L2a_3end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000359 |
|---|---|
| TE superfamily | L2 |
| TE order | 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 | Clamp | 185 | 198 | - | 16.68 | GAGGGAGCGAGCCA |
| L2a_3end | ZKSCAN5 | 196 | 204 | - | 16.46 | GGAGGTGAG |
| L2a_3end | SGR5 | 424 | 436 | - | 16.39 | AAAACAGACAAAA |
| L2a_3end | ZNF189 | 141 | 149 | + | 16.13 | TGCTGTTCC |
| L2a_3end | ZNF189 | 90 | 98 | + | 16.13 | TGCTGTTCC |
| L2a_3end | ZNF530 | 297 | 310 | - | 16.08 | GCAGGGTAAGGGGG |
| L2a_3end | Clamp | 53 | 66 | - | 15.95 | GAGTGAGCGAGGGG |
| L2a_3end | PRDM9 | 18 | 37 | - | 15.83 | TGAGGTCAGAGAGGTAACGG |
| L2a_3end | JKD | 424 | 435 | + | 15.70 | TTTTGTCTGTTT |
| L2a_3end | KLF17 | 44 | 57 | + | 15.28 | ACCACTCTCCCCCT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
