATCAACTGGATTTGAGTTTGCGGCTAAAATTATAAACACCAAGAA ACTAACAGCAAGAGATTTTCAAAAGCTAGAACGAGAAGCTAGGATTTGTA GGAAATTGCACCACCCTAATATTGTTCGATTGCATGACAGCATACAGGAG GAAAACTATCACTATCTTGTTTTTGATCTTGTAACTGGTGGTGAACTTTT CGAAGATATTGTTGCACGTGAATTTTATTCAGAGGCTGATGCATCACATT GTATTCAGCAAATATTGGAATCTGTCAATCACTGCCACCAGAACGGTGTG GTGCATCGAGATCTCAAGCCAGAGAATTTACTATTAGCAAGTAAGGCAAA GGGTGCAGCTGTGAAACTCGCGGACTTTGGTCTAGCCATTGAAGTACAAG GTGATCACCAGGCCTGGTTCGGATTTGCCGGTACCCCTGGGTATCTATCG CCCGAAGTATTGAAAAAGGAACCATATGGCAAATCGGTAGATATATGGGC ATTCATACTCTACATACTGCTGGTCGGATATCCACCGTTCTGGGACGAGG ATCAACACCGCTTGTATTCACAAATCAAGGCCGGGGCCTACGATTATCCT TCGCCAGAATGGGACACGGTTACGCCAGAGGCAAAAAATCTGATCAATCA AATGCTCACTGTAAACCCAAATAAGCGAATAACTGCAGCTGAAGCCCTTA AGCATCCATGGATTTGTCAACGAGAGCGAGTGGCTTCTGTAGTACATCGC CAGGAAACCGTGGACTGTCTCAAGAAATTCAATGCTCGACGCAAGCTTAA GGGAGCTATACTCACCACAATGCTGGCAACTAGGAATTTCTCCACAGCTA GACGACAGGAAATAATCAAGATCACAGAGCAGTTGATTGAAGCCATCAAC AGTGGCGACTTCGACGGATATACTAAAATATGTGATCCACATCTAACTGC TTTTGAGCCGGAGGCATTGGGAAACTTGGTCGAAGGAATTGATTTTCACA AATTTTATTTCGAAAATGTACTTGGCAAAAATTGTAAAGCCATTAACACA ACAATATTGAATCCCCACGTGCACTTACTGGGAGAAGAAGCCGCTTGTAT CGCCTATGTAAGACTTACACAGTACATCGACAGACACGCACATACTCATC AATCGGAGGAGACTCGCGTTTGGCACAGACGCGACAACAAATGGCAAAAC GTTCACTTCCATCGAAGTGCATCTGGCAAGATCAGCGGGGCAACGACTTT CGATTTTATGCCACAGAAGTAG

5) PlexA 6)

>/usr/tmp/aaaa14534 [Unknown form], 5915 bases, BF5 checksum. ATGCTCTGTATACTCTGTTTACTATCAATCACAATTTTGGGAAATCTACC ATCACGTTCAGCCCACGGACAAATATTGCACCTATATAAGAAAAGTAATG AGCAGCTAAATTCTGGATTTACGTACGCGCAGCCGTCTGTATTGGATGTT CGAGCTGATAGGATTGGACGAAGTGCTGAAGCCCTTAGGGTTAATATAAC GGAAACGGACCCAAATGTGCTGACCCGTAATGCTGGGAACTTCAGCACGA ATATAATTACAAATGTAGCCAAATTTGACACAAGACTCAACCATCTGTTG

34

GTGGACACAGTTACGGGCAGAGTGTTTGTTGGCGGTGTGAATCGGTTGTA TCAGCTATCGCCGGACCTGGAGCTGCACGAAACCGTGAAGACAGGACCAC AAAATGATTCAGTCGAGTGCACCATACTAGACTGCCCGCTTAATGCCGTG CGCAAGCCAACAGATAACTATAATAAGGTGCTTCTTATAGATCGCGCCAC CTCGCGTCTTATCGCATGTGGATCCTTGTTCCAGGGCACCTGTACGGTCC GTAATCTGCAAAATGTTAGCATAGTTGAGCACGAGGTGCCGGACGCCGTT GTTGCGAATGATGCCAACTCCTCAACGGTTGCTTTTATTGCGCCTGGACC CCCCCAGCATCCGGTGACGAATGTTATGTACGTGGGCGTTACCTATACCA ACAACTCGCCGTACCGTAGCGAGATCCCGGCCGTAGCGTCCCGATCTTTG GAAAAAACCAAAATGTTTCAGATAGCATCATCGGCTGTTACGACTGGCAC GCGAACCTTTATAAATTCGTATGCCCGCGAAACATATCTGGTGAACTATG TGTACGGGTTCAGCTCAGAACGGTTTTCATATTTCCTAACCACTCAGTTG AAGCATAGTCATCACTCGTCGCCCAAAGAGTATATAACTAAACTGGTCCG AATATGCCAAGAGGACTCCAACTATTACTCGTACACTGAAATTCCGGTGG AGTGCATTAGTGAGGCTCAGGGCGGAACTAAATTCAATTTGGTCCAGGCC GGCTTTTTGGGCAAACCTAGCTCGGATTTGGCGCAAAGCTTGGGAATCTC GATACAGGATGACGTTCTCTTTGCGGTCTTTTCGAAGGGTGAAAGCAACA CTCCAACCAACAACTCGGCCCTTTGCATCTACTCATTGAAATCAATTCGT CGCAAATTTATGCAGAACATCAAATTCTGCTTCAATGGAAATGGAATGCG TGGACTCGACTTTATATCACCCAGCATGCCTTGTGTCTTAACGGTATAAA CTGCAAACCATTGGGGAAGACTTTTGCGGACTGGATGTTAATTCACCTCT CGGCGGAGAGCAGCCAATCACAGCTGTCCCAGTGGCAATGTTTAACACGA GGGTCACATCTGTGGCTGCGACCAGCACCAGCGGTTATACGGTCGTATTC ATTGGAACCGTTGACGGATATATTAAGAAAGTAGTCGTTGAATCGGCGAC CGTTGCAAATGAATATGCAAGCTTGGCCGTTGATTTGGGATCTGCCATTA ATCAGGACATGCAGTTTGATAATCAGAACCTTTATGTTTACGCTATGTCC GAGCGCAAAGTATCCAAAGTTAAGGTTTATGATTGTGCTGATTTTAGGAC TTGTGGCGAATGTCTGGGTGCAAAAGATCCATACTGTGGTTGGTGCTCGC TGGAAAATAAGTGCAGCCCACGCTCAAATTGTCAGGATGACGCCAATGAT CCACTTTACTGGGTTAGCTACAAGACGGGCAAATGTACGACAATTACGAG CGTGGTGCCACATCAATTACAGCGTACGACCGCTCGCACCTTGGAGCTGA TCATTGATCATTTGCCGCAGCTAAAAGAGAATCTGATTTGCGCTTTCACA ACCGAGGACAAAGCCCTATTTACAAATGCCACAAAGAAGCGAAACGGCGT CAACTGTACCACGCCCCGCACGGACATGTTGCCGCAAATTGAACAGGGCA AACATCATTTCACAGCGAAGTTATCGGTGCGCACGCGGAACGGTCCTGAT CTTGTCTCAACCGACTTCACGTTCTTCGACTGCAGCACGCACTCATCGTG TACGCGCTGTGTATCATCTGAGTTTCCGTGCGACTGGTGTGTGGAGGCGC ATCGCTGCACCCATGATACGGCCGAGAATTGCCGCAACGATATCCTGGTG ACCGGCGTCAGCCGAATTGGTCCGAGCTATCGGTCCGGCCCTGGTTTCTG CCCGACCATTAACGCCACCGGCGATGGCAGTGAGGTTCTTGTTGCTGCTG GCACCAGCAAATCCATCAAGGTTAAGGTTCACATCATTGGCCAGTTTATT GTGCAGACACGTTTCGTTTGCCAGTTCAATATTGAAGGTCGCGTGACCAG CCTAAACGCCCAATTGCTTGGCGATACAATCTACTGCGACAGCATGGAAT TTCAGTACACATCACGATCACCGAACCTAACCGCAACTTTTGCAGTTATA TGGGGCGGATCGAAGCCTCTCGACAATCCTCATAATATTCACGTTGTGAT TTATCGTTGTCGCGTGATGGCAGATAGTTGTGGGATATGTCTTGCGCTAG CCGAGAAGTACAATTGCGGATGGTGTTCGTCGACGAACACATGCGAGGTG GTTGAACAATGTAACAAAAATAATGAAGGCAAAACGGATTGGCTGAATCG GAGCGAGATTTGTCCAAATCCAGAGATTCATTCCTTTGGTCCCAAAACTG GACCATGGGAGGGCGGCACCAATATAACTATAAAGGGCATAAATCTAGGA AAAAATTATAATGACATATATTCCGGCGTTCGAATTGCTGGAATTAATTG CATGCCATTTCAACAGTTTTACATTGACACAAAACAAATTGTTTGTACTG TGGATAGTCCCGGCGAGCAGATGTATCGAAATGGGCGAATCGTGGTTCAA ATCGGGGACTATCGTGGCGAATCAAAGGAAGATTATGAGTTTGTCGATCC GAAAATATCGAATTTTTATCCGCGGTTCGGCCCGTCATCAGGAGGTACCC AAATACGGATAATTGGCAAACATTTGAATGCTGGATCACGAATACAGGCC

35

TTTATAAATGATCATCTACCTTGTAAAATCATTAGTACGGACTCCTCGCA AGCGATATGTCAGACATCGCCGTCTCCGGGTATTATTGAAGGACGTCTAA AAATGTCTTTCGACAATGGGCCGCGTGAATTTAATGACTATAATTTTAAA TATGTACTCGACCCAACTGTTGAGCAAGTTAGCTCCGGACCCAGTGGCCA AATTAAAGTACCAAAGGGTATTCCTGCTGGCGGTATTCGGATTATAGTTA CGGGAACACAATTTACCAGCATACAAGCACCGAGCATCTATGTCTTTTAC AAGGGTCAAATGTACGCGAGCCAGTGCCGGGTTCAATCCGATAATGAAAT GGAATGCCCGTCGCCGACTATTGAGGCAGATAGCCAAATTTTGGATCCGG AGAATCCCACGTTGCTCGAATACGGATTTCTCATGGACAATGTGCTCAAG GTGCAGAACTTGTCGAAAAAGCACAACAATCATTTTGAGCTTTACCCCAA TCCGGAATACTTTACGTTCGAGGAACGTGTCAAATACTTCAAAAGCGAGT ACCTCACCATAAATGGTCGAAATCTCGATCGCGCGTGCAAGGAAACGGAT GTCGAAGTGAAAATTGGCAACGGCTACTGCAATATAACGTCTCTGTCGCG TCAGCAGCTGACTTGCCGGCCGCCCACGGAAGCAGTCGCTGCCAGTAACA GTCCGAATGGTCCGGAGGTGATTGTACGTATTGGATCATCATTGGAGTAT CGCATTGGCATACTCAGTTACGAGTCATCGAACCTGATTATGGATTGGGG GGATAACGTCGTCTTTGTTGTAATTGCCGGCTGCGTTATATTCTTTCTTA TCTTTTGTGCCCTGCTTGTGGCGTATAGAAAAAAGACCGCCGAATCTCAC CGTGAGCTCCGAAACATGCAGGAGCAAATGGATATTTTGGAATTGCGTGT GGCTGCCGAGTGTAAGGAAGCATTCGCCGAACTTCAAACGGAAATGACGG ACTTGACGGGCGATCTAACGTCGGGTGGCATACCATTTTTGGATTATCGC TCGTATGCTATGAAAATCTTATTTCCCAATCATGAAGATCACGTCGTCTT GCAATGGGAGCGACCGGAATTGTTGCGCAAAGAAAAGGGATTGCGGCTAT TTGCCCAGCTCATTATGAACAAAACATTCCTGCTGCTTTTCATAAGAACT TTAGAGTCGAATCGTTATTTCTCGATGCGAGAACGTGTTAATGTCGCCTC ATTAATAATGGTCACGCTGCAGTCAAAACTGGAATATTGTACGGACATAT TGAAAACATTATTAGGCGATCTCATTGAAAAATGCATTGAGGGCAAGAGT CATCCAAAATTATTGCTTCGACGTACCGAGAGTGTGGCCGAGAAAATGTT GAGTGCTTGGTTTACGTTTCTTCTCTATAAATTCCTAAAGGAGTGTGCCG GAGAGCCTCTATACATGCTGTTTCGTGCGGTTAAGGGTCAAGTAGACAAG GGTCCGGTTGATGCGTGCACCCACGAGGCTCGCTACTCTTTGAGCGAGGA GAAGCTTATCCGGCAGTCTATTGATTTTCGACCCATGACCGTGAATGCCA GCATTATACAACAGCCAATTTTTTGCAACAATTTGGACATGTTGCCGTCA CACACCGAGAACGTATCCGTTAAGGTGCTCGACTGCGATACGATTGGTCA GGTGAAGGAGAAATGTTTGGAAACGATTTATAGAAATATACCATCCAGCC AAAGACCTCGCAAAGATGATTTGGATCTGGAATGGCGAACTGGAGCAACG GGTCGTGTGATCCTATATGATGAGGATGCTACATCGAAAACGGAGAACGA TTGGAAAAAGCTAAACACATTGCAGCATTACAATGTGCCAGATGGAGCCG GTCTAAGCCTTGTACCAAAGCAAAGTTCCATCTATAACTTTAGTATATTA TCTGATAAAAACGAGAAATCTCACAAATATGAAACACTGAATATATCGAA GTACACCTCCTCCTCACCGACATTCAGCCGCGCCGGAAGCCCCTTGAACA ATGATATGCACGAGAATGGAATGAAATATTGGCATTTGGTCAAACATCAT GACAGCGATATTCAAAAGGAAGGCGAACGTGTCAATAAATTGGTCTCTGA AATATACCTAACAAGACTGCTGGCGACTAAGGGTACTTTGCAGAAGTTCG TAGATGACCTCTTTGAGACAATATTCAGCACCGCTCATCGTGGGTCCGCC TTGCCTTTGGCAATTAAATACATGTTTGACTTTTTGGATGATCAAGCCCT TTTGCACGGAATAACAGATCCCGAAGTCGTGCACACTTGGAAAAGCAACA GTTTACCTTTGCGTTTCTGGGTGAATTTAATAAAGAACCCAAATTTTGTA TTTGATATACATAAATCGAATATTGTGGACTCCTGTCTGTCAGTTGTAGC TCAAACATTTATGGATTCCTGCTCAACGTCAGATCATCGATTGGGCAAAG ATTCGCCAAGCTCAAAACTATTATACGCCAAGGATATACCCGAGTATCGC AAGTGGGTTGACCGGTATTACAGGGATATTCGGGATATGTCATCCATTTC TGATCAGGACATGAATGCAATGCTCGCTGAAGAATCTAGGCTGCATACAA CTGAGTTTAATACGAATTGTGCTCTACATGAGCTCTACACTTACGCTGTT AAATATAATGAGCAGTTGACGGTTACACTGGAGGAGGACGAATTTTCACA AAAACAACGACTTGCATTTAAATTGGAGCAGGTTCACAATATCATGTCAG

36

CTGAATAAGCCTCGC Genomic Sequence 1) Ephrin >/usr/tmp/aaaa14839 [Unknown form], 4501 bases, 1144 checksum. TGACAAACCAAGATTGTTCGGCTTGAATATACCCTGCACTGTTGTGCGTT CCTTTACAATAGTTTTGGGTTATGCATTTAAAGTAATATACCCCATTAAA TGAAACATTTTGTGAGTCTTTTATATACATATTTACCGCAAGCAACTCAA ACATAAAAGATAAGAAGATGAAATACCCTAGATAACCGAAATATTAAGAT CTGCCATAATGTATTTTACATGTGTAAAAAAAGTCATCTTTGATCTTAAA TCATAACCAGGTGGATCTCAGAGAGTAATAGGGGCTGGAGAATTTGAAAT TGTTACAACCTTTAGATTTCTGAAGACAACCCTTTCTGCTTGGCTTAAGT AATACCGTTAATATTCTATTAACAGTTAATTCAAAAAGGCCCTTTGAGGA ATTTAGATTTGTTTGATACTCAAACTAATTTTCCAAGATTTTCGAGAAAA TATCCATTTTGATGGCTTTCACCCTTTTCACAAAGCGAGTCCTCTTGTGG GGAAAAGGGCCGGAATATTATTATTTTATTATCCCCATTGTTATTGAAAA GAATGATTTATTGGTAATTTACAAGTGCCCTAATAAATTAAAATTATCTG AAAACTTGGGCCCTTTTCTTCGAAGGTAAATAAATAATAATGTCTATTCA AATTTTGATTTGTAGATTTCGGATTGATAACACCGATCATATTATTGACG TGAATAAGGGCAATCTGGCATTCGAATTCGACCAGGTGCACATTATATGT CCAGTTTATGAGCCCGGCGCATTCGAGAACGAAACGGAGAAGTACATAAT ATACAACGTGTCTAAAGTGGAGTACGAAACATGTCGCATAACGAACGCAG ATCCGCGAGTAATAGCTATATGTGATAAGCCTCAGAAATTAATGTTTTTT ACGATAACTTTCCGGCCATTTACACCGCAGCCAGGTGGTTTAGAGTTCCT ACCTGGAAATGACTACTATTTCATTTGTGAGTACTGCGATTATATTATTG TAAATATATATTGTATGCTTTCTTTTTTTCTACAATTAGCGACGTCATCG AAGGACGATTTGTACCGTCGCATTGGCGGTCGTTGTTCCACAAATAATAT GAAAGTTGTGTTTAAAGTGTGCTGTGCAGCCGAAGATAAGAACAAGACAA CGGAAACAACGCTTCTGGGCAGTGTCCCAGCCGAAAGTGGCAATGGCGTC GACAATGCGGGGCTTAATGTAGATCAAAATCTAAATGCGAATGCTAACCA TGGACATGGTCATAATGGTGTCAATACCATTAGCACTAATACTGGATTCA TACCGGGTGGATCAGCAGTTGGCAGCGGAAGCGGCGGCAGCGGAGGCGGT GTTCAACTAAAGCCCATAAACGGAATGATGGGCACGTCGATCAACACGAA CATTGATCAATTCAATCGCATACCCATTCAACCAAACGTAATGGGCAACA ATATTGGAGCAGCTGGAGGTGGTGCTAGCGGTAGCTCTGGTACTGGCGGC ATAATGCTGTCACCTGGCCATGGGAGCATAAATATGCTGCCACCGGGTCG GGGCGGCGTTCATATGACCTATCCCGGCCATCATCACATACAGACTGGCA TTCGAATTAATAATGTGCCAACGCAACCAAATAATCAGCATCCGCACCAC AAGGGCAATATGAATGTGAATAGCAATGGTAAGGACACATTAAAAAAACA GATTGCAGATGCAGATCAGTACGATAAACAAAAAGTTGACAGCCGTTTGA TGGCGGGCAGCGGCATTGGCACTGCTATTCCCGTCAATATTGGCAGAGAT ATTCACTATTTGCCGCCAGTTCTGGTTGACACAAACCACAGTAACATTGT ACAGAGCACCATTAATTGGCCATTAAATACTTGGGGCATGGACACAAATA ACACATCATCCAGCAGATTCTTAATAACTACATCCACCATAAATACTACT ACTAACAATAGCAAGCAATTGTTCCATCCGAAACACATCAATGTCAAAAT TAACACCAACTCAGACAGTCATAACAATACAAGTATTAGCAATTACACAC AATCTTTCCACAGTCCGCCAGACCTCGGTACTAACAATAATAACAGAAAA AGTAAGTAGAACTTATAGAAATGCATTTGCCATTACCTAAAACTGTGCCT GCGTCCATGATACCCATACCATAATTCCGTTCCATACCCACCTTAATAAT AATTTCTAAGATGAAGTTTAGTTCGGCATGCTAATTTTCAATTTTCACAA TAGTGCGTGGTTACAGCAAAGCTTGAAAAGGTCGTCTTGATTATTGATTG ACTTCACAATTTTAGGGCGCAGATAAAATATCTTTGTGAAATTATGCTTT TTGTTTGAGAAATTCGAGGAATTTTTGGGTAGCTTGTAATTGCTGAGTTT GGTGTAATTCTTTCTGCAAATCTTATGGTATAGTTGACTGATGTTGATAC

37

GTTTGTAGGCTTTGGTTAAGATATTTTAAAAAACCAAATCTTTTATATAA GAACATGATTTTCCACCGACCATTCCTATGACAGCTATATATACTGTCTG CAATAGAAGGACGGACCTAGGCAATGTTTTATGACAGAACCTTCAGACTG AGAGACCAGTTTCCGCAGAAACACACAGACGATAGTGCCTATCGGTAAAG TTTTTGATAATAATCAGAAGTATATCTACTTTATAAGGTCGGAAATTTAT CCTTCTATGTGTTACGCATTTCATGACAATGGTATAAGAATGTAGGATAC GTGTCTTATTAATGTGTACAGGAGTATCTAATATTTTCGTTTGCTTTGAA GGCACTAATGATAATTATATACGCTTTTCAAAAAGGTAATGATAATGAAA ATCGCATTTCATCACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCC AAAAACCATTATTAGTGAAAAGATATGATAATGGAAATCACATTTCATTA TAAATAAAAAATGATAGCAAATAATTTTACGAATATATTTCCGAAATTGA AAGTAATGAACAAATATTTTTAGCATTAGCATTTTCAATGAAAACTTTAT TAATTGATTTTAATCATTTAAATATGCTTCATTTAACTTGNNNNNNNNNN NNNNNNNNNNNNNNNNNNNGTAAGTAACTATTTATAAATCAATTATCAGA GTTAATGAAATTAAGTTTTCATTACTTACTATTCATTATCACTATTCATT CAATTCATTTTCATTAGCATTACCTTTTTTTAGTGGTCATGNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNGAACAGANNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCTA GTCGGGAGCTCACGACTAGAACATCTTACTTGTTTACTTTGTAAACAGAG TATGAAAGTGCAAATATTTTCAGCGAAACTCAAAAATTTACAGCTTTATT ATTTTGCCAACCTACCACCACATTATACTATGTAAACGACCAATTACATT AAATGTTGATCATGATAAAGGTGATAAATCCCAAAATATTTGGGTTGATT ATAAACTGAACCATTTTGGGTTACAGTCCAGTTCTTTTCACAATCCGTCA AAAGAGCACACGATATAAGGATTTTACTTGGCATTATTGTCAATATTAAA CGGCTAACTTTGAACCCAAATGAAAATTCAACATCCATTTTGTAATTACA GATGATCACCACAATTATGACAAGCATCCCAATGAGGTAGTCAAAAACGA AGAGCTCACCTACAACAGTGGATCAGGGCAAGCAACTCGCAGCCATATCT GGATTTGGACCTGGCTGGCAGGCGGAGCAGCCACCCAGGGTCTAACTTCT ATGCATGCCTATGGTATTAATTTAACACTCTTGCTGGCCATCATAGTAAT CACATTTCAATACCTGTTTTGGGCACCTGCCGCATATACGATGCGTCGCC GCCCCGAACCTCTTGGCATTAATTACCGGTGAATGGTTATCAACGGCTCT CTATCTCTCGCTGCAGCTGCTAGTTAATTTAAGAAGACATAACATCTCAC ACACAACGTCCTTTGGTAGTACTATGTAAACATATTTGCATAATTTTGTA TTTTCAATAGGATCGATTCGAATGGAGCCAAATTAAAGCAAGCGAGGAAG TGAGTAGTTGAAAAGAAGGAGAAAGGTGAAATAGAATAAATAAGTAAACA AATGAAATTTTCAAGCCCATTAAAACATAGTTTATAGCGATATAGATTAA CTTTACGCATAAGTCAAGAAAAAATGGCAATACGCCGATTTAAGACGATT ACAGTTTGAAGAGAGTATAAGTTTTAATTGCCATTGGCCTTAGAGCCATA GGGCTCTGGTCTCTTTGCAGTTCGTATTCCCAAAGTTTCCCAAAACCGAA T 2) ATPB >droVir2_dna range=chr3:15500-18761 5'pad=0 3'pad=0 revComp=TRUE strand=? repeatMasking=none CCCATATTCTAAGGCTACAATTGGTGATGAGTCTCATTTAGAGAATTAAT TGTTAGAATCGGCTTGCTATAAAAGCAATAATAATCTTAACATGATAATT GAACGTGTTGAGAGAGACTATATGAGAATATTGATAAGAGTGTATTTGTT TCAATAATACAACAGGGCTGCCAACTGGTGCTATAGAAACTATTAAGTTA AGAATTGCTCAAAATGTTTGATTGACCTTTCTGATGACAGTGTTTTATCA CTAAAAAAAAGTGTAATTCAACTAGAAATTAGCTGAATTGGCAACATTGC ACCCGGATGAGAAGGCCTGCAAGAAACGAAAATATCTAGAAATTTCAGTA ACACCCTTGATACAAAAAAAAACCATGACTATCGATACATCACTTTAATG TCACTGTGACTATCGACAAATTTCAATACGACCGTAAATTATGTATTCAT ATTGCGACGGTACCGTAGTACTTCTACAAACCTCCGTCAGTTGGTCAAAA

38

ATGTTCGCGTTACGTGCTGCCGCTAAAGCTGATAAAAATTTGATGCCATT TTTGGGGCAATTGTGTAAGTATAGATATGTAATTTTAGTTAATTACAAAT ATTAACAAGGAAAAAATGATTTTCACGCATAAACTCGTTCTTTAACTTGG TCCCTTAACCGGACGAAGGTGGCTTGACAAAAAGCGAACATAACCTTATA TGTGGTTGAAAAGAACTGATTGCATAATATTGAAAATACAAAGTGTTTAA CTCGAATTAATTTTATAACGGTTAATTTACTATTTCGGATGCAATAGGTA CTATAAACGAAAGTGCAAATCTTTTTTGTATAGGCATACACATATTTTTA ATGACCAGCAGAAATATGTACATATGTATGTATGGACTTCGTGCATATGT ATTTTGGAAACTTTTGGTGTTTCAATGAAAAAAGAAACAATCGAATCTGC ATTTGTCATATCGGTCTCCTATTATTTTCCTGTTGTGATATTCAAAATCC TCACTAAATTATAGTATGTAGTATCATTGTGACGTAATATAGGTTGGTAT GCATATTCATATATATATAACATATGCATATATATGTATATATGTAATTC ATGTAACCGCATGCATTAGAAGCAAAGAATTTTATAAACATTCATACACA TATTTGAACCGATTATGTTTGCAGCTCGCGGTCATGCTGCCAAGGCAGCC GCTAAGGCGGCCGCTGTAGCAAATGGCAAAATTGTAGCCGTAATTGGTGC CGTCGTGGACGTGCAATTTGATGATAACTTGCCGCCAATTCTGAATGCAT TGGAGGTTGACAACCGCTCGCCCCGTTTGGTGCTGGAAGTGGCCCAACAT TTGGGCGAGAACACCGTACGCACCATTGCTATGGACGGTACTGAGGGTTT GGTTCGTGGACAGAAGGTTCTCGATACTGGCTCCCCAATTCGAATTCCAG TCGGAGCGGAGACTCTGGGACGCATTATGAATGTCATTGGTGAGCAACAA TTTATGAATATATTAAAACTGTTATGTTATCTATATATATGAAATGTTTA CCATGTTTAAAGGCGAACCAATTGATGAGCGTGGTCCCATTCCGTCTGCG AAGACCTCGCCTATTCATGCTGAAGCTCCCGAATTCGTGGACATGTCCGT CGAACAGGAAATTCTGGTTACCGGAATTAAAGTCGTCGATCTTCTGGCAC CCTATTGTAAGGGTGGTAAAATCGGTCTGTTTGGCGGTGCCGGTGTCGGC AAAACTGTGCTAATTATGGAGCTAATTAACAATGTGGCCAAGGCACATGG TGGTTACTCTGTGTTCGCCGGCGTTGGCGAACGTACTCGTGAGGGCAATG ATCTGTACAACGAGATGATTGAATCTGGTGTTATTTCGCTGAAGGATAAG ACCTCGAAGGTGGCTCTCGTCTACGGTCAAATGAATGAACCTCCAGGCGC ACGTGCTCGTGTAGCCTTGACTGGTCTCACCGTTGCCGAATATTTCCGTG ACGAGGAGGGACAGGATGTGCTGCTTTTCATTGACAACATATTCCGTTTT ACTCAGGCCGGTTCCGAAGTGTCCGCTCTTTTGGGTCGTATTCCATCGGC TGTCGGTTACCAGCCGACTTTGGCAACTGACATGGGTACTATGCAAGAGC GTATTACCACAACCAAGAAGGGCTCCATCACTTCGGTCCAGGCTATTTAT GTGCCAGCTGACGATTTGACCGATCCTGCTCCAGCCACAACTTTCGCCCA TTTGGACGCCACCACTGTCTTGTCGCGTGCCATTGCCGAATTGGGTATCT ACCCGGCTGTCGATCCTTTGGATTCCACTTCACGTATCATGGATCCCAAC ATCATTGGCCAGGAACACTACAATGTCGCTCGCGGTGTGCAAAAAATCTT GCAAGATTACAAATCTCTCCAAGATATCATTGCCATTTTGGGTATGGATG AGTTGTCCGAGGAGGACAAACTGACTGTCGCACGCGCACGTAAGATCCAG CGTTTCTTGTCACAGCCATTCCAAGTCGCTGAGGTCTTCACTGGACATGC CGGTAAACTAGTCCCATTGGAGCAAACAATTAAGGGCTTCTCACAGATTT TGGCTGGTGAATACGATCATCTGCCAGAGATTGCGTTCTACATGGTTGGC CCAATCGAAGAAGTTGTTGAGAAGGCCGACCGTCTAGCCAAGGAAGCAGC CTAAAATGCATATTACAAAAATGGTTTTTGCAAATTAATATTCAATTGTA TTAAGCATAAAGATGTCAGAGACAAATGAAAAAAATAAAACATAATTAAA CAACACGGGTCTTTAATATTTCATTATTTTTGCAGGCAAGGACACTATCA AACACAACACGGTCATGGCTAGATCGATGCCCTCCTGTTATATTGAATTC TACCACTAACCAAACAACATATAGACTGGACATCACATACAAACAGCGTT GCCACAAAAAGTATCGGAGGCATCTGGTCCAAACTCGCGAGTAAGGGAGT AAGATATATATATGATGTATTTTTGAACCGCTTACTCTACAGGAAAGTGC TTGGCGCACTCTCTTCCATATGATTTGTGCGATAGAACGGCAACGCTGTT AACTCTAATCTCGCTCGCACTTATCCTCAGCTCTCAATGCTCTCTCTATG TTTAGCGATCGTTTCAATGTGTGTGTGTGCATTTGTCCGACGAGGAAAAC TGCGCACAAATTCAATTTTTCTCAAATGCTGAGGCATTTCTACCCTTTTG AAGGCACAGCTA

39

3) EIF-5A >droVir2_dna range=chr3:19000-20593 5'pad=0 3'pad=0 revComp=TRUE strand=? repeatMasking=none AAAAATACTTATTTCTGACGATTTAACAATATTCACAAATGTTTTTACTG CATTTATATGTTAACGGATGTATTAACTGGTGAATAAAATGAAAGTACAA AGAAAATTGAACGTTATAAATACAAAATAAGACTTTATAAATTAATTAAT TTAATACTTGGATTCCTGCAAAATATATGTACACTTTTTGCCACCGAACG ACACACACACGGATGCACTAAACAAACATACACCGACATACCAGATACAA CTCTACCACATTCAAGATGTCGGATACCATAAAATATCGATAATTTGATA GTCGCATTGACCACCATTCAATGTTGTACAGTGGTTTAAGATCGCAATGC AACACGCTGCAACGCCCAAATACATCGATATTTAAAAAAAAACAGCGCTG CTTCGATATTTTTTCATCACTATAGTGTGACCAATATTTCAGTTTCCTTT TCTTCGCAGCGTGCCGCGTGTAAGTTTTTAATAGAAAAAGTTTTGTCAAA ATGTCGGATTCTGAACAGCATGAATTCGGCGGCGACTCGGGTGCATCTGC AACTTACCCGATGCAATGTTCAGCGCTGCGCAAAAATGGCTATGTGATGC TTAAGGGACGCCCTTGCAAGATAGTGGATATGTCTACCTCCAAGACAGGC AAGCATGGCCACGCCAAAGTCCATCTTGTTGGCATCGACATATTTACACA GAAAAAGTACGAGGATATCTGTCCCTCCACCCACAATATGGATGTGCCGC ATGTGAAACGAGAGGACTTCCAGCTCACCGATATTAGTGATGATGGCTAC CTATGTCTGATGAACGACAACGGCGACTTACGCGAAGATCTCAAGATTCC CGACAGTGCATTGGGTACATCTTTGCGCGCCGATCACGTTGCCGGAAAGG AGCTTTTGTGCACCGTGATGAAAGCCTGTGGAGAGGAGTGCGTTATTGCC GTCAAAAACAATACTGCTTTGGATAAATAAGCTTATCGGGGTAGTTTCAA CCACTGACCTGATACTGGAAAAGTGTAATGATATAATGAAGTAATATCAA TTAAAAGATTCAAAAATACAAACTGCTGCGTTTTTTTGTTTTTAGTATTT ATTTGCATATGTACATATGTATTGAGGATTATTTCAGCTTGATAACATTT CCATTGCCATTTTTGTTAAAACATTAGAACGAACATTAATCAATTTGTGA GCTATACAATGACTGAATGTCCGATTACTGACGCGTTAGCGTAGTTTTTA AAACCAAATACTGGTTTAAAAAATTCGCAAACACGTGGATCTTGCCAATT TTTTTTTTTTTAGTGCTGAGCATTTAACTTGATAATAAAAAGCACTGAGG TTAGAGCGAGAGCGCACTATATCCATAATGCAAATGTGAGAACATTTCGC ACGTAGTACATGTATGTATGTATTTGAAATGTATGTATGGAATGTATGTA TATATATATATTCATATGTATATATGTTTGTTTCAATGAATCCTGATCAG AGTTAAATATAAGATACTTTTGCATGCCATTTTATGAATTGGCTATACAT ACATGTACATATATAAAATGACATGGGCTTAAATTTTTTTACGA 4) CaMKII >droVir2_dna range=chr3:1-11090 5'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none GATCCTTCTTCTACTATTCTTGCCCTTAGGAAAAACCAGTTTATTTACAA TAATTTATGTTTTTTACAGGGGTGCCTTTTCAATAGTAAAAAGATGTGTC CAAAAATCAACTGGATTTGAGTTTGCGGCTAAAATTATAAACACCAAGAA ACTAACAGCAAGAGGTAAGAATCTATTATTTGTGTTTTTTTTTTAATAAA TATTTTTATTTCTTTATGACAAACTGTATTGCGTTCTTTCAGATTTTCAA AAGCTAGAACGAGAAGCTAGGATTTGTAGGAAATTGCACCACCCTAATAT TGGTATGATATCTATATAAATTGTCCATGTAGACAATGCTAAGTCTAGTT TTATTATCCAAGCCAAGCGAAGTCTTCTGTATAAAATAAATTATAAAATT TGGCACGGATTACATTTAAATCAGCCAAACACAATCGATTAAAGAGGAGT TTTTTATAGCCCTTTGTTCTACAGATGTCTAACGCGATAAAAATGTACTT TTTCGGCCCGAAGAAAAGATTTGCAAAAGCTGGTTTGGATCAATTCCCGG AACGCTATTTTATTTTTTTACTATGTGAACAAAATACTTATTCTATCTAT AAAACTCGACTTAGTTCTCTTTTGGCTTAAGTATATGTTATAAAATGAAT GCGACAATTGGATATCTTTAACGATAGAATAATAATGTTAATCATAATTA AACGTTAAAGGTTTTTATTCGATTTGTTTGACTTTCAGTTCGATTGCATG ACAGCATACAGGAGGAAAACTATCACTATCTTGTTTTTGATCTGTAAGTA

40

ACGACTCGCGCACCGTAGAGTTTCATATGTGTACTAATACAATGTTATGT ATATAGGTTGCTTGTAGAAAGAATAACTAATTATATTTTGATTGTAAACA AAAGCTTTCGGGTTCCTTTGTGAATAAGGCAATGGACTTGACTATTGTTT ATTGAGATTCATAGTTCATCCTTTCCCCACCGAGTTCCTATTTACTTACT AACTATAGCTCGCTCTTATATCTGCACTCTAACTACCTTTGTATAAATAC ATAGTATAAATACGAAATGGAATTAACAATTTTCTGAACGAAAGCAATCT TAAAACTAGAACTTGAAACAAAATTGACCTACTGAATACTAAATGCATTT TGCAGTGTAACTGGTGGTGAACTTTTCGAAGATATTGTTGCACGTGAATT TTATTCAGAGGCTGATGCATCACATTGTATTCAGCAAATATTGGAATCTG TCAATCACTGCCACCAGAACGGTGTGGTGCATCGAGATCTCAAGCCAGAG AATTTACTATTAGCAAGTAAGGCAAAGGGTGCAGCTGTGAAACTCGCGGA CTTTGGTCTAGCCATTGAAGTACAAGGTGATCACCAGGCCTGGTTCGGAT TTGCCGGTACCCCTGGGTATCTATCGCCCGAAGTATTGAAAAAGGAACCA TATGGCAAATCGGTAGATATATGGGCATGTGGTAAGCACGAGCATTTCTC ATCTATTATTATTATTTATTTTATATGTAAGATGTTATTTTTGTCACTAC TCAATACACACTCCGATTATGTTAACCCAATTTGTAAATAGCTTATGAAC AACTTTAAGCATATAAATTGTTTATATACAGGAGTCATACTCTACATACT GCTGGTCGGATATCCACCGTTCTGGGACGAGGATCAACACCGCTTGTATT CACAAATCAAGGCCGGGGCCTACGATGTAAGAATCTCTTTCAATCCACCC AAAATTACAAAACGTACAAAATTTGTACGCTGATTCAGTATTTACACTGC ATGATGTCGATGAAAAATTACTATATTGATAATATTTCGTTATTTAAACA TAAAGATGCAATAATTTCAATATTGAAATGCAGACAGTAGATTTATCTGC ATAAGATTTTCTAAATTATCTTTGGTATATCTTTTATCAAATTCTTGCAA CTTCTTTTTTAGTATCCTTCGCCAGAATGGGACACGGTTACGCCAGAGGC AAAAAATCTGATCAATCAAATGCTCACTGTAAACCCAAATAAGCGAATAA CTGCAGCTGAAGCCCTTAAGCATCCATGGATTTGTGTAAGTAATTGTCAT ATATTTGCGGTATACATTCCGGACTAACCAAGGCTCTCCATATTTTTCAA ATAGCAACGAGAGCGAGTGGCTTCTGTAGTACATCGCCAGGAAACCGTGG ACTGTCTCAAGAAATTCAATGCTCGACGCAAGCTTAAGGGAGCTATACTC ACCACAATGCTGGCAACTAGGAATTTCTCCAGTAAATAGATTTAATATTG TAATGAAAAGAAAAAAGAAAATCGTGTTTCATTTTCGTTTAAAGGCAGAA GCATGATCACCAAAAAGGGAGATGGATCTCAGGTGAAGGAATCAACCGAT TCCTCTAGCACAACACTAGAGGATGATGACGTCAAAGGTAAATATTTATG TAAATTGGGCCAATAGTTGGAGTCTATAATTGTTTATGATCTTTGTCGCT AAAACCTATTTTGAATGAAGTGGGGAATAGATGAGTTCAGCTCGTTAGGT TACATTTTACAATTGAATGAGTTTCTAGCCAACAAAATAGACAGTAATGC TAAGGATATACCTTTAAAAAAATTAACATATAAAACATATATATTTAAAT TATATAGTGAAATAATATAAAACATTTATAAATTATATAATTTATATATG TATATAACAGTTGACCATTAAGTGTCGCATTAAATAGTGCATTTTAAATA GAATTGGTTCATTTTTAAGTTATCAATTTATGCTGGCAATTTATTTTCAT ATAATCTGCACGTGTATAATTCTCGTTGTAATCTGCCTGTGTATTATTTT TTTATACCATACATTTTGTACATTGGCATGGTTAATATTAACTTTTAGAA AAATCAACTTGTTAAACATGAATACACAACTATTGTTTTCACATTGCAGA TGGCTTAAATAATTGTAAGAAATAAGGTTTGTTTAAACAATTTAGGCTCA TCTTAAAACATCTTAAAGAATAAAAGTAATTCGATTTGAGCCTCAATCCA ATTTCGTAGCAATATGCAACGTGGAGGGAAAGTCATCTGCGACTTCAAAC AGGCAGACATACAGAAAGACAGAAAAATAGATGGCTAGGCAGACAGACAG ACATAAAGACTGACACTCTGGTAGACAGACAGACAGATTGACAGACCGAA AGACTCAAAGTCAGACAGAGAGAGAGAGAGAGAGACATACAAGTAGACGA GAAGGTAAACAGACAGACAGACCTTTCCTTTAATACAACCCATTGAAAAT TTTTAATGGCGATCTGATGGTCCATTTGTAGATTTGGAATGCAGCAAAAG TCTAGAAAAATTTTCAATTTAAATTATAGATTATTATAGGCAGAATGTGT TAATGTCGGGTATATCCGAAACCTTGTCTGTTTTATCACTCAAAATCATA CAAATTAGGTGCACAGTTTTTTTATATTTTTTTTTCCTAAAAGATCTTTA ACTGCATTAAACAATTGCCTCGATTGAATAATGTTTTTATGTAGTCAATT GATGAATTCATCTTTGCTTTATTTGCGTCGTGATTAGCTTTGAAGTACAC

41

GTACTTGTAAAATAGAAATTTCTTTGCACACTTTTAAACTTTTCAGGCAA AATTATTACAAAATAATTCACAAGCGCGGAAGTACGGATATCTTCGGCAC GCCGAAAACCCAATAACCTTGCAGACAGAGAGATGTAAGAATAGTGAAGC TCGCAAAAGCTGAGATTAAAGAAAATATCTGGGGGAGAAAGAAAGACAGA AATAATTTTTCGACCGAGACTTCCTATACAGCCATATAATACAATCTTCA TTAGGTTTGGATCAAATATGAGCAGCATCGTTTAACTTCTACATGCTAGA CAAGAAAGTTTTTCATACAAGCACTTAATTTTCCTATATATGTACATGTG GTCCGATCCAGCCTGCAACAGAAAGACGGATTATTGCAAGGTTTCAAGTT TGCATAGAAACAGACAGACAGACGGACAGACGGACATGGCTATATTAACT CGCCTGTTCAAGAATATATATAGACTTTATGGTATCGGAGATGTGCATCG ATCTGTGACAAAACTATAATACCCAGTATACATATTTTTATATATTATAT TTTTGGGTGCTTGGGTGGATTCGAGGGGTATTTGAAAAAATATTTTCTGT ATGTGCGCAAATATACAACAATACTTAACAATTAAAAGCAATAAAAACGG TTGCATTTTCAATTATGAAATTTGTTTATTTTTTTTTTTAGAAGATAAAA AAGGGATCGTTGATCGCAGTACCACAGTCATATCAAAAGACCCAGAAGGT AAATTTTCTTTTGAATTTTATTTTTAGTTTTTGATTGCCTTCTTTTCATT ATTAATATTATTGTTTTTGTTGTTTCTTATGTTACCTCATCGAGACAAGC ACCACATACTAAAGTCCTTAATCGTTTAGGCATTCATTTAAAGCAGATCG ACTTTGTGATATCATTTGATTTGACTAACGAACCCAATAAACGAACTAAG GGTAGTTCTGAAAAGTCATTCTCTCTAAGGTTTTGTCGGCCCCTACTTTT TCGAGCTGATATTATCGAGTTTATGTACCTGGTTTGAAGGCGCCGTCTTC ATTGGTTTGTTTTAAATTCAGCGCTCGAGCTGCTCTCCTTGCATTAACTT GGGAACAACAGCCCTTTTTATCAAATCGCCCTATTCCCCCCAGATTTATA CATACATTTTCGAACAATATCGTTTAGGATTTCTTCGAAGATCAGTTTGC TGTTAATTTATTTTTTTTTGTCATAGTTGGTAGCTTCTTAAATTGACAAA GATTTGTAATATGAAAATGAATGTATAGATATAAAAAAACATCCTAAGTT ATTTGATTACTCTTAATGAAACTGAACGACATATCAACTTCAAGTCGTAT GAGTATGGAAACTGTAATCAATGCATATTCAAATAGTACTCGCTCTTTAA AGAATCATTCGTGATAACAAAGACAATAATTATGCTAAATGATATTCGCG ATGTTGACCAGACCAGCTACTGCATGCTGTAAAGAGACTTTTACTAACAA TAATATATATGATATATATATGATATATATATATATTAATATATTTGCCT GACTGTACACATCGCATTTTAACAGTCGGCCAACTGACCCAGCTCCAATC AAAGTCGACGAGCGTGCCATTCGGTGTTGGGTACACCAGCAGAGTCAAGG CCAATGTCATCGACAATACGAATGCCAGTAGCAAAATTATTACTAATGAG AATTGTAAACGCATTGATGCCCAAAGTCAAATGCATTCAAAGTCCCGCCT TAGAGGTGAGTATGCTTCAAAATTAATGCTAGGCATTTTTCTATAGAGTT CTATAGCCCAGTTTCTGGATGCAAAAGCAAATGAATTCTGTAAATAAAGG CGTCTATTTTTTATACATACGTGAATTATATTTTTTCTGATCTATTGCAG ATCGCATGCTCAATTTTTGCTGTATATCCAAAAAAGGCAACAACTAAGTT CAGCTGCAAATGCAAGCATATCTTACGTATGTATCGTATTGTATTATTCC ATCAACTTTCGTAGCTTCATATAAGACATAGGCATCGTATTATGCTGTTT ATAATATTTGTATTTGTTGAAGCTAGCTGATGTCTCAGTTGTTCTTTAAA AAAAGCTTGGCGCTCGGCATTAGAAACCTCACATACTTATATATAGTATG TTCCCAGTATGTAAAGAGCCTGTACTCAAAACTGTTGCATCTTTCTGTGT TTTTTACAAGAATTAACACGAATGATATATGAATAAAAATTTATCGCAAA AATATGTTGTGCTTGTGTTAATTCTGGACGAAAACTGATCAGATAATCAA ATTTCGATAGTTTCCAGCCAAATTCGACTTTTTTCTGAGGTCACTTTCCA GTTGTCCAGTTTCCAACACTGGTGTTAAGTAGGTCGGTTCCCAGATACCC GGATTACTCTCTCCTTTGGTCTAGCAAAGCATTTGAAAGCAGTTCCCGTA TCTCTGTTGACATATTAACTTAAATGGATAATTATCTGATAAACACGAAT CCTCAATTATTTATTTAGTTTTCAGCAGTTTCCAACACTGGTCTTGAGTA GATTGATTTCCGTATTCCCGGATTCCTTTCCCCGTTTGGTCTAGCAAAAG CATTTGAAAACATCTCAATGTCATCTAATTTGAAGAAAACTTACATGCAT AATTATCTGAAAACACGAATCCTTAATTATTTGTTTAGTCTTTTGATTTT ATATACACATATACATATATACGTTATATTAAATAATGTATATATATTTA TAAATGATGAAATGTGTGCGTTTTAGAAATAAGGATTGTGTGTCCTGCAA

42

AAACTTGCCAGCAAATATCAGGAACCTCACAATGCTCTTCAGGTATGTAC TAGGGCTTTACTCCTTAGCTCTCAATCCTTTTTTAATCAGTCATAAGCAG CCTTCTCACATATATATATGTGTGTATATATACTATGTATTTCTTCTTTT ATGAATGATTGAATGTGTCTTATCGTAAGAAATTCTGCATTTTGATTTAG AATTTTCGAAACAGTTTGCTACTCTATCAATCACCTTATCAATCAGAATC ACGTGCATGCTATCACATTTCAATTATTATTATTATTTGATGTATATTTT GTGGCACCTCAGACATTATATAACACAGGGAGATTCTTTACGGCTGGTTT CTTTTTTTTGTAATTCTTTCAACTAATAATAATAAGTATAATGCAATCCA CATTGTTGCCAAATAATTTCAGTTTTCATTGGATGACAAAGTCTTAGAAC AGACTAGTTGGGTATGCCCGGGCTCTCCCGGTCCAATTTTTTCAAGTTTC AAGTTTTAAACGTAAAATTTAAACTCCACGTCTGAAGTAGTTTTTTTTTT CTTGGTAAGAATGTCGAAGAATAAACTGCCATCTTTAATGGGATGGTAAA CAAAAAAAAATAAGATAAATATAATAATCAAATAAAAATGTCGAATACTA CGTTGTCTTGACCGATACGTCTATATTATGTAATATATTTATATTTATAT TATATATTATATAGATATTATATAGAATAGAAAAGTATAAGTGAGCCGCT TTCTGATTAGGAATATTTTACCAATCCACATTCTTAACACAATTTCGTTT TCAAATAAGTTGTACCCAAAAATTGTGCACTTATTGAATATTTGCTCAAC GGTAAATCATGTCTCAAATAAATTAAAAATTGTACACTCCACAGTGTTCT ACATTGAAAACAATATCGAAAACGAAAGTAAATGTGGCAATATAATAACT GTTTTCCACTCCAGCTTGATAATTTAAATAAGAAAAGTGATATTTATATC CACCTTAAAAGAAACACTTTTTCAGAATAATTTTGAAATAAAACCAGCTA CAGGCCTCAGTTTTTAAATATGTCACAATACTAAACGAATTCATCATTAT ATATATTCATATATTATATATATTTGCAATTATTTAACACTGAATATGAA AAATGACGGTAAATTTACAAGCCTTAAAATCGATGTTTATCGATATTTTG AAATACCAATATATATTAGAGATACCGACAAAAATACTCGTTTTGCGAGT GGCATTTATTAGTGGCGATTTTTAGTTTAATTTTCTGAATAAGTTCACTC GTTCATGTTCTGGTAATATCAACGTTTCGGGCGAGTATTTCCTTTGTTGA CTACAGATCCATATGTTAATAGCTTGGCTTATTTGTTTTAGGGATGTGTT TGTAGTTTAATGAGTCAATATTTTATGACGTTTTTTATGAGTACGTGAAG AACAAATTTAATCAATTTTATTTAAATAGTCCGTTAAATTCAATAGATAA CTCGGTAATTGGGTGCTTACTTCAGCATTAAATGTTTTAAACTTAAAGAT GTAATATACTTGGTGAAAGTTAAAGATATTGGTCAAGGTGTCTTGATAAA CCATTAAGTTGTTCATACAAGAAGTTAATTTATAATGGTCCCTTTTTTAA ATCTCTTCTTTTCAAAGATTTTGCTTAACTGTAGGGAGCATGGTGAAACA TATAAATGTCGGGCTTGGTAAAGATTTTAAGAAAAACAAAAAGTTTACTG TACAACTTCTTTATGTTCGACCGATAATCCTATGGCAGCTATATGATATA GTGGTCCGATGTTATTGGGTGTTAGCAAATATGTGAGGAGCATAGTAAAA CTAAAAAATGCTGAGTTTGGTCAAGATATCATGATAAACCAAGAAGTAAA CCAAATAAAAACCTACTTTTCGACCGATCGTTCATATTGTTCGCATAGAA ACCGACAGACCGATGTGGCTTTATCAGCTCGACTGTTAAAGCTGATCTAG GATATATCTAATTTATATTCCCTTCAACAAAGGCAAAAAATAAACATAAA ATGTCCATACATATGTATACGATTGACATATCGCCACACTTTATTTTTTG AAGAGTTTACCAAAAAAATATACCATCACATGCATTTAGTTTCTGGTTTT TGATTTCCCTAGTACGTTGGTTGGTTGGATTGTTCAATTGTAATTCTCAT CATACTATCGTTATAATCGAAATTCATCCGTGGTTGTAGTCTCTGACTTT TAACGAAATACACTATTAAATATAATCTGATTTGGAGCACTATCTGCTTT AATTTAATTTATAACAACTTATAACAAAAAGCAGCTAGACGACAGGAAAT AATCAAGATCACAGAGCAGTTGATTGAAGCCATCAACAGTGGCGACTTCG ACGGATATACGTGAGTTAATCTTATCTATTGGGCAAAGTGTTCAAGCTAA TTTTTCGTTAATCCTCCTGGCTACAGTAAAATATGTGATCCACATCTAAC TGCTTTTGAGCCGGAGGCATTGGGAAACTTGGTCGAAGGAATTGATTTTC ACAAATTTTATTTCGAAAATGGTAAATATGTTAAATGAGCTGTCTAAATT TAAATTTCACTAGAATTTAATGTACGCATTTCGTTTATTTTTATTTAGTA CTTGGCAAAAATTGTAAAGCCATTAACACAACAATATTGAATCCCCACGT GCACTTACTGGGAGAAGAAGCCGCTTGTATCGCCTATGTAAGACTTACAC AGTACATCGACAAGTAAGTTTTGATTTTTTACTAGCAAATATATTTCACA

43

AACCATCTAAGAACCCCATTACGACTTATTACATTATATGCCAGCCGGCA AAATGCAATCGATCTAGCGCAATTTATTTTCATCTATTTAAGTTCATGGA AACTGAAATTAGAGACTAGATTTTTAATGTACTTTGTCGTTTTCAATACA CAGAGAACTAGCTTATCACTTTTTGTCGAGATCTTGTCCCATATTTGATA AGCTTAAAACTGCTTCAGTTTTTGAAACCCTAGCCACATTATTCCTCAAA ATGAAACAAGGCACTGGTTTTTTTGGAGCCATGAAAATGTCATAGAGATC AGACTTTAAGAACCGAAGCTATTACAGAATGCTGAGGGAATACGAAGCAC GGAAGGAAACCATAATGTTTTTCTGGATGGGCTTAGGATATGCACATGTT TAAGCTGAACTGGACGCAATTCCGACTAGAGCCTTTTCATACCCTGAACC CATTAAAAATGGGTAAAAAGGTATATTGTATTTGTGCAAAATGCAAATGT ATGTAACAGGCAGAAGGAAGCATTTCTGATCCCATAAAGTATATATATTC TTGATCAGCATTAAAAGCCGAGTTGATCTAGCCATGTCCGTCTGTCTGTC CGTCCGTCCTTATGTATGAACGCAAGGATCTCAGAGCCTATAAGAGCTAG AGACTTGAAATTTTAGATGTAGTTGCTCCTAGTGCTTGCGCAGATTGAGC TTGTTTTCGATAATCGATAACTTACTTATTTCCAAGTAATCGATAAAAAT CGATATCGACATCCAGTTTATTGAACAAATCGGGTAAATAATAAGAGCTA GAGTTACCAAACATGATATGTTGCTTCTATAATATTATATATATGTCAAG TATCTTTCATTTTATACCTATCGCCACCATCCCGCTACCACCAAAGAGCT CAAAAATTAAATTAATAACCCAACTCTTATTGCCAGTCAATTTAAGCCAC AATTTAAATGCAATTGACTTTTGCAAAATATACAAATGTTCTATGGTATA ATAAGATATACTGTAGAAAATTTCATAGAGATCCGTTAAGAAAAATCCAA AGTTATATCCAACTGCGCAATTAAATGGGGCAGAAGATTTAAGAATTTCT GTATACATGCACACACACATTCATGCGCTTCTGCTTCGCATTCTAACAGC ATGGTAATGCTAAGTATTTTAGTTCCTTTTTTTTATCGTAAGTACTTAAT TATTGGTGGGTTTCTGGGTAGAGGCAACCTCTTGTTTTTTTTTTTTATTA AGTGGTCAACTATTGGATTGATCTCGTTATGCTTATAAAATAATGCTGTC TTATTGGTTATATATTTAAATAACGCATTTTAAAAATCGCACTAGACAAG GACACGCACATACTCATCAATCGGAGGAGACTCGCGTTTGGCACAGACGC GACAACAAATGGCAAAACGTTCACTTCCATCGAAGTGCATCTGGCAAGAT CAGCGGGGCAACGACTTTCGATTTTATGCCACAGAAGTAGGCGGTATCCG CAGAAATTCAAAGATAGCATAATTAATTCGCTCCGATAGCCTAATATGAT CTATGTGTATATGAATCTTTATAATAAACAGCTGAAACAACAATAGTTCA ACTCAACTTGTGTGCACTTCTAAGCGAATCGAAGATATGGGAGAAAAAAA AAAGAAAAGAATATTCAAAATGTGTGTTTCTTTGATCTTTTATAATTTAC AATCTATTGAATTACTATGTTGAATATGCAAACGAAAGAGTAAAAAGCTT TATGAAAGAGTAATATCTATAAATATGTATTATACAAAATTAATGTAATC ACGATGTGTCCAGTAAATATTCAGAAACGTATCCGCAACTATTTGATCTA AAAGCTATAACTATTTTTAATTGTAAACAAGAGAAAAACA 5) PlexA >droVir2_dna range=chr3:21568-32497 5'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none AGTTTTGTGTAAATGTGTGCGACAGACAGAAACAAAATTCACAGTACAAT ATGTATACATATATATAAAATATGTATATTCTTGGTTATCCGTCTGTCCG TGTCCGTTTCGAAAAAATAAAAGTTCAGCTCCCATGTTTATGTCTGCGTT TTTGATGTACAGGTGCAGGGTTTTTGCTGGACGATCACTTAAAGTGCATT TAACTGATGCACAAATGAACTTTTGCGGTCTTTTATCATTTTATAATATT TTATATATAATTAAGTGATGAGATTTTAAGTATTTTCTTGGCATATTTTC CTTTCTTTTGTAGGTGCTGAGATAATAATAATGTAGCATCAACTGGGAGT CGACACAAGTTGTAGATAAAATCTCTATAGATCAAATGAATATGGATAAA TGTTTGAAAAGTGGCATTAACTGCGGCTGCTTGCAAGACATTTAAACGCA CACGCTGCAACGTTCTTTTTGTTTTAAATAAAATAAAAAAGCTGGAAATA TTTGGAAGCCAATAGAGAATTGCGAATCCTAAGCAAAGGATTATTCATAT TTCGATCTGATCGCCATTGTGGCGATTAGCCAGCGACTGTGGAAATGAAT ATGCTCTGTATACTCTGTTTACTATCAATCACAATTTTGGGAAATCTACC ATCACGTTCAGCCCACGGACAAATATTGCACCTATATAAGAAAAGTAATG

44

AGCAGCTAAATTCTGGATTTACGTACGCGCAGCCGTCTGTATTGGATGTT CGAGCTGATAGGATTGGACGAAGTGCTGAAGCCCTTAGGGTTAATATAAC GGAAACGGACCCAAATGTGCTGACCCGTAATGCTGGGAACTTCAGCACGA ATATAATTACAAATGTAGCCAAATTTGACACAAGACTCAACCATCTGTTG GTGGACACAGTTACGGGCAGAGTGTTTGTTGGCGGTGTGAATCGGTTGTA TCAGCTATCGCCGGACCTGGAGCTGCACGAAACCGTGAAGACAGGACCAC AAAATGATTCAGTCGAGTGCACCATACTAGACTGCCCGCTTAATGCCGTG CGCAAGCCAACAGATAACTATAATAAGGTGCTTCTTATAGATCGCGCCAC CTCGCGTCTTATCGCATGTGGATCCTTGTTCCAGGGCACCTGTACGGTCC GTAATCTGCAAAATGTTAGCATAGTTGAGCACGAGGTGCCGGACGCCGTT GTTGCGAATGATGCCAACTCCTCAACGGTTGCTTTTATTGCGCCTGGACC CCCCCAGCATCCGGTGACGAATGTTATGTACGTGGGCGTTACCTATACCA ACAACTCGCCGTACCGTAGCGAGATCCCGGCCGTAGCGTCCCGATCTTTG GAAAAAACCAAAATGTTTCAGATAGCATCATCGGCTGTTACGACTGGCAC GCGAACCTTTATAAATTCGTATGCCCGCGAAACATATCTGGTGAACTATG TGTACGGGTTCAGCTCAGAACGGTTTTCATATTTCCTAACCACTCAGTTG AAGCATAGTCATCACTCGTCGCCCAAAGAGTATATAACTAAACTGGTCCG AATATGCCAAGAGGACTCCAACTATTACTCGTACACTGAAATTCCGGTGG AGTGCATTAGTGAGGCTCAGGGCGGAACTAAATTCAATTTGGTCCAGGCC GGCTTTTTGGGCAAACCTAGCTCGGATTTGGCGCAAAGCTTGGGAATCTC GATACAGGATGACGTTCTCTTTGCGGTCTTTTCGAAGGGTGAAAGCAACA CTCCAACCAACAACTCGGCCCTTTGCATCTACTCATTGAAATCAATTCGT CGCAAATTTATGCAGAACATCAAATTCTGCTTCAATGGAAATGGAATGCG TGGACTCGACTTTATATCACCCAGCATGCCTTGTGTCTTAACGGTATGTA TATAGGGTATTTGAAAAATTCCAATCGCAAGTGTGGAAAAATCGCGGAAC ATCTTAAAATACCATTTCCTTCCAATCAGACTCTCAAAGATTAAATGGGC AAAGTATCGAATTAACAAATATTATTATGAAAATTTATTGAAGTCGCGTT TCACATTCCCCCGACAATTGTGGAAAAATCGAGTAAAACGGTTTTACGAA CCTCTTTAAATCCATTTTCAATCTGTGTGAAAATTCATTTCCTTAATAAG TTAGTTAGTTGACAGAGATCCTATTGATAATTTATTTGAGACTCGTTTCA TATATTAACGGATATTCACCTTTCCCAGTTTGGAAATTCCACACGCAACT GTGGAAAATTGGCAGAAAATTCAAAGCCCTTTGTGAAAATTAATTTAATA CTTGGGTAAAAATGTGGGTGGGTCAAAGGTCTTGAGTTTTTATTTTTAGA CTTCACTTACATATAACTGTAAAATATAACTGACGAGAACTTGGTAAAGT TAAATATTTCACGGGTGCGAAATGACTGTAAAATTAATCTAAACATTTGA GCAAAAATCTTGAACTGCGCCAGGCCCCGGGATATAGCAAAACGATGAGG AGATTCGAAGTAGATCAGAGATTTGTTACAAACCGGGGCTGCAAACCCAA AGGAGTTAGTTGTTCGGCGTATGGTTCGAACATAGTATCCAAAACCCATT TTCAAATGTTTTTTGAAAATAGAATTCGACTGATAATAGTGAAATCCGTA GTTTGATCTGTATCTTAAAATTGGCATCTACTGAATATGCTAAAACAAAT GCAACGGTTAATGCACAAGTTTTTTTCAGTGGGCTGCCTCTTGAAAAGGT CAACAGTTGTTAATTTTAAGCCAAGCTATTTTTGAAAAATATATGGGTTT AGATTCTGCGGCTCGTGGGGCAGTTGGTTTGGCCAAAGTTGTTGCTGACA AAACTTAATAAATAATAATATATATATCTAAAAAATATTACTGATTTTGT AGAAACTGCAAACCATTGGGGAAGACTTTTGCGGACTGGATGTTAATTCA CCTCTCGGCGGAGAGCAGCCAATCACAGCTGTCCCAGTGGCAATGTTTAA CACGAGGGTCACATCTGTGGCTGCGACCAGCACCAGCGGTTATACGGTCG TATTCATTGGAACCGTTGACGGATATATTAAGAAAGTAGTCGTTGAATCG GCGACCGTTGCAAATGAATATGCAAGCTTGGCCGTTGATTTGGGATCTGC CATTAATCAGGACATGCAGTTTGATAATCAGAACCTTTATGTTTACGCTA TGTCCGAGCGCAAAGTATCCAAAGTTAAGGTTTATGATTGTGCTGATTTT AGGACTTGTGGCGAATGTCTGGGTGCAAAAGATCCATACTGTGGTTGGTG CTCGCTGGAAAATAAGTGCAGCCCACGCTCAAATTGTCAGGATGACGCCA ATGATCCACTTTACTGGGTTAGCTACAAGACGGGCAAATGTACGACAATT ACGAGCGTGGTGCCACATCAATTACAGCGTACGACCGCTCGCACCTTGGA GCTGATCATTGATCATTTGCCGCAGCTAAAAGAGAATCTGATTTGCGCTT

45

TCACAACCGAGGACAAAGCCCTATTTACAAATGCCACAAAGAAGCGAAAC GGCGTCAACTGTACCACGCCCCGCACGGACATGTTGCCGCAAATTGAACA GGGCAAACATCATTTCACAGCGAAGTTATCGGTGCGCACGCGGAACGGTC CTGATCTTGTCTCAACCGACTTCACGTTCTTCGACTGCAGCACGCACTCA TCGTGTACGCGCTGTGTATCATCTGAGTTTCCGTGCGACTGGTGTGTGGA GGCGCATCGCTGCACCCATGATACGGCCGAGAATTGCCGCAACGATATCC TGGTGACCGGCGTCAGCCGAATTGGTCCGAGCTATCGGTCCGGCCCTGGT TTCTGCCCGACCATTAACGCCACCGGCGATGGCAGTGAGGTTCTTGTTGC TGCTGGCACCAGCAAATCCATCAAGGTTAAGGTTCACATCATTGGCCAGT TTATTGTGCAGACACGTTTCGTTTGCCAGTTCAATATTGAAGGTCGCGTG ACCAGCCTAAACGCCCAATTGCTTGGCGATACAATCTACTGCGACAGCAT GGAATTTCAGTACACATCACGATCACCGAACCTAACCGCAACTTTTGCAG TTATATGGGGCGGATCGAAGCCTCTCGACAATCCTCATAATATTCACGGT AAGTCTTCCCTTTGTCTTCCCTTCCCTTCAAAAATGCGTAACACACATAT GAGACATCTCCGACCCCCTTAAGTAATATTCAACGAAATAAATAATTAAC AATTCTAGATCAGCTTCACAACAGGCGAGCTGATGTCTCTTTCTGTCTGT TCCATATCCAACTAGTCCCTCAATTTTTAAGCCATCATCGTGAAGTTTGC ATGAATAACAATTTGTTTATTAAGATCTCTTTTCGCCAAACTCAGCATTT ATAAGTTTCACTACATATGACAAATTTTTTATCAACTTCGGACCATCATA AGTTCTCGTATTAAAAGCTTTTCTGTTTATCAAAATATCTCAACTTATAA GTTATATGACTATATATTAATCAACCTGGATAGGAAGAACCGATCGATAC ATTTTTGTATAGTTTAATATTATATTTTTCCTGATATTTTGTTCAGTCAG CATTTACGAGCTGCACTATTCTCACATATTATTTCCTTTCTATTTCCTAT TTCCTTTTTATTAGTTAATTTCATGAAATTGTTCTATGAATATATATATA TATTTTTGTCTAAAGATTTTTAAACCCACTCTTAACCCATTTTCAAACCC ATTAAAAATGGATAAAAAGGGTATGTTGTATTTGTGCAAAATGTAATTGT ATGTAACAGGCATCTCCGACCCCATAAAGTATATATATCATTGATCAGCA TCAATAACCGAGTCCATGTCCTTTGTCTGTCCGTCCGTCCGTCTGTCTGT CCGTCCGTCCGTATGTATGAACGCAAGGATCTCAGAACCTATAAAAGCTA GAGACTCGAAATTGCATTGAAAATGTAGGTCCTCCTAGTGCCTGCGCAAA TCGAGTTTGTTTCCGAATATCGATAACTTACGCCGTTTCCAAGCAATCGA TAAACATCAATACCGACATCCCGTTTTTGAGCAAATTGGGTAAATAATAA TAGCAAGTGTCACCAACCATGATATGTTGCTTCTAGAATCTCTATATATA AAACTGTTTGTCCTGACTGACTGACTAACTGATTGGTGATCAACGCGCAG CCCATACCGTAAGAGCTAGGAAGCTGAAATTTTCACCTTTTGTGATGAAC GTGCACTTAAGGAAGGGGTTTCCGGAAATTCCACCCGCAAGCATGGAAAA ATCGCGAAAAACGTTGGTATGAAACTTTTTTGTTAACCATCGGATCGTCC TCAAACTCAATTTCAAAGTTCTGTGTTCAAATTCATTTGAGGGGTGCTTC ACACTTTTCGAAAAATCCATTCCTCCTTGGTGGAAATGGGAGTCAAAGAT TTGGTGGGTGGCCTTTTGCCTTCAAATTCATTTGCATGGATCTAAAAAAT CATTTGAGACGTGTTTCACTTTTTTTTTTTCAAAATCTAAGCTCTTTCGA TGGAAAGTGCATTTCAAAGTAATGTTTTGAGAATTATAAGCTGTGTCCGA TTTGCATCAAATTTATTTTCAAAGCTCTGTATAAGAATATAATGAATACA TGTTTTAGCAATTTGGGAAATTCCACTTGAAACGTTTGTATGACAGTACT TTGTTTACTGTTTCTGCTCAGTTTCAAAATCATTTTCAATGCTCTTCGAG AACATTGCTTTGATAACATAAGTGTCACGGGCAAGGCCGGGCTATACCCG CTAGTATTATTTATATGTCAAGTATCTTTCATTTTTTACCAGTCCGCCAC CTCCCCGCTACCACCCCAGAGCTATAAATCGAGTTAATAAGCCATCTTGT ATTACCAATTTACCAATTTAAGCCACAATTTAGATATAGATAATAAGATA TACTGGTGTGGCTGTTGAGTAGAGACGGCGGTTGCAGTTGCAGTTTTAAC CAATCTTTTTTTTGATTACAGTTGTGATTTATCGTTGTCGCGTGATGGCA GATAGTTGTGGGATATGTCTTGCGCTAGCCGAGAAGTACAATTGCGGATG GTGTTCGTCGACGAACACATGCGAGGTGGTTGAACAATGTAACAAAAATA ATGAAGGCAAAACGGATTGGCTGAATCGGAGCGAGATTTGTCCAAATCCA GAGATTCATTCCTTTGGTCCCAAAACTGGACCATGGGAGGGCGGCACCAA TATAACTATAAAGGGCATAAATCTAGGAAAAAATTATAATGACATATATT

46

CCGGCGTTCGAATTGCTGGAATTAATTGCATGCCATTTCAACAGTTTTAC ATTGACACAAAACAAATTGTTTGTACTGTGGATAGTCCCGGCGAGCAGAT GTATCGAAATGGGCGAATCGTGGTTCAAATCGGGGACTATCGTGGCGAAT CAAAGGAAGATTATGAGTTTGTCGATCCGAAAATATCGAATTTTTATCCG CGGTTCGGCCCGTCATCAGGAGGTACCCAAATACGGATAATTGGCAAACA TTTGAATGCTGGATCACGAATACAGGCCTTTATAAATGATCATCTACCTT GTAAAATCATTAGTACGGACTCCTCGCAAGCGATATGTCAGACATCGCCG TCTCCGGGTATTATTGAAGGACGTCTAAAAATGTCTTTCGACAATGGGCC GCGTGAATTTAATGACTATAATTTTAAATATGTACTCGACCCAACTGTTG AGCAAGTTAGCTCCGGACCCAGTGGCCAAATTAAAGTACCAAAGGGTATT CCTGCTGGCGGTATTCGGATTATAGTTACGGGAACACAATTTACCAGCAT ACAAGCACCGAGCATCTATGTCTTTTACAAGGGTCAAATGTACGCGAGCC AGTGCCGGGTTCAATCCGATAATGAAATGGAATGCCCGTCGCCGACTATT GAGGCAGATAGCCAAATTTTGGATCCGGAGAATCCCACGTTGCTCGAATA CGGATTTCTCATGGACAATGTGCTCAAGGTGCAGAACTTGTCGAAAAAGC ACAACAATCATTTTGAGCTTTACCCCAATCCGGAATACTTTACGTTCGAG GAACGTGTCAAATACTTCAAAAGCGAGTACCTCACCATAAATGGTCGAAA TCTCGATCGCGCGTGCAAGGAAACGGATGTCGAAGTGAAAATTGGCAACG GCTACTGCAATATAACGTCTCTGTCGCGTCAGCAGCTGACTTGCCGGCCG CCCACGGAAGCAGTCGCTGCCAGTAACAGTCCGAATGGTCCGGAGGTGAT TGTACGTATTGGATCATCATTGGAGTATCGCATTGGCATACTCAGTTACG AGTCATCGAACCTGATTATGGATTGGGGGGATAACGTCGTCTTTGTTGTA ATTGCCGGCTGCGTTATATTCTTTCTTATCTTTTGTGCCCTGCTTGTGGC GTATAGAAAAAAGACCGCCGAATCTCACCGTGAGCTCCGAAACATGCAGG AGCAAATGGATATTTTGGAATTGCGTGTGGCTGCCGAGTGTAAGGAAGCA TTCGCCGAACTTCAAACGGAAATGACGGACTTGACGGGCGATCTAACGTC GGGTGGCATACCATTTTTGGATTATCGCTCGTATGCTATGAAAATCTTAT TTCCCAATCATGAAGATCACGTCGTCTTGCAATGGGAGCGACCGGAATTG TTGCGCAAAGAAAAGGGATTGCGGCTATTTGCCCAGCTCATTATGAACAA AACATTCCTGCTGCTTTTCATAAGAACTTTAGAGTCGAATCGTTATTTCT CGATGCGAGAACGTGTTAATGTCGCCTCATTAATAATGGTCACGCTGCAG TCAAAACTGGAATATTGTACGGACATATTGAAAACATTATTAGGCGATCT CATTGAAAAATGCATTGAGGGCAAGAGTCATCCAAAATTATTGCTTCGAC GTACCGAGAGTGTGGCCGAGAAAATGTTGAGTGCTTGGTTTACGTTTCTT CTCTATAAATTCCTAAAGGAGTGTGCCGGAGAGCCTCTATACATGCTGTT TCGTGCGGTTAAGGGTCAAGTAGACAAGGGTCCGGTTGATGCGTGCACCC ACGAGGCTCGCTACTCTTTGAGCGAGGAGAAGCTTATCCGGCAGTCTATT GATTTTCGACCCATGACCGTGAATGCCAGCATTATACAACAGCCAATTTT TTGCAACAATTTGGACATGTTGCCGTCACACACCGAGAACGTATCCGTTA AGGTGCTCGACTGCGATACGATTGGTCAGGTGAAGGAGAAATGTTTGGAA ACGATTTATAGAAATATACCATCCAGCCAAAGACCTCGCAAAGATGATTT GGATCTGGGTATGTGATTTATCGTCAGTTCATTTGGATTTGCATAAATCA ATTTGTACTTACTTTTTTTTTTTCTCATTCTACCTAATTAGAATGGCGAA CTGGAGCAACGGGTCGTGTGATCCTATATGATGAGGATGCTACATCGAAA ACGGAGAACGATTGGAAAAAGCTAAACACATTGCAGCATTACAATGTGCC AGATGGAGCCGGTCTAAGCCTTGTACCAAAGCAAAGTTCCATCTATAACT TTAGTATATTATCTGATAAAAACGAGAAATCTCACAAGTAAGTAACAAAA AGGAAAGAACAACTATCTTTGGATGCCAAAACTAGCAGACATATGACAAC TAATTTCTATTTTTGTTCCTCGTGGGATTGTCCAATATTTTCAATCCAAG TCGATATAGTCATGTCCGTTTGTACGAATGCTTCGATCTCGTAGTAGAAT ATAGTTAGGAGCTCCTGCGAACAATATTGATTCATGCCTAGTTTTATATA GATATATGTATATATATATACGACGAAGTTGGTTTTTTTCTAGTATTTCG TGGTTTTCGACTACTATCTGAAAGGTTATTGAAAAAAGTGTGATGTTCTT TACTTAATTTGTAGCAAAACAATTTATTTTTCTGCCATTTAGATATGAAA CACTGAATATATCGAAGTACACCTCCTCCTCACCGACATTCAGCCGCGCC GGAAGCCCCTTGAACAATGATATGCACGAGAATGGAATGAAATATTGGCA

47

TTTGGTCAAACATCATGACAGCGATATTCAAAAGGAAGGCGAACGTGTCA ATAAATTGGTCTCTGAAATATACCTAACAAGACTGCTGGCGACTAAGGGT ACTTTGCAGAAGTTCGTAGATGACCTCTTTGAGACAATATTCAGCACCGC TCATCGTGGGTCCGCCTTGCCTTTGGCAATTAAATACATGTTTGACTTTT TGGATGATCAAGCCCTTTTGCACGGAATAACAGATCCCGAAGTCGTGCAC ACTTGGAAAAGCAACAGTTTACCTTTGCGGTTCGTATTTTCACAACTTGA TATAATTTCGACAAGTGATTTATTAATTTTCGTTTAATTTCTAGTTTCTG GGTGAATTTAATAAAGAACCCAAATTTTGTATTTGATATACATAAATCGA ATATTGTGGACTCCTGTCTGTCAGTTGTAGCTCAAACATTTATGGATTCC TGCTCAACGTCAGATCATCGATTGGGTAGGATAAAATAAATCCAATTATT CCAATTGGTGACACAAAAAACTAAATGTCAATGTGTTTATTATTGCAGGC AAAGATTCGCCAAGCTCAAAACTATTATACGCCAAGGATATACCCGAGTA TCGCAAGTGGGTTGACCGGTATTACAGGGATATTCGGGATATGTCATCCA TTTCTGATCAGGACATGAATGCAATGCTCGCTGAAGAATCTAGGGTAAGT TTTAAAGCTATTAAATGGCAATCAAATCTTCTTTTAAATCATGATTACAA GTAAAAATTAATGTTGTGCTTTGGTTCGTCGTTCGAGCTATGTGCCCATG TTCTGCCTTCAGAGTGGTTAATTTTGTTCAAATTTAATAAGTATTGTTAT GTTATAAGTATTTTTGAGATAACTGGATTTTTTTGTAAGGGTGTTGTGTG ACAATTCACACTTTGCAAATCCCTCACTTTGTTTTGGGATAAAAAAAGTT ACTTGGCCCAAAAAAAGTCCGGTTAATTCTATATAGTAAACTTGTATTGG AGGTATTCAAACGTTAATATTTTGATGTTTTGAGATATTAAAGCTAAATT TGCAATAGTTGGAATGACCTCATCTAATATTCTATTCAAAAATGTAGTTT TCTTCTCCTTTTTTGAGTTGTAAGTCAATGTGAACCTAATGATGCTATTC CTATGCTTTCAGCTGCATACAACTGAGTTTAATACGAATTGTGCTCTACA TGAGCTCTACACTTACGCTGTTAAATATAATGAGCAGTTGACGGTTACAC TGGAGGAGGACGAATTTTCACAAAAACAACGACTTGCATTTAAATTGGAG CAGGTTCACAATATCATGTCAGCTGAATAAGCCTCGCGTCACCATTCTCA AAAAAAAAAAAAAAAACTGGAAACTACGATTTTATGCATCTAAAATATGT TAGTATGAAAGTGCTTGTGTATTACCCAATAATGATGGAACAGGAAGTCC ATTTCTTTATATACTCGTACATATACCACCTATGCAAAAATATATAAATG TGAGTGTGTGTAAGCCCAAATTCTTTCTCGTACATAGTTTGTTTAAGTCC CTCATCTAATTAATGTATGTGATGCAGCCATAAACTTTTACAGCCGTAAA GTCGTACTGCCATAAACTTAGCACATTCAAACACTTACACTAATATCATT CCATTGACTATGCTACTTGTCGAGGAAAGGATAAAACAAATATGTTTTTT TTTTTGTGGGCATGTGTGGAATTTGCTCATTGATATTTATGTAAAATTTT TGTATGATTATTACACTATAATGCATGTCAGTAATATTAATGTCTAAGAA TCGATATTCAATATATATATATATAAAATA