L2a_3end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000359 |
|---|---|
| TE superfamily | L2 |
| TE class | LINE |
| Species | Theria_mammals |
| Length | 517 |
| Kimura value | 32.66 |
| Tau index | 0.7342 |
| Description | 3' end of L2 (LINE2) retrotransposon, L2a_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 |
CTACATGATCTGGCCCCCCGTTACCTCTCTGACCTCATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCACGCTCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCTCTTCCCCCAGATATCCGCATGGCTCGCTCCCTCACCTCCTTCAGGTCTTTGCTCAAATGTCACCTTCTCAGNGAGGCCTTCCCTGACCACCCTATTTAAAATNGCACACCCTCNCCCCCANCACTCCCTATCCCCCTTACCCTGCTTTATTTTTCTCCATAGCACTTATCACCATCTGACATACTATATATTTTACTTATTTATTTGTTTATTGTCTGTCTCCCCCCACTAGAATGTAAGCTCCATGAGGGCAGGGACTTTTGTCTGTTTTGTTCACTGCTGTATCCCCAGCGCCTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATATTTGTTGAATGAATGAAT
|
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 |
|---|---|---|---|---|---|---|
| L2a_3end | BPC6 | 48 | 68 | + | -3.46 | CTCTCCCCCTCGCTCACTCCG |
| L2a_3end | EWSR1-FLI1 | 187 | 204 | - | -10.84 | GGAGGTGAGGGAGCGAGC |
| L2a_3end | EWSR1-FLI1 | 183 | 200 | - | -14.96 | GTGAGGGAGCGAGCCATG |
| L2a_3end | EWSR1-FLI1 | 191 | 208 | - | -15.59 | TGAAGGAGGTGAGGGAGC |
| L2a_3end | BPC5 | 40 | 69 | - | -31.54 | GCGGAGTGAGCGAGGGGGAGAGTGGTAGGA |
| L2a_3end | BPC5 | 34 | 63 | - | -41.73 | TGAGCGAGGGGGAGAGTGGTAGGAGATGAG |
| L2a_3end | BPC5 | 42 | 71 | - | -47.11 | GAGCGGAGTGAGCGAGGGGGAGAGTGGTAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
