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% |