Table 2 W-chromosome-specific repeats of S. mansoni
GenBank accession number | Name | Length (bp) | Percentage female hits | Repeat familya | Transcription evidence | FISH localization | Copy number estimateb | Reference |
|---|---|---|---|---|---|---|---|---|
U12442 | SMAlphafem-1 | 338 | 99.86 | SMAlpha retroposon | RT-PCR | p-arm | 60,000 - 70,000 | |
J04665 | W1 | 482 | 100 | Retro | Middle of q-arm at frontier between heterochromatin and euchromatin as satellite, middle of q-arm | 500 | ||
U10109 | W2 | 715 | 100 | 400 | [62] | |||
HQ880214 | W3 | 786 | 100 | LTR, highly similar to W2, highly similar to R = 407 | No transcription (RT-PCR) | As satellite in the middle of q-arm at frontier between heterochromatin and euchromatin or also in the pericentromeric region | 200 | |
HQ880209 | W4 | 1132 | 99.52 | Highly similar to R = 879 | RT-PCR | Same location as W1 | 800 | |
HQ880217 | W5 | 1129 | 99.27 | LTR, similar to Perere-2, identical to R = 564 | EST and RT-PCR | Either at the frontier of heterochromatin and euchromatin of the q-arm or in the pericentromeric region, or at both locations | ||
HQ880215 | W6 | 310 | 99.88 | Retro | EST | In the pericentromeric region | ||
HQ880210 | W7 | 1000 | 100 | DNA transposon, 97% identical to GenBank accession number XP_002570219 (hypothetical protein Smp_186230) | In the pericentromeric region | |||
HQ880218 | W8 | 266 | 99.97 | Tandem repeat (previously described as TR266), DNA transposon | Either at the frontier of heterochromatin and euchromatin of the q-arm or in the pericentromeric region | |||
HQ880211 | W9 | 803 | 100 | LINE2, similar to SjR2 retrotransposon | EST | |||
HQ880212 | W10 | 682 | 100 | LTR | ||||
HQ880213 | W11 | 376 | 100 | LINE, similar to R = 170 | ||||
HQ880216 | W12 | 264 | 100 | Retro, 97 to 100% identical to several hypothetical S.m. proteins | ||||
HQ880219 | W13 | 258 | 100 | Retro | In the middle of the heterochromatic part of the q-arm as satellite | |||
HQ880220 | W14 | 209 | 100 | DNA transposon, similar to R = 170 | ||||
HQ880221 | W15 | 185 | 96.62 | DNA transposon | ||||
HQ880222 | W16 | 164 | 100 | Similar to R = 116 | ||||
HQ880223 | W17 | 160 | 100 | LTR | ||||
HQ880224 | W18 | 160 | 100 | LTR | EST | |||
HQ880225 | W19 | 139 | 100 | Retro, 100% identical to GenBank accession number XP_002569391 (hypothetical protein Smp_181820) | EST | |||
HQ880226 | W20 | 138 | 100 | |||||
HQ880227 | W21 | 138 | 99.84 | DNA transposon, similar to R = 116 | ||||
HQ880228 | W22 | 132 | 100 | DNA transposon | ||||
HQ880229 | W23 | 125 | 100 | DNA transposon | ||||
HQ880230 | W24 | 115 | 99.56 | Retro, similar to Sh122 repeat and R = 31 | ||||
HQ880231 | W25 | 112 | 99.65 | LTR | ||||
HQ880232 | W26 | 111 | 100 | DNA transposon | ||||
HQ880233 | W27 | 110 | 100 | DNA transposon, similar to R = 133 and Sh microsatellite C2 | ||||
HQ880234 | W28 | 108 | 100 | Similar to Sh microsatellite C140 | ||||
HQ880235 | W29 | 97 | 100 | Similar to Sb Sbov20 repeat | ||||
HQ880236 | W30 | 96 | 99.05 | LTR | ||||
HQ880237 | W31 | 92 | 100 | LTR | ||||
HQ880238 | W32 | 89 | 96.88 | DNA transposon | ||||
HQ880239 | W33 | 86 | 99.86 | LTR | ||||
HQ880240 | W34 | 82 | 100 | DNA transposon | ||||
HQ880241 | W35 | 80 | 100 | Retro | EST |