L2b_3end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000360 |
|---|---|
| TE superfamily | L2 |
| TE class | LINE |
| Species | Theria_mammals |
| Length | 466 |
| Kimura value | 32.92 |
| Tau index | 0.7773 |
| Description | 3' end of L2 (LINE2) retrotransposon, L2b_3end subfamily |
| Comment | L2 3' region. Starts at 2910 of L2 consensus with ~170 bp overlap. MIR and MIRb share 3' terminal end homology over ~50bp. |
| Sequence |
TCGCACGATCTGGCCCCGCTACCTCTCCGGCCTCATCTCCTACCACTCTCCCCTTGCTCACTCTGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCANGCTCNCTCCCGCCTCAGGGCCTTTGCACNTGCTGTTCCCTCTGCCTGGAACGCCCTTCCCCACCTCTTCGCCTGGCCAACTCCTACTCATCCTTCAGGTCTCAGCTCAAATGTCACCTCCTCCGGGAAGCCCTCCCTGACCCCCCAGGCCGGGTCAGGCGCCCTCCTCTGGGCCCCCCCAGTCCTACCCTGCCACTCTGGGTTATNATTGTCTGNTTACATGTCTGTCTCCCCCACTAGACTGTGAGCTCCGTGAGGGCAGGGACCGNGTCTGTCTTGTTCACCGCTGTATCCCCAGCGCCTAGCACAGNGCCTGGCACACAGTAGGCGCTCAGTAAATATTTGTTGAATGAATGAAT
|
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 |
|---|---|---|---|---|---|---|
| L2b_3end | ARF10 | 333 | 343 | - | 13.55 | TGGGGGAGACA |
| L2b_3end | FoxB | 443 | 453 | - | 13.53 | ACAAATATTTA |
| L2b_3end | sug | 246 | 257 | + | 13.48 | GACCCCCCAGGC |
| L2b_3end | TFAP2A | 247 | 257 | + | 13.45 | ACCCCCCAGGC |
| L2b_3end | TFAP2E | 119 | 127 | + | 13.43 | GCCTCAGGG |
| L2b_3end | TFAP2E | 119 | 127 | - | 13.41 | CCCTGAGGC |
| L2b_3end | UGA3 | 115 | 121 | - | 13.34 | GGCGGGA |
| L2b_3end | CTCF | 267 | 297 | - | 13.24 | GGGTAGGACTGGGGGGGCCCAGAGGAGGGCG |
| L2b_3end | E2F6 | 114 | 121 | - | 13.22 | GGCGGGAG |
| L2b_3end | PLAGL2 | 279 | 286 | + | 13.18 | GGCCCCCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
