L2c_3end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000361 |
|---|---|
| TE superfamily | L2 |
| TE class | LINE |
| Species | Mammalia |
| Length | 478 |
| Kimura value | 36.01 |
| Tau index | 0.8694 |
| Description | 3' end of L2 (LINE2) retrotransposon, L2c_3end subfamily |
| Comment | L2 3' region. Starts at 2910 of L2 consensus with ~170 bp overlap. |
| Sequence |
CTNCACGATCTGGCCCCTGCCTACCTCTCCAGCCTCATCTCCTCCACTCCCCTCCTCGCCCACTATGCTCCAGCCACACTGAACTNCTTGCATTCCCCAAACACGCCGCAGTTCTTTCCTGCCTCCGNGCCTTTGCACATGCTGTTCCCTCTGCCTGGAATGCTCTTCCCCCCTCCTTCCACCTGGCTAACTCCTACTCATCCTTCAAGNCTCAGCTCAGATGTCACCTCCTCCGGGAAGCCTTCCCTGACCCCCCAAGNCTAGTCTAGGTGCCCTCCTCTGTGCTCCCATAGCACCCTGTCTATACTCCCATTATAGCACTTATCATTAACTTGTATTGTAATTGTCTGTTTACNTGTCTGTCTCCTCCACTAGACTGTGAGCTCCTTGAGGGCAGGGACCGTGTCTTATTCATCTTTGTATCCCCAGCGCCTGGCACATAGTAGGCGCTCAATAAATGTTTGTTGAATGAATGAAT
|
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 |
|---|---|---|---|---|---|---|
| L2c_3end | ZNF148 | 49 | 58 | + | 13.81 | CCCCTCCTCG |
| L2c_3end | PRDM9 | 165 | 184 | - | 13.70 | AGGTGGAAGGAGGGGGGAAG |
| L2c_3end | PRDM9 | 164 | 183 | - | 13.61 | GGTGGAAGGAGGGGGGAAGA |
| L2c_3end | ZNF324 | 239 | 252 | - | 13.58 | GGTCAGGGAAGGCT |
| L2c_3end | ZNF530 | 167 | 180 | - | 13.54 | GGAAGGAGGGGGGA |
| L2c_3end | ZNF770 | 30 | 37 | + | 13.45 | CAGCCTCA |
| L2c_3end | FKH2 | 349 | 355 | - | 13.43 | GTAAACA |
| L2c_3end | INO2 | 134 | 142 | - | 13.34 | GCATGTGCA |
| L2c_3end | ZNF701 | 271 | 287 | - | 13.19 | GAGCACAGAGGAGGGCA |
| L2c_3end | RELB | 92 | 98 | + | 13.14 | ATTCCCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
