Table 1.
List and characteristics of Y-loop localizing lncRNAs
| lncRNA | Chromosome | Gene size | Intron | Proximal genes | Poly-A | Conserved |
|---|---|---|---|---|---|---|
| CR42657 | X | 1 kb | 0.2 kb, 64 bp | CR44016, nej, btd | No | No |
| CR43193 | X | 1 kb | 50 bp | Shakb* | Yes | Yes |
| CR43431 | 3L | 5 kb | 2 kb, 54 bp, 67 bp | CR32111, CR44552, CR44553 | No | Yes |
| CR43622X | 2R | 0.6 kb | N | hbs | Yes | Yes |
| CR43835X | X | 0.9 kb | 58 bp, 62 bp, 62 bp | CR43279, CG32719 | No | No |
| CR43839√ | 2L | 0.8 kb | N | CR45722, CR45723, tj | Yes | Yes |
| CR43862√ | X | 0.9 kb | 91 bp, 77 bp | CR45610, run | No | Yes |
| CR44017 | 3R | 0.6 kb | N | gpp* | Yes | Yes |
| CR44114 | 2L | 0.9 kb | 58 bp | rotini | No | Yes |
| CR44206 | 2R | 15 kb | 7.2 kb, 6 kb | Dh31-R, CR45312 | No | Yes |
| CR44344√ | 2R | 2 kb | 0.4 kb, 57 bp, 0.2 kb | mbl* | No | Yes |
| CR44412√ | 2L | 0.8 kb | N | Sytα | No | Yes |
| CR44553 | 3L | 1 kb | N | CR43431, CR44552, CR32111 | No | Yes |
| CR44606 | 2L | 1 kb | N | sky*, CG42238* | Yes | No |
| CR44619 | X | 2.7 kb | 1.4 kb | lncRNA:Vinr, paics | Yes | No |
| CR44792√ | 2L | 1 kb | N | CG31475 | No | Yes |
| CR44889 | X | 1 kb | 56 bp | meso18E, CG12531 | No | Yes |
| CR44977 | 2L | 1.4 kb | 81 bp | Brat* | No | Yes |
| CR45174X | 3L | 1 kb | N | Ago3* | No | No |
| CR46499 | X | 9.9 kb | 1.3 kb, 1.4 kb + 9 more | CR43614, CR32773*, NorpA* | No | Yes |
| CR45805 | 3L | 3.3 kb | N | Pdk1*, CR45400, 45401, 45402 | Yes | Yes |
| CR45965 | 3L | 1.4 kb | N | Ten-m*, CR45962*, 45964, 45963 | No | Yes |
| CR46278 | 2R | 2 kb | N | lola*, psq* | No | No |
| CR40441 | Y | 0.2 kb | N | Ppr-Y* | No | No |
| CR45931 | Y | 0.6 kb | N | WDY* | No | Yes |
| CR45946 | Y | 0.5 kb | N | kl-3* | No | Yes |
| CR45947 | Y | 0.5 kb | N | kl-3* | No | Yes |
| CR45948 | Y | 0.9 kb | 61 bp | WDY* | No | Yes |
Columns from left to right indicate lncRNA annotation numbers, chromosomal location, gene size, presence and size of introns, proximal genes, presence of a consensus Poly A signal, and sequence conservation between Drosophila species. Check marks adjacent to lncRNA annotation symbols indicate moderate to severe infertility when knocked out, whereas X’s indicate no or minor phenotypes. Y-loop lncRNA genes found proximal to each other are in bold. lncRNAs with no introns are labeled as “N”. Proximal gene products involved in RNA transcription or processing are indicated in italics. Asterisks indicate genes with unusually long introns. The five Y chromosome-linked Y-loop lncRNAs discovered last are listed at the bottom of the table.