!transposon_sequence_set.README.v9.41 !April 25 2005 !Comments, corrections to ma11@gen.cam.ac.uk TRANSPOSON SEQUENCE CANONICAL SETS FOR DROSOPHILA This is a file of 'canonical' sequences of the transposable elements from Drosophila. History: These sequences were originally compiled by Takis Benos (EBI), Leyla Bayraktaroglu (Harvard) and Michael Ashburner (EBI & Cambridge) with help from Aubrey de Grey (Cambridge), Joe Chillemi (Harvard) and Martin Reese (LBL). We thank Suzi Lewis (Berkeley) for inspiration and discussion, and Guochun Liao (Berkeley) for his repeat sequence set and newly discovered transposable element sequences from the Berkeley P1 clones, and Lynn Crosby (Harvard) for her annotations of some elements. Subsequent curation of these sequences has been in the context of the Drosophila Genome Project and was a collaboration between M. Ashburner (Cambridge), Josh Kaminker (Berkeley) and Casey Bergman (Berkeley). From Version 8.0 this set has been maintained by Michael Ashburner and Casey Bergman in Cambridge. Other sequence data sets originating from M. Ashburner are no longer maintained. Future plans: We plan to make each of the melanogaster sequences a real sequence from the Release 4 melanogaster genome sequence and to enrich the annotation. For elements that are not 'complete' in Release 4 we will construct a 'consensus' sequence, either as a mosaic of two or more sequences or as a 'majority rule' consensus of aligned elements. We thank Margi Butler, Elena Casacuberta, Madeline Crosby, Bob Levis, Mary-Lou Pardue, Kevin O'Hare, Horacio Naveira, Dmitri Petrov, Steve Schaeffer, Todd Schlenke, Alfredo Vilesante & the authors of REBASE for sequences and/or annotations. Errors or additions to ma11@gen.cam.ac.uk, please. =============================================================================== March 16 2004. v.8.0 ==================== 1. Updates of FB identifiers. 2. Added from REPBASE (drorep.ref.4.5.3, January 2003): BS3, BS4, Doc4-element, Doc5-element, Fw2, Fw3, Helitron, R1-2, Tc1-2, G5A, G7, accord2, gypsy7, gypsy8, gypsy9, gypsy10, gypsy11, gypsy12, invader6. 3. ORF1 of Juan added from Repbase record. 4. A new line for synonyms has been introduced into records, e.g.: SY synonym:BEL This is not a complete list of synonyms (for which see FlyBase), just those in widespread use. April 6 2004. v.9.0 =================== 1. New records for elements from species other than D. melanogaster: Dana\Tom, Dvir\Dv, Dhyd\Bungy, Dbuz\Osvaldo, Dkoe\Gandalf, Dmau\mariner, Dhyd\Minos, Dfun\Isfun-1, Dsub\bilbo, Dsil\Loa, Dhet\Uhu, Dvir\Ulysses, Dsim\ninja, Dvir\Helena, Dvir\Penelope, Dvir\Tv1, Dvir\Tel, Dmir\TRAM, Dmir\TRIM, Dvir\Paris, Dmir\spock, Dmir\worf, Dwil\Vege, Dwil\Mar, Damb\P-element_T, Dbif\P-element_M, Dbif\P-element_O, Dsub\SGM, Ddip\Bari1, Dpse\mini-me, Dbuz\BuT1, Dbuz\BuT2, Dbuz\BuT3, Dbuz\BuT4, Dbuz\BuT5, Dbuz\BuT6, Dbuz\INE-1, Dbuz\ISBu2, Dbuz\Galileo, Dbuz\Kepler, Dbuz\Newton, Dyak\TART, Dyak\HeT-A, Dvir\TART, Dvir\HeT-A. 2. D. melanogaster Helena consensus sequence added. The Circe sequence has been replaced from a consensus from A. Villesante. 3. The micropia sequence has been replaced by one that lacks the 4bp deletion within the CDS present in the previous record. 4. New sequences for TART-A and TART-C subfamilies added (the only previous TART sequence (U14101) was TART-B). The sequences for Tc3 & Beagle2 have been extracted from the R3 genome and added. The sequence of the Q element has been extracted from the R1 genome and added. 5. Annotations improved for some of the sequences. 6. All annotations now use SO terms. The syntax is: FT SO_feature ; :.. e.g.: FT SO_feature five_prime_UTR ; SO:0000204:1..730 April 7 2004. v.9.1 =================== 1. The following R1-element variants have been added: Dnet\R1A, Dtak\R1A2, Dmer\R1A3, Dnet\R1B. The original melanogaster element has been re-named:R1A1-element. April 7 2004. v.9.2 =================== 1. The Dbuz\ISBu3, Dsub\GEM and Dvir\Uvir elements have been added. April 18 2004. v.9.2.2 ====================== 1. Update of annotation of TART-C. 2. Dtei\I-element sequence added. May 1 2004. v.9.2.3 =================== 1. Added prygun as a synonym of Tirant. June 23 2004. v.9.2.4 ===================== 1. accord2 and qbert found to be the same element; accord2 sequence (AC008256) removed and qbert sequence (AF541947) renamed as accord2. September 3 2004. v.9.2.5 ========================= 1. Added Doc5-element as synonym of Porto1. December 10 2004. v.9.3 ======================= 1. Added the cDNA sequence for a D. melanogaster Osvaldo-like element. April 22 2005. v.9.4 ==================== 1. Updates on FBgn identifiers. 2. Added sequence of the TAHRE element. April 22 2005. v.9.41 ===================== 1. A formatting error in the Helana sequence corrected. The current data set includes 179 elements: FB gene ID Symbol EMBL Size Comment Retroviral elements: FBgn0000004 17.6 X01472 7439bp complete FBgn0000007 1731 X07656 4648bp complete FBgn0000005 297 X03431 6995bp complete FBgn0005384 3S18 U23420 6126bp complete FBgn0000006 412 nnnnnnnn 7567bp complete FBgn0063447 accord nnnnnnnn 7404bp complete FBgn0063782 accord2 AF541947 7650bp complete FBgn0010103 aurora-element AB022762 4263bp ?complete FBgn0000199 blood nnnnnnnn 7410bp complete FBgn0010302 Burdock U89994 6411bp complete FBgn0022937 Circe nnnnnnnn 7450bp complete FBgn0000349 copia X02599 5143bp complete FBgn0043969 diver AC004377 6112bp complete FBgn0063439 diver2 nnnnnnnn 4917bp complete FBgn0062343 Dm88 nnnnnnnn 4558bp complete FBgn0014947 flea Z27119 5034bp complete FBgn0061513 frogger AF492763 2483bp ?complete FBgn0015945 GATE AJ010298 8507bp complete FBgn0063436 gtwin nnnnnnnn 7411bp complete FBgn0001167 gypsy M12927 7469bp complete FBgn0063435 gypsy2 nnnnnnnn 6841bp complete FBgn0063434 gypsy3 nnnnnnnn 6973bp complete FBgn0063433 gypsy4 nnnnnnnn 7369bp complete FBgn0063432 gypsy5 nnnnnnnn 6852bp complete FBgn0063431 gypsy6 nnnnnnnn 7826bp complete FBgn0067384 gypsy7 AE003788 5486bp incomplete FBgn0067383 gypsy8 AE003788 4955bp incomplete FBgn0067382 gypsy9 AE002591 5349bp incomplete FBgn0067387 gypsy10 nnnnnnnn 6006bp incomplete FBgn0067386 gypsy11 nnnnnnnn 4428bp incomplete FBgn0067385 gypsy12 nnnnnnnn 10218bp incomplete FBgn0001207 HMS-Beagle AF365402 7062bp complete FBgnnnnnnnn HMS-Beagle2 nnnnnnnn 7220bp complete FBgn0026065 Idefix AJ009736 7411bp complete FBgn0063430 invader1 nnnnnnnn 4032bp complete FBgn0063429 invader2 nnnnnnnn 5124bp complete FBgn0063428 invader3 nnnnnnnn 5484bp complete FBgn0063427 invader4 nnnnnnnn 3105bp complete FBgn0063426 invader5 nnnnnnnn 4038bp complete FBgn0067380 invader6 NT_033778 4885bp incomplete FBgn0063919 Max-element AJ487856 8556bp complete FBgn0063917 McClintock AF541948 6450bp complete FBgn0002697 mdg1 X59545 7480bp complete FBgn0002698 mdg3 X95908 5519bp complete FBgn0002745 micropia X14037,X15066 5461bp complete FBgn0003007 opus AY180918 7521bp complete FBgn0063755 Osvaldo AY089271 1543bp incomplete FBgn0044355 Quasimodo AF364550 7387bp complete FBgn0000155 roo AY180917 9092bp complete FBgn0063394 rooA nnnnnnnn 7621bp complete FBgn0061485 rover AF492764 7318bp complete FBgn0003490 springer AF364549 7546bp complete FBgn0003519 Stalker AF420242 7256bp complete FBgn0063455 Stalker2 nnnnnnnn 7672bp complete FBgn0063454 Stalker3 nnnnnnnn 372bp LTR FBgn0063897 Stalker4 AF541949 7359bp complete FBgn0045970 Tabor AC007146 7345bp complete FBgn0004082 Tirant nnnnnnnn 8526bp complete FBgn0063450 Tom1 nnnnnnnn 410bp LTR FBgn0040267 Transpac AF222049 5249bp complete FBgn0023131 ZAM AJ000387 8435bp complete FBgn0004357 Dana\Tom Z24451 7060bp complete FBgn0013796 Dbuz\Osvaldo AJ133521 9045bp complete FBgn0005772 Dmir\TRAM Y08905 3452bp ?complete FBgn0004642 Dmir\TRIM X59239 3111bp ?complete FBgn0015168 Dsim\ninja D83207 6644bp complete FBgn0004146 Dvir\Ulysses X56645 10653bp complete FBgn0020675 Dvir\Tel AF009439 2485bp incomplete FBgn0013099 Dvir\Tv1 AF056940 6898bp complete non-LTR retrotransposons: FBgn0063440 baggins nnnnnnnn 5453bp complete FBgn0000224 BS nnnnnnnn 5142bp complete FBgn0067624 BS3 nnnnnnnn 1790bp ?complete FBgn0067623 BS4 nnnnnnnn 754bp incomplete FBgn0063594 Cr1a nnnnnnnn 4470bp complete FBgn0000481 Doc X17551 4725bp ?incomplete FBgn0063534 Doc2-element nnnnnnnn 4789bp complete FBgn0063533 Doc3-element nnnnnnnn 4740bp complete FBgn0069587 Doc4-element nnnnnnnn 2791bp incomplete FBgn0000652 F-element AC005198 4708bp complete FBgn0067421 Fw2 nnnnnnnn 3961bp ?complete FBgn0067420 Fw3 nnnnnnnn 3132bp ?complete FBgn0001100 G-element X06950 4346bp ?complete FBgn0063507 G2 nnnnnnnn 3102bp complete FBgn0063506 G3 nnnnnnnn 4605bp complete FBgn0063505 G4 nnnnnnnn 3856bp complete FBgn0063504 G5 nnnnnnnn 4856bp complete FBgn0069433 G5A nnnnnnnn 2841bp incomplete FBgn0063503 G6 nnnnnnnn 2042bp complete FBgn0067419 G7 AC003788 1192bp incomplete FBgn0020425 Helena nnnnnnnn 1318bp incomplete FBgn0004141 HeT-A U06920 6083bp complete FBgn0001249 I-element M14954 5371bp complete FBgn0043055 Ivk nnnnnnnn 5402bp complete FBgn0046110 Juan AY180919 4236bp complete FBgn0001283 jockey M22874 5020bp complete FBgn0063425 jockey2 nnnnnnnn 3428bp complete FBgn0046701 Penelope AF418572 804bp incomplete FBgn0015786 Porto1 nnnnnnnn 4682bp ?complete FBgn0063900 Q-element AE002612 759bp incomplete FBgn0003908 R1A1-element X51968 5356bp complete FBgn0067405 R1-2 nnnnnnnn 3216bp incomplete FBgn0003909 R2-element X51967 3607bp complete FBgn0041728 Rt1a AJ278684 5108bp complete FBgn0063467 Rt1c nnnnnnnn 5443bp complete FBgn0042682 Rt1b AF281636 5171bp complete FBgn0069343 TAHRE AJ542581 10463bp complete FBgn0004904 TART-A AY561850 13424bp complete FBgn0004904 TART-B U14101 10654bp complete FBgn0004904 TART-C AY600955 11124bp complete FBgn0042231 X-element AF237761 4740bp complete FBgn0013836 Dmer\R1A3 AF015277 3772bp incomplete FBgn0015678 Dmir\spock AY144571 4952bp ?complete FBgn0064494 Dmir\worf AY144572 4174bp ?complete FBgn0013854 Dnet\R1A AF248067 1757bp incomplete FBgn0013854 Dnet\R1B AF248068 2038bp incomplete FBgnnnnnnnn Dpse\mini-me AC131959 4622bp complete FBgn0005661 Dsil\Loa X60177 7779bp ?complete FBgn0023239 Dsub\bilbo U73803 5540bp complete FBgn0013903 Dtak\R1A2 U23198 1753bp incomplete FBgn0013017 Dtei\I-element M28878 5386bp complete FBgn0011601 Dvir\Helena U26847 691bp incomplete FBgn0015679 Dvir\Penelope U49102 4158bp ?complete FBgn0067468 Dvir\HeT-A AY369259 6610bp complete FBgn0066148 Dvir\TART AY219709 8500bp complete FBgn0067460 Dvir\Uvir AY369259 6564bp ?complete FBgn0024768 Dyak\HeT-A AF043258 5691bp complete FBgn0026443 Dyak\TART AF468026 8444bp incomplete SINE-like elements: FBgn0026416 INE-1 U66884 611bp ?incomplete FBgn0012361 Dhyd\Bungy U14600 227bp ?complete IR-elements: FBgn0005673 1360 nnnnnnnn 3409bp complete FBgn0005773 Bari1 X67681 1728bp complete FBgn0064134 Bari2 AF541951 1064bp complete FBgn0001181 HB X01748 1653bp ?incomplete FBgn0001210 hobo M69216 2959bp complete FBgn0014967 hopper X80025 1435bp incomplete FBgn0067381 hopper2 AF541950 1593bp incomplete FBgn0063402 looper1 nnnnnnnn 1881bp incomplete FBgn0063401 mariner2 nnnnnnnn 912bp complete FBgn0002949 NOF X15469;X51937 4347bp complete FBgn0003055 P-element X06779 2907bp complete FBgn0003122 pogo X59837 2121bp complete FBgn0004905 S-element U33463 1736bp ?incomplete FBgn0063466 S2 nnnnnnnn 1735bp complete FBgn0026410 Tc1 nnnnnnnn 1666bp complete FBgn0069340 Tc1-2 nnnnnnnn 1644bp complete FBgn0061191 Tc3 AC009537 1743bp complete FBgn0063372 transib1 nnnnnnnn 2167bp complete FBgn0063371 transib2 nnnnnnnn 2844bp complete FBgn0063370 transib3 nnnnnnnn 2883bp complete FBgn0063369 transib4 nnnnnnnn 2656bp complete FBgn0020218 Damb\P-element_T AF012414 3329bp ?complete FBgn0012207 Dbif\P-element_M X60990 2935bp complete FBgn0012207 Dbif\P-element_O X71634 2986bp complete FBgn0063576 Dbuz\BuT1 AF162798 769bp ?incomplete FBgn0063575 Dbuz\BuT2 AF368884 2775bp ?incomplete FBgn0063575 Dbuz\BuT3 AF368870 795bp ?incomplete FBgn0063573 Dbuz\BuT4 AF368868 1447bp ?incomplete FBgn0063572 Dbuz\BuT5 AF368868 669bp ?incomplete FBgn0069879 Dbuz\BuT6 AY187768 387bp ?incomplete FBgn0045754 Dbuz\INE-1 AF368900 1467bp ?incomplete FBgn0045754 Dbuz\ISBu2 AF368867 726bp ?incomplete FBgn0045754 Dbuz\ISBu3 AY313771 993bp ?incomplete FBgn0020486 Ddip\Bari1 Y13852 1676bp incomplete FBgn0044997 Dfun\Isfun-1 AJ309320 928bp incomplete FBgn0003948 Dhet\Uhu X63028 1658bp ?complete FBgn0010242 Dhyd\Minos Z29098 1773bp complete FBgn0014755 Dkoe\Gandalf U29466 979bp incomplete FBgn0002651 Dmau\mariner M14653 1286bp complete FBgn0026463 Dsub\GEM AJ131629 1730bp ?complete FBgn0015678 Dvir\Paris Z49253 1728bp complete MITE elements: FBgn0066141 Dwil\Mar AF518731 610bp ?complete FBgn0066140 Dwil\Vege AF518730 884bp ?complete FBgn0069871 Dsub\SGM AF043638 823bp ?complete Foldback elements: FBgn0000638 FB V00246 1106bp ?incomplete FBgn0027840 Dbuz\Galileo AY187769 2304bp ?incomplete FBgn0063570 Dbuz\Kepler AF368884 722bp ?incomplete FBgn0063569 Dbuz\Newton AF368890 1510bp ?incomplete Helitron elements: FBgn0067418 Helitron AE002840 564bp ?incomplete Class uncertain: FBgn0000513 Dvir\Dv X03936 845bp ?incomplete ===============================================================================