Table 3. Alus subjected to in vitro transcription analysis.
| Alu | Expression in cell linesa | Predicted length of primary transcript(s)b |
|---|---|---|
| AluSq2_chr1 (chr1:61523296–61523586) | H1-hESC, HeLa-S3, Hep G2, K562, NHEK | 355 (T4); 361 (T10). |
| AluSx_chr1 (chr1:235531222–235531520) | none | 328 (TAT3); 338 (TAT3); 431 (T4) |
| AluSx1_chr3 (chr3:139109300–139109588) | H1-hESC, GM12878 (sporadical) | 304 (T3GT); 311 (TCT3); 437 (TAT3); 443 (T17) |
| AluY_chr7 (chr7:73761603–73761897) | K562 (sporadical) | 322 (T5) |
| AluY_chr10-a (chr10:103929441–103929803) | H1-hESC (sporadical) | 370 (TCT3); 376 (T4); 397 (T6); 406 (T3GT2) |
| AluY_chr10-b (chr10:69524852–69525156) | NHEK | 397 (T5) |
| AluSx_chr10 (chr10:12236879–12237173) | none | 320 (T4); 456 (T6) |
| AluSp_chr17 (chr17:4295121–4295437) | K562 | 387 (T3CT); 424 (TAT3); 430 (T6) |
| AluY_chr22 (chr22:41932115–41932411) | none | 378 (TGT3); 409 (T4); 590 (T3CT) |
The second column lists, for each Alu element, the cell lines in which it was found to be expressed by RNA-seq data analysis. The transcript lengths (in nts) reported in the third column were calculated by assuming as TSS the G at the first Alu position, located 12 bp upstream of the T with which the A box starts (TRGY…). This assumption is based on early in vitro transcription analyses showing that most Alu transcripts initiate in close proximity to the 5′ end of the consensus Alu sequence (3,6). To estimate the 3′ end of the transcript, both canonical (Tn with n ≥ 4) and non-canonical T-rich (25) Pol III terminators were considered downstream of Alu body sequence (indicated in parentheses after the transcript length); for canonical terminators, the 4 Us corresponding to the first 4 Ts of the termination signal were considered as part of the transcripts; for non-canonical terminators, all the nts of the terminator were considered as incorporated into the RNA. The underlined values are those for which a closely corresponding transcript was detected in transcription gels.
aThis column lists, for each Alu element, the cell lines in which it was found to be expressed by RNA-seq data analysis.
bThe reported transcript lengths were calculated by assuming as TSS the G at the first Alu position, located 12 bp upstream of the T with which the A box starts (TRGY…).