Subject: CG3013 and CG17501 are not genes, they're part of a transposon-related repetitive element family I became suspicious that CG3013 and CG17501 may not really be genes when I saw that both share homologous domains with C. elegans Tc1 transposase. When I BLASTed each against the Drosophila genome, I got strong hits to numerous scaffold segments (see attached text file of results with CG3013). The segments share >90% identity over a region of > 500 nts. I suspect, because of the homology to Tc1 transposase, that this repetitive family is or was a family of short inverted repeat type DNA transposons. Furthermore, the N-terminus of the CG8415 protein, is also related to this transposon-like repetitive sequence family. Here is a BLASTn alignment of a portion of AE003788, which contains CG3013, with AE003815, which contains CG8415. Query: 121992 tcaagcaacatgatccgcaaagcactgctgtttgtcgagaagaacgaaacacggcgaaga 122051 |||| ||| ||||||||||||||||||||||||||||| ||||||||||||||||||||| Sbjct: 92707 tcaaacaaaatgatccgcaaagcactgctgtttgtcgaaaagaacgaaacacggcgaaga 92648 Query: 122052 aagccctctatgtccaacgtggagataaagcgcttggttcggcaaggcaagaagga 122107 |||||||| ||||||||||||||||| | |||||||||||||||| |||||||||| Sbjct: 92647 aagccctcaatgtccaacgtggagatcaggcgcttggttcggcaaagcaagaagga 92592 CG8415 gene product 1 M S N V E I R R L V R Q S K K D Score = 166 bits (86), Expect = 4e-36 Identities = 102/110 (92%) Strand = Plus / Minus Query: 121687 tctctcaatgtaacggttctttttgtttttgggcacttgctgcaaaagtgcgcgaaatga 121746 |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||| | Sbjct: 92850 tctctcaatgtaacggttctttttgtttttggtcacttgctgcaaaagtgcgcgaaatta 92791 Query: 121747 ggcgttaaccaaaatagcactgaccacgtatttgctgaataaaactaata 121796 |||| |||| ||||||| ||||| ||||||||||||||||||| ||||| Sbjct: 92790 ggcggtaacaaaaatagtactgattacgtatttgctgaataaaattaata 92741 Score = 164 bits (85), Expect = 1e-35 Identities = 93/97 (95%) Strand = Plus / Minus ImageImageImageImage ImageImageImage Query: 122318 agatgagaccaaaattgtgttgtttggtgggaaaggctcttggtcttatgttcgtcgtcc 122377 |||||||| ||||||||||||||||||||||||||||||||||||||||||||| ||||| Sbjct: 92588 agatgagagcaaaattgtgttgtttggtgggaaaggctcttggtcttatgttcggcgtcc 92529 CG8415 gene product 18 D E S K I V L F ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Query: 122378 accacgaactgaatttaatcctcgcttcacctttaag 122414 |||||||||||||| ||||| |||||||||||||||| Sbjct: 92528 accacgaactgaatataatcatcgcttcacctttaag 92492 CG8415 gene product 92528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Score = 164 bits (85), Expect = 1e-35 Identities = 107/118 (90%) Strand = Plus / Minus Query: 122459 aaatcattgtagtatttaagttaagtgagtaaaatgatgaaaaagtggcagaaaatagag 122518 |||||| ||||||||||||||| ||| || || |||||||||||||| |||||||| || Sbjct: 92363 aaatcactgtagtatttaagtttagtcagcaatatgatgaaaaagtgttagaaaatacag 92304 CG8415 gene product 92363 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Query: 122519 aaacgctgggacatacacgaaatgtgcttatggtgctattattgttaccgcaactgta 122576 ||||| |||| || |||||||||||||||||||||||||||||||||||||||||||| Sbjct: 92303 aaacggtgggccaaacacgaaatgtgcttatggtgctattattgttaccgcaactgta 92246 CG8415 gene product 92303 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Score = 110 bits (57), Expect = 2e-19 Identities = 101/118 (85%), Gaps = 8/118 (6%) Strand = Plus / Minus Query: 121553 tacagctgcggttaaaataatagcactactgcaggtgaaaagttcatttcataatcataa 121612 ||||| |||||||||||||||| ||||||||||| || |||||| ||||| ||| | || Sbjct: 92987 tacagttgcggttaaaataataacactactgcagttgcaaagttgatttcctaa--aaaa 92930 Query: 121613 aattattaaatgtttatattttttaaagtcagattgcatgaataataagtaccatatg 121670 ||||||||||| ||||| | ||||||||||||||||||||||||||||||||| Sbjct: 92929 aattattaaatatttattt------aagtcagattgcatgaataataagtaccatatg 92878 CG8415 has been characterized as a ribosomal protein gene. I haven't looked to see what portion of CG8415 is homologous to ribosomal proteins. It seems likely to me that the N-terminal coding exon of CG8415 isn't really part of the ribosomal protein, but instead is a remnant of a transposable element. I think the real N-terminus of the ribosomal protein is probably located downstream of the repetitive sequence. ================================================================================ Query= (585 letters) Database: D. melanogaster genomic nucleotide sequences 1170 sequences; 122,655,632 total letters If you have any problems or questions with the results of this search please refer to the BLAST FAQs Taxonomy reports Distribution of 91 Blast Hits on the Query Sequence Image \------------------------------------------------------------------------ Score E Sequences producing significant alignments: (bits) Value gb|AE003788.2|AE003788 Drosophila melanogaster genomic scaf... 1160 0.0 gb|AE003040.1|AE003040 Drosophila melanogaster genomic scaf... 890 0.0 gb|AE003066.1|AE003066 Drosophila melanogaster genomic scaf... 874 0.0 gb|AE002770.1|AE002770 Drosophila melanogaster genomic scaf... 844 0.0 gb|AE003786.2|AE003786 Drosophila melanogaster genomic scaf... 724 0.0 gb|AE003512.2|AE003512 Drosophila melanogaster genomic scaf... 722 0.0 gb|AE002582.2|AE002582 Drosophila melanogaster genomic scaf... 640 0.0 gb|AE003845.2|AE003845 Drosophila melanogaster genomic scaf... 525 e-148 gb|AE003846.2|AE003846 Drosophila melanogaster genomic scaf... 496 e-139 gb|AE003603.2|AE003603 Drosophila melanogaster genomic scaf... 486 e-136 gb|AE003212.1|AE003212 Drosophila melanogaster genomic scaf... 482 e-135 gb|AE003843.2|AE003843 Drosophila melanogaster genomic scaf... 365 e-100 gb|AE003395.2|AE003395 Drosophila melanogaster genomic scaf... 361 1e-98 gb|AE003389.2|AE003389 Drosophila melanogaster genomic scaf... 351 1e-95 gb|AE003090.1|AE003090 Drosophila melanogaster genomic scaf... 351 1e-95 gb|AE003657.2|AE003657 Drosophila melanogaster genomic scaf... 270 3e-71 gb|AE003605.2|AE003605 Drosophila melanogaster genomic scaf... 266 5e-70 gb|AE003019.2|AE003019 Drosophila melanogaster genomic scaf... 194 2e-48 gb|AE003815.2|AE003815 Drosophila melanogaster genomic scaf... 174 2e-42 gb|AE003594.1|AE003594 Drosophila melanogaster genomic scaf... 170 2e-41 gb|AE003844.2|AE003844 Drosophila melanogaster genomic scaf... 135 1e-30 gb|AE002772.2|AE002772 Drosophila melanogaster genomic scaf... 109 7e-23 gb|AE002837.1|AE002837 Drosophila melanogaster genomic scaf... 94 4e-18 gb|AE003787.2|AE003787 Drosophila melanogaster genomic scaf... 88 3e-16 gb|AE002942.2|AE002942 Drosophila melanogaster genomic scaf... 86 1e-15 gb|AE003574.3|AE003574 Drosophila melanogaster genomic scaf... 84 4e-15 gb|AE003147.2|AE003147 Drosophila melanogaster genomic scaf... 54 4e-06 gb|AE003573.2|AE003573 Drosophila melanogaster genomic scaf... 50 6e-05 Alignments tmpseq_0 1 atgggtcgcggaaagcattgtaccgtcgaaaaaagaaatttgattaaaaacatgatctct 60 AE003788 121890 ............................................................ 121949 AE003040 40718 .....................c........-......................... 40772 AE003066 3668 ...................................................t........ 3609 AE002770 13094 ............................................................ 13035 AE003786 26889 ..........a................................................. 26830 AE003512 297556 ........................................................t... 297615 AE003846 36955 .......................................t..........c..--... 37010 AE003846 154469 .......a...........................................g........ 154410 AE003846 174621 .......a...........................................g........ 174562 AE003846 213790 ...........c......... 213770 AE003603 22141 ...........................t................................ 22200 AE003212 788 ..............t............-......a.......g................. 846 AE003843 211063 ...........................t..................t...... 211011 AE003843 312639 ........t....................................... 312592 AE003395 19920 ............................................................ 19861 AE003389 8967 ............................................................ 9026 AE003090 22654 ..........t... 22641 AE003090 22674 ................. 22658 AE003657 222682 ...........c.......t........................................ 222741 AE003019 648 ......t......t.................. 617 AE003594 166750 .........at................................................. 166691 AE003844 146102 ..................................................t......... 146043 AE003451 169882 .................. 169865 AE003796 68203 .................. 68220 AE003756 188259 .................. 188242 AE003193 10738 ................. 10722 AE002656 179535 ................. 179519 AE003506 80304 .......g............. 80284 tmpseq_0 61 gaaggtaaaaa-atacgctgaaattggccgcattgtcggttgttcaagcaacatgatccg 119 AE003788 121950 ...........-................................................ 122008 AE003040 40773 ...........-.....a.........t.......................a........ 40831 AE003066 3608 ...........-...............t....................t..a........ 3550 AE002770 13034 ...........-...............t......t.......g........a........ 12976 AE003786 26829 ...t......c-c..............t..a........g.......a...a.......a 26771 AE003512 297616 ...c......c-c..............t...................a...a........ 297674 AE003846 37011 ...........-...............t................t..a...a........ 37069 AE003846 154409 ..........c-c..............t.......................a........ 154351 AE003846 174561 ..........c-c..............t...................a...a........ 174503 AE003846 250813 ..............a...a.....a.. 250839 AE003603 22201 ..........c-c..........g...t..a................a...a.......a 22259 AE003212 847 ....t......-..c............t.............a.........a........ 905 AE003843 211006 ........t..a...t............a...a........ 210966 AE003843 312593 .........c-c..............t........t..........a...a..a..... 312536 AE003843 211010 ..... 211006 AE003395 19860 ..........c-c...t..........t..............c.g..a...a........ 19802 AE003389 9027 ...........cc...t..........t..............c.g..a...a........ 9086 AE003090 22640 a..........-...............t...................a...a..a..... 22582 AE003657 222742 a..........-...............tg.......g............t.a........ 222800 AE003019 616 .........tc-c..............t.......................a....c... 558 AE003815 92707 ....a...a........ 92691 AE003594 166690 ..........c-c..............a................... 166645 AE003844 146042 ...........-. 146031 tmpseq_0 120 caaagcac-t-gctgtttgtcgagaagaacgaaacacggcgaagaaagccctctatgtcc 177 AE003788 122009 ........-.-................................................. 122066 AE003040 40832 ........-.-a...........a.....a.......................a...... 40889 AE003066 3549 ........-.-............a.............................a...... 3492 AE002770 12975 ........-.-...........ga.............................a..a... 12918 AE003786 26770 ...------.-............a...g..........tg.............a...... 26718 AE003512 297675 ........-.-............a.....g...............g.......a...... 297732 AE002582 10683 ..........a.............................a...... 10637 AE003846 37070 ........-.-............a.............................a...... 37127 AE003846 154350 .......g-.-............a.............................a...... 154293 AE003846 174502 ....t...-.-............a...........g......g.......t..a...... 174445 AE003846 250840 ........-.-............a.............................a...... 250897 AE003603 22260 ...t....-.-............a...g..........tga............a...... 22317 AE003212 906 ........-.-.a......g...a.....................t.......a...... 963 AE003843 210965 ........-.-............a.............................a...... 210908 AE003843 312535 ...c....-.-............a...g..........tg.............a...... 312478 AE003395 19801 ........-.-............a............ 19768 AE003389 9087 ........t.-............a............ 9121 AE003090 22581 ........-.-............a...g..........tg.............a...... 22524 AE003657 222801 ........-.-............a.............................a..... 222857 AE003019 557 ...c....-aa......aa....a..t.............a......t.....a...... 499 AE003815 92690 ........-.-............a.............................a...... 92633 AE003594 166638 ............a...... 166620 AE002772 1062 ......a.....g.....c..tg.............a...... 1104 tmpseq_0 178 aa-cgtggagataaagcg-cttggttcggcaaggcaagaaggagccttttaagccggcga 235 AE003788 122067 ..-...............-......................................... 122124 AE003040 40890 ..-.........c.....-......................................... 40947 AE003066 3491 ..-.........c.....-......................................... 3434 AE002770 12917 ..-.........c.....-......................................t.. 12860 AE003786 26717 ..-.........c.....-.............a........................... 26660 AE003512 297733 ..-.........c.....-.......t.....a...........t............... 297790 AE002582 10636 ..-.........c.....-......................................... 10579 AE003845 87346 ................................t.. 87312 AE003846 37128 ..-.........c.....-...........................g...........a. 37185 AE003846 154292 .. 154291 AE003846 174444 ..-.t.... 174437 AE003846 250898 ..-......---c.....-.......t.....a........ 250933 AE003846 174420 .....-.............a....... 174395 AE003846 174393 ....t.. 174387 AE003603 22318 ..-.........c.....-.............a........................... 22375 AE003212 964 ..-.........cg....-..............a.......................... 1021 AE003843 210907 ..-...............-.......t.....a................a.......... 210850 AE003843 312477 ..-.........c.....-............. 312448 AE003090 22523 ..-....a....c.....-.............a.............g..a.......t.. 22466 AE003657 222857 ..-.......a......................a.......... 222899 AE003019 498 ..-.........c.....-........... 471 AE003815 92632 ..-.........c.g...-.............a.......... 92592 AE003594 166619 ..-...t.....c....c-.........a...----------.................. 166572 AE002772 1105 ..c.....c...c.....c.............a........................... 1164 tmpseq_0 236 cggaactggagaaggagcttcagatagctgaaagcgtggaaactgttcgcaaacgcttag 295 AE003788 122125 ............................................................ 122184 AE003040 40948 ........a................................................... 41007 AE003066 3433 .......ca................................................... 3374 AE002770 12859 ........ag.................................................. 12800 AE003786 26659 ........a.....................c............a...............a 26600 AE003512 297791 ........a.....................c............a...............a 297850 AE002582 10578 .......ta...........a....................................... 10519 AE003845 87311 ........a....c.................................g............ 87252 AE003846 37186 ........t......................................t......t....a 37245 AE003846 174386 ........a...t............. 174361 AE003603 22376 ........a.....................c............a...............a 22435 AE003212 1022 ........a.............................a....a................ 1081 AE003843 210849 ........a.a...................c............a................ 210790 AE003843 312442 ........t.....a 312428 AE003395 19763 ....................a.............................. 19713 AE003389 9126 ....................a.............................. 9176 AE003090 22458 .........t...........a 22437 AE003090 22465 ........ 22458 AE003657 222900 ........a...........................g........ 222944 AE003594 166571 ........a........... 166552 AE002772 1165 .... 1168 tmpseq_0 296 gacaaaacaaccttaatgcgtgcagcccaaataaagtcccccttttgactgttaagcatg 355 AE003788 122185 ............................................................ 122244 AE003040 41008 ...............................-............................ 41066 AE003066 3373 ..............................ga........g................... 3314 AE002770 12799 ..............................ga...............g.......t.... 12740 AE003786 26599 .........................t..c.ga........g................... 26540 AE003512 297851 ............................c..a.....a..g...........g....... 297910 AE002582 10518 ..............................ga........g................... 10459 AE003845 87251 ..............................ga........g..................a 87192 AE003846 37246 ............................ 37273 AE003846 37276 ...........t...... 37293 AE003603 22436 ........c......t.........t..c.ga........g................... 22495 AE003212 1082 ..........t...................gg........g....... 1129 AE003843 210789 .....................a..... 210763 AE003843 210204 ........g................... 210177 AE003843 312427 ......................... 312403 AE003395 19712 ......g.....................c.ga........g................... 19653 AE003389 9177 ......g.....................c.ga........g................... 9236 AE003090 22436 ............................c.ga........g................... 22377 AE003605 264815 .............................ga........g................... 264757 AE003732 119015 ................... 118997 tmpseq_0 356 tggcaaagc-gaatcgaatatgccaagattcccaaggactggcctgt-ggagatgtggca 413 AE003788 122245 .........-.....................................-............ 122302 AE003040 41067 .........-.....................................-.....a...... 41124 AE003066 3313 .........-...c............................gt...-.....a...... 3256 AE002770 12739 .........t.........................c...........-.....a...... 12681 AE003786 26539 .........-..c................a.a...............-.....a.....g 26482 AE003512 297911 .........-...................a.a.............a.-.....a....tg 297968 AE002582 10458 .........-...c............................gt...-.....a...... 10401 AE003845 87191 .........-....................t................-.....a...... 87134 AE003846 37294 .........-..............t.... 37321 AE003603 22496 ...... 22501 AE003603 22508 ........c.....a-.....a.....g 22534 AE003212 1128 ...........................t....-.....a.....g 1171 AE003843 210176 .........-a..........---.....a.a...............-.....a.....g 210122 AE003843 312371 ...............-.....ac..aag 312345 AE003395 19652 .........-a.t.t.......a......a.a.......g.......-.....a.....g 19595 AE003389 9237 .c.......-............a.......t................g.....a...... 9295 AE003090 22376 .........-...................a.a..........t....-.....a...c.g 22319 AE003605 264756 .........-....a................................-.....a.....g 264699 AE003784 186645 . 186645 AE003477 267305 ................. 267321 tmpseq_0 414 caacattttgtggtcagatgagaccaaaattgtgttgtttggtgggaaaggctcttggtc 473 AE003788 122303 ............................................................ 122362 AE003040 41125 ............................................................ 41184 AE003066 3255 .......................................c.....a.............. 3196 AE002770 12680 ....................................a.......a............... 12621 AE003786 26481 .......................g...............................c.... 26422 AE003512 297969 .......................t...............................c.... 298028 AE002582 10400 .............................................a.............. 10341 AE003845 87133 .................................c...................tc..... 87074 AE003846 154294 .........................t......a.... 154258 AE003846 250937 ..........................c.... 250967 AE003603 22535 ....g..................g...............................c..a. 22594 AE003212 1172 .......................................................c.... 1231 AE003843 210121 .......................g.............................t.c.... 210062 AE003843 312344 ..................... 312324 AE003395 19594 a........t...........a.g.............c.................c.... 19535 AE003389 9296 .......................g.............c.................c.... 9355 AE003090 22318 ...................a...g...............................c.... 22259 AE003605 264698 ......................................... 264658 AE003605 264652 ........ 264645 AE003815 92588 ........g.................................... 92544 AE003652 159253 ................. 159237 AE003784 186644 ................ 186629 tmpseq_0 474 ttatgttcgtcgtccaccacga--------actgaatttaatcctc-g-cttcaccttta 523 AE003788 122363 ......................--------................-.-........... 122412 AE003040 41185 ........ag............--------.......a........-.-........... 41234 AE003066 3195 .........g..........a.--------.......a........-.-........... 3146 AE002770 12620 .........g............--------.......a.....t..-.-........... 12571 AE003786 26421 .........g............--------.......a........-.-........... 26372 AE003512 298029 .........g............cgtccacc...a...a........-.-........... 298086 AE002582 10340 .........g..........a.--------.......a.......t-.-........... 10291 AE003845 87073 .........g............--------.......a........-.-........... 87024 AE003846 154257 .........g.ta.....g...--------.......a........-.g........... 154207 AE003846 250968 .a.......g............--------..c..... 250997 AE003603 22595 .........g..........a.--------.......a........-.-........... 22644 AE003212 1232 .........g............--------..a....a........g.-........... 1282 AE003843 210061 .........g............--------.......a........-a-........... 210012 AE003843 312324 .......g..c.........--------.......a.....a..-.-........... 312277 AE003395 19534 .........g............--------.......a........-.-t.a........ 19485 AE003389 9356 ....... 9362 AE003090 22258 .........g............--------.......a........-.g........... 22208 AE003605 264644 .........g.....t......--------.......a........-.-........... 264595 AE003815 92543 .........g............--------.......a.....a..-.-........... 92494 AE003638 84624 ... 84622 AE003608 216061 ..... 216065 AE003510 192026 ..... 192022 AE003506 201078 .... 201081 tmpseq_0 524 agatctttaagattagatgtgttactaa-tttttttatttcgattgaaaatcattgtagt 582 AE003788 122413 ............................-............................... 122471 AE003040 41235 .. 41236 AE003040 41795 .......c.........-...........t................... 41842 AE003066 3145 .. 3144 AE003066 2508 .......c.......---...........................g... 2463 AE002770 12570 .. 12569 AE003786 26371 .. 26370 AE003786 25734 .........-............................... 25695 AE003512 298087 .. 298088 AE003512 298698 .......c.........-............................... 298745 AE002582 10290 .. 10289 AE002582 9658 .......c.........-............................... 9611 AE003845 87023 .. 87022 AE003845 86386 .........-..........................t.... 86347 AE003846 154206 .. 154205 AE003846 37876 .......c.........t............................... 37924 AE003603 22645 .. 22646 AE003603 23273 .........-....g.......................... 23312 AE003212 1283 .. 1284 AE003843 210011 .. 210010 AE003843 311840 .......c.........-....g.......................... 311793 AE003843 301184 .......c........t-............................... 301231 AE003843 312276 ... 312274 AE003395 19484 ... 19482 AE003389 9836 .......c.........-...cg.......................... 9883 AE003090 22207 .. 22206 AE003090 21614 .......c.........-......................t........ 21567 AE003605 264594 .. 264593 AE003605 263955 .....t...-............................... 263916 AE003815 92493 .. 92492 AE002772 1269 .......c.........-....g................... 1309 AE002837 19949 .......c.........-............................... 19996 AE003787 211601 ....c.........-............................... 211645 AE002942 38 .........-............................... 77 AE003574 207863 .......c.........-............................. 207818 AE003147 11656 .......ac.....a..-...........ta................c. 11609 AE003573 192944 .......a.........-............ 192972 AE003638 84621 ..............t..a...... 84598 AE003445 181388 \-.................. 181371 AE003559 55830 .......-........... 55847 AE003796 202104 .................. 202087 AE003656 122170 \-..............a...... 122190 AE003650 35640 .-................ 35624 AE003608 216066 ............ 216077 AE003510 192021 ............ 192010 AE003506 201082 ............. 201094 AE003499 5553 ................. 5569 AE003828 207899 ...-.............. 207915 AE003599 238297 ............g........ 238317 AE003772 101930 \-.......t............. 101950 tmpseq_0 583 att 585 AE003788 122472 ... 122474 AE003040 41843 ... 41845 AE003066 2462 ... 2460 AE003786 25694 ... 25692 AE003512 298746 ... 298748 AE002582 9610 ... 9608 AE003845 86346 ... 86344 AE003846 37925 ... 37927 AE003603 23313 ... 23315 AE003843 311792 ... 311790 AE003843 301232 ... 301234 AE003389 9884 ... 9886 AE003090 21566 ... 21564 AE003605 263915 ... 263913 AE002837 19997 ... 19999 AE003787 211646 ... 211648 AE002942 78 ... 80 AE003147 11608 ... 11606
