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Table 1 Summary of VIPER copy analyzes from the distinct genomes presenting at least one potentially encoding copy

From: Study of VIPER and TATE in kinetoplastids and the evolution of tyrosine recombinase retrotransposons

Species No of analyzed copies No of copies with at least one potentially encoding ORF No of copies with the three potentially encoding ORFs No of potential encoding copies with YR and RT/RT related domains No of copies with SDRs Structure of SDRs size in base pairs, percentage of identity No of putative autonomous copiesa Mean identity among copies in nu (total) and aa levels (for each ORF)b
B. saltans 10 7 4 1 1c 5′ → A1 3′ → B1 → B2 → A2 A: 83 bp, 100%; B: 57 bp, 100% 0 nu: na Gag-like: na YR (5, 150 aa): 32.7% RT/RH (7, 294 aa): 33%
T. cruzi Dm28c 15 15 12 12 7 5′ → A1 3′ → B1 → A2 → B2 A: 173 bp, 100%; B: 219 bp, 100% 7 nu (13): 95% Gag-like (13, 492 aa): 97.9% YR (15, 338 aa): 98.2% RT/RH (14, 948 aa): 96.8%
T. theileri 15 5 3 2 1 (incomplete) 5′ absent 3′ → A1 → A2 A: 95 bp, 100%; 0 nu: na Gag-like (3, 240 aa): 31.1% YR (2, 272 aa): 47.1% RT/RH (5, 701 aa): 57.6%
C. fasciculata 15 7 4 1 3 5′ → A1 3′ → B1 → A2 → B2 1: (A: 136 bp, 99%; B: 288 bp, 100%) 2: (A: 144 bp, 100%; B: 308 bp, 100%) 3: (A: 414 bp, 93%; B: 294 bp, 99%) 1 nu: na Gag -like (3, 240 aa): 31.1% YR (5, 278 aa): 41.6% RT/RH (5, 701 aa): 40.8%
C. mellificae 15 4 1 0 ? all copies in short or end of contigs na 0 nu: na Gag-like: na YR (3, 507 aa): 100% RT/RH (2, 393 aa): 43%
A. deanei 4 4 1 0 0 na 0 nu: na Gag-like (3, 240 aa): 31.1% YR (2, 272 aa): 48.4% RT/RH (6, 611 aa): 26.7%
Lep. pyrrhocoris 15 14 2 0 0 na 0 nu: na Gag-like (2, 396 aa): 99.7% YR (13, 430 aa): 61.6% RT/RH (11, 1091 aa): 72.1%
  1. aputative autonomous copies are those containing the tree expected ORFs plus direct repeats
  2. bidentity was estimated only for regions with confident alignment. The number of sequences and the size of alignment is shown in parenthesis
  3. cthe pattern of repeats is distinct than expected and the distance from the end of the ORF and the next repeat is quite large and unexpected. Thus, it is not possible to state whether this repetition is indeed part of the element