Table 2. Translational status of transposable elements documented to be active in Nipponbare.
| Element | Superfamily | Locus | Tissuea | mRNA-seq (FPKM) | TRAP-seq (FPKM) | TEI | Translation Evidenceb |
|---|---|---|---|---|---|---|---|
| Tos17 | LTR/Copia | LOC_Os10g29650 | Callus | 15.03 | 0.58 | 0.04 | Maybe |
| Lullaby | LTR/Copia | LOC_Os06g38480 | Callus | 13.01 | 15.61 | 1.20 | Yes |
| Osr10 | LTR/Copia | LOC_Os04g32750 | Panicle | 0.01 | 0.00 | NA | Not expressed |
| Osr37 | LTR/Gypsy | LOC_Os03g43750 | Callus | 10.12 | 4.83 | 0.48 | Yes |
| RIRE2 | LTR/Gypsy | LOC_Os03g36279 | Callus | 2.26 | 2.56 | 1.14 | Yes |
| RIRE3 | LTR/Gypsy | LOC_Os06g32890 | Shoot | 0.13 | 0.08 | NA | Not expressed |
| RN363 | LTR/Gypsy | LOC_Os02g24150 | Panicle | 1.92 | 2.02 | 1.05 | Yes |
| Ping | PIF/Harbinger | LOC_Os06g39624 | Panicle | 16.50 | 9.41 | 0.57 | Yes |
| Pong | PIF/Harbinger | LOC_Os11g19864 | Callus | 6.40 | 6.36 | 0.99 | Yes |
mRNA-seq, messenger RNA sequencing; FPKM, fragments per kilobase per exon model per million mapped reads; TRAP-seq, Translating Ribosome Affinity Purification followed by mRNA-sequencing; TEI, translatome enrichment index; NA, not applicable.
a
If the transposon is expressed in multiple tissues, the one with the highest TRAP-seq level is listed.
b
TRAP-seq FPKM ≥ 1 is considered to be translated; mRNA-seq FPKM ≥1 is considered to be expressed.