Table 2.
Motifs detected in the region between − 100 nt and + 40 nt based on both McPromoter-predicted TSS and database-annotated TSS for the retrogenes and parental genes with annotated 5′ UTRs.
| Motif Name | Motif name (Fitzgerald et al. 2006) | Motif number (Ohler et al. 2002) | Consensus sequence | Retrogenes (n = 65) | Parental Genes (n = 83) | |||
|---|---|---|---|---|---|---|---|---|
| ND (47) | D (18) |
ND (17) | D (66) | |||||
| TSS a | TSS b | |||||||
| TATA | DMp1 | 3 | TATAWAA | 8 | 2 | 2 | 2 | 8 |
| INR | DMp2 | 4 | TCAKTY | 16 | 2 | 1 | 3 | 17 |
| INR1 | DMp3 | - | TCATTCG | 1 | 1 | 1 | 1 | 0 |
| MTE | - | 10 | CSSAACGS | 2 | 0 | 0 | 0 | 3 |
| DRE | NDM4 | 2 | WATCGATW | 5 | 9 | 8 | 6 | 20 |
| - | DMv2 | 8 | TGGYAACR | 0 | 1 | 1 | 0 | 3 |
| - | DMv3 | 7 | CAYCNCTA | 2 | 2 | 2 | 1 | 13 |
| - | DMv4 | 1 | GGYCACAC | 2 | 4 | 2 | 4 | 20 |
| - | DMv5 | 6 | GTATWTTT | 3 | 0 | 0 | 0 | 8 |
| E-box | NDM5 | 5 | CAGCTSW | 1 | 5 | 5 | 1 | 7 |
| DPE | DMp4 | 9 | KCGGTTS | 0 | 0 | 0 | 0 | 2 |
| GCT | - | - | YGGCTTTK | 7 | 0 | 0 | 1 | 1 |
Total numbers of genes are given in parentheses. D refers to a TSS detected by McPromoter. ND means that the TSS was not detected by McPromoter. The high abundance of some motifs is highlighted in bold.
a
TSS is based on the database.
b
TSS is based on McPromoter prediction.