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Table 2 Summary of manual annotations

From: Analysis of 14 BAC sequences from the Aedes aegyptigenome: a benchmark for genome annotation and assembly

BAC number Transcript number Aedes transcript Supercontig Contig Sequencing of cDNA Differences in annotation between manual annotation (MA) and gene build Replicated transcript in Aedes assembly
        Aedes transcript Supercontig Contig Notes
1 1 AAEL013103 1.789 24718 - - AAEL014498 1.1137 29191 -
  2 AAEL013088 1.789 24718 - - AAEL014499 1.1137 29191 -
  3 AAEL013092 1.789 24718 - - AAEL014500 1.1137 29189 -
  4 AAEL013582 1.875 25903 Identical Longer 5' in MA AAEL015005 1.1393 31331 5' end of transcript matched MA
        AAEL013099 1.789 24718 3' end of transcript matched MA
  5* AAEL015006 1.1393 31331 Identical - AAEL013097 1.789 24718 Identical to AAEL013097
        AAEL013583 1.875 25903 Identical to AAEL013583
  6 AAEL013098 1.789 24719 - Only 3' coding region lines up AAEL013098 1.789 24719 Only 3' coding region lines up
3 7* AAEL009524 1.403 16729 - - AAEL000392 1.7 624 -
4 8 AAEL008104 1.301 13837 - - - - - -
  9 AAEL008110 1.301 13837 Identical Different intron/exon structure - - - -
  10 AAEL008114 1.301 13837 Identical 3' longer in MA - - - -
  11 AAEL008115 1.301 13837 - - - - - -
  12 AAEL008103 1.301 13837 Identical - - - - -
  13 AAEL008100 1.301 13837 - - - - - -
5 14* AAEL014561 1.1166 29449 Identical - Transcript missing 1.216 10858 -
  15 AAEL014559 1.1166 29447 Identical - AAEL006682 1.216 10863 -
6 16* AAEL014711 1.1232 30069 Identical Different intron/exon structure AAEL014491 1.1132 29135 -
  17 AAEL014712 1.1232 30070 - - AAEL014495 1.1132 29137 -
  18 AAEL014709 1.1232 30070 Identical - AAEL014494 1.1132 29136 -
7 19 AAEL006423 1.204 10417 - - - - - -
  20 No transcript 1.204 10417 - Similar to AAEL003685 - - - -
  21* AAEL006424 1.204 10417 Identical - - - - -
  22 AAEL006417 1.204 10417 Identical - - - - -
8 23* AAEL006019 1.186 9724 Identical - AAEL008297 1.312 14138 -
9 24* AAEL010573 1.488 18854 Identical - AAEL000068 1.1 48 -
  25 AAEL010594 1.488 18854 Identical - AAEL000046 1.1 48 -
  26 AAEL010587 1.488 18855 Identical - AAEL000020 1.1 48 -
  27 AAEL010575 1.488 18855 Identical - AAEL000076 1.1 48 -
  28 AAEL000054 1.1 48 - - AAEL010578 1.488 18855 -
  29 AAEL010595 1.488 18855 - - - - - -
10 30 AAEL007897 1.288 13401 Identical Extra 3' exon in MA - - - -
  31 AAEL007893 1.288 13401 - - - - - -
  32 AAEL007907 1.288 13401 - - - - - -
11 33 AAEL002503 1.59 3864 - - - - - -
  34 AAEL002532 1.59 3866 Identical 3' exon absent in MA - - - -
  35 AAEL002534 1.59 3863 - - - - - -
  36 AAEL002523 1.59 3864 - - - - - -
12 37 AAEL001205 1.25 1764 - Longer 5' in MA - - - -
  38 AAEL001215 1.25 1764 Identical Longer 3' in MA - - - -
  39 AAEL001215 1.25 1764 Identical - - - - -
  40 AAEL001198 1.25 1761 - - - - - -
  41 AAEL001201 1.25 1764 - - - - - -
  42 AAEL001210 1.25 1764 - - - - - -
13 43 AAEL008780 1.348 15270 - - AAEL001693 1.39 2713 -
  44 AAEL008781 1.348 15269 - - AAEL001703 1.39 2712 -
  45 AAEL008769 1.348 15269 - - AAEL001701 1.39 2711 -
  46 AAEL008778 1.348 15269 - - AAEL001681 1.39 2711 -
14 47 AAEL005065 1.140 7865 - - AAEL005223 1.146 8136 -
  48 AAEL005085 1.140 7866 - - AAEL005220 1.146 8136 -
  49 AEL005237 1.146 8136 - - AAEL005088 1.140 7865 -
  50 AAEL005229 1.146 8136 - - AAEL005059 1.140 7865 -
  51 AAEL005218 1.146 8136 - - No gene build annotation 1.140 7865 -
  1. The 51 manually annotated transcripts (Transcript number) from each BAC clone (BAC number) along with their corresponding transcript (Gene build transcript) from the gene build (AaegL1) and their location (supercontig, contig) are listed along with cDNA amplicons if sequenced. Transcripts that were replicated in the genome are also listed along with their corresponding gene build transcript, location and differences with the manual annotation (MA) if any. Manual annotations marked with an asterisk indicate single-copy cDNA-derived genetic markers used to isolate the BAC.
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Genome Biology

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