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 | ZNF282 | 91 | 105 | + | 18.56 | CATTCCCCAAACACG |
| L2c_3end | ZNF189 | 140 | 148 | + | 16.13 | TGCTGTTCC |
| L2c_3end | PRDM9 | 45 | 64 | - | 14.74 | AGTGGGCGAGGAGGGGAGTG |
| L2c_3end | ZKSCAN1 | 440 | 448 | + | 14.33 | ATAGTAGGC |
| L2c_3end | MAZ | 170 | 177 | + | 14.06 | CCCCTCCT |
| L2c_3end | MAZ | 49 | 56 | + | 14.06 | CCCCTCCT |
| L2c_3end | usp | 246 | 254 | - | 14.00 | GGGGTCAGG |
| L2c_3end | ZKSCAN5 | 223 | 231 | - | 14.00 | GGAGGTGAC |
| L2c_3end | PRDM9 | 35 | 54 | - | 13.93 | GAGGGGAGTGGAGGAGATGA |
| L2c_3end | TEAD1 | 155 | 163 | - | 13.85 | GCATTCCAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
