L2d_3end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001215 |
|---|---|
| TE superfamily | L2 |
| TE class | LINE |
| Species | Eutheria |
| Length | 516 |
| Kimura value | 36.41 |
| Tau index | 0.8395 |
| Description | 3' end of L2 (LINE2) retrotransposon, L2d_3end subfamily |
| Comment | Copies at orthologous sites in all eutheria. |
| Sequence |
CTCCACGATCTGGCCCCACCCTACCTNTCCAGCCTTATCTCCCACTACTCCCCAGCACGAACCCTCCGCTCCAGTCAGGCCGGTCTCTTCACTGTCCCCCGAACACGCCTTGCGCATTCCCGCCTCTGCGCCTTTGCTCACGCCGTTCCCCCCGCCTGGAATGCCCTTCCCCTTCCTCTCTCTCTATCCAAATCCTACCCATCCTTCAAGGCCCAGCTCAAGTCCCACCTCCTCCACGAAGCCTTCCCTGACCACTCCAGCCCACACTGATCTCTCCCTTCTCTGAACTCCTATAGCACTTATAGTCTGTACCACGCAATTTAGCACTTAATTATATACTGTCTTGTATTGTTCTCTAATTGTTTCATGTGTGTTAGTCTTGTCTCCCCAACTAGATTGTAAGCTCCTTGAGGGCAGGGACCATGTCTTATACTNTTTTNTCGTTCCCCACAGCGCCTAGCACAGTGCTGAGCACATAGTAGGCGCTCAATAAATACTTGTTGATTGATTGATTGA
|
TF motifs of the concenus sequence
Use FIMO to detect transcription factor motifs in the concenus sequence of the TE family.
| TE_family | TFBS | Start | End | Strand | Score | Matched sequence |
|---|---|---|---|---|---|---|
| L2d_3end | RAMOSA1 | 177 | 190 | - | 14.14 | TGGATAGAGAGAGA |
| L2d_3end | LjSGA_053525.1 | 12 | 19 | + | 14.06 | GGCCCCAC |
| L2d_3end | ZFP14 | 165 | 179 | - | 13.92 | AGAGGAAGGGGAAGG |
| L2d_3end | TEAD1 | 156 | 164 | - | 13.85 | GCATTCCAG |
| L2d_3end | LjTCP20 | 417 | 424 | + | 13.85 | GGGACCAT |
| L2d_3end | Clamp | 175 | 188 | - | 13.72 | GATAGAGAGAGAGG |
| L2d_3end | cassava45561.m1 | 11 | 19 | + | 13.67 | TGGCCCCAC |
| L2d_3end | SPIB | 169 | 181 | + | 13.66 | CCCCTTCCTCTCT |
| L2d_3end | ZNF610 | 63 | 72 | + | 13.64 | CCTCCGCTCC |
| L2d_3end | dar1 | 13 | 23 | + | 13.64 | GCCCCACCCTA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
