Table 2.

Characteristics of LTR Retrotransposons from Hemiascomycetous Yeasts

Species Element ORF1 size (AA) ORF2 size (AA) Frameshift LTR
name[iii] size (bp) copy[iv] number size (bp) terminal inverted repeats
Ty1-like elements
 S. cerevisiae Ty1-br5917324351321 CUUAGGC 332 TG…CA
 S. cerevisiae Ty2-b5959134311359 CUUAGGC 332 TGT…ACA
 K. marxianus Tkm1 599410–154211339 CUUAGGC 385 TGTTG…CAACA
 S. exiguus Tse1 569115–203831235 CUUAGGC 424 TGA…TCA
 S. kluyveri Tsk1 5905 84351320 CUUAGGC 322–333 TG…CA
 K. lactis Tkl1.1[i] 5425 1202[v] 1335[vi] CUUAGGC 393–398 TGTTG…AAACA or TGTTG…CAACA
 K. lactis Tkl1.2[i] [ii]  1391[vii] CUUAGGC ?…AAACA[viii]
 S. servazzii Tss1[i] [ii] 1–2
Ty4-like elements
 S. cerevisiae Ty4-j6227 33631440 CUUAGGC 371 TGTTG…CAACA
 S. bayanus Tsu4 609515–203581433 CUUAGGC 321 TGTTG…CAACA
Ty5-like elements
 D. hansenii Tdh5 5349∼20–1490 – 457 TGTTGAA…TTCAACA
 P. angusta Tpa5 488310–15–1417 – 322 TGTTG…CAACA
 S. exiguus Tse5.1 52868–10–1531 – 370 TGTTG…CAACA
 C. albicans Tca555880–5–1477 – 685 TGTTG…CAACA
 S. paradoxus Ty5537610–15–1698 – 251 TGTTGA…TCAACA
Tca2-like elements
 D. hansenii Tdh2 59283–53361340no, stop codon379 TGTTGG…CCAATA
 C. albicans Tca264265–103241576no, stop codon280 TGTTGG…CCATCA
gypsy elements
 S. cerevisiae Ty3-g5351 22851262 GCGAGUU 340 TGTTGTAT…ATACAACA
 S. exiguus Tse3 648710–152571181 AUUAGUA 945–947 TGTAAC…GTTACA
 Y. lipolytica Yltl9451351097[ix] 1069[ix] ? 714 TGT…ACA
 S. kluyveri Tsk3[i] [ii] 1–2
 D. hansenii Tdh3[i] [ii] 1–2
 S. servazzii Tss3[i] [ii] 1–2
 Y. lipolytica Tyl3[i] [ii] 1–3
 Z. rouxii Tzr3[i] [ii] 3–5
 C. tropicalis Tct3[ii] 1–3

[i] Defective element.

[ii] Incomplete sequence.

[iii] The name of the elements specifically identified in this study are in bold.

[iv] The copy number was determined for Ty elements; it does not include solo LTRs.

[v] The first part of gag from Tkl1.1 was deleted.

[vi] This ORF has a frameshift between positions 1909 and 1931.

[vii] This ORF has a frameshift at position 1490 (ggg instead of gg).

[viii] The beginning of the LTR was not determined.

[ix] Sizes of Ylt1 ORF1 and ORF2 are only indicative because the locus that underwent the frameshift could not be precisely determined.

[x] bp, base pairs; AA, amino acids; ORF, open reading frame; LTR, long terminal repeat.