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 | ZNF16 | 45 | 65 | - | 4.69 | CAGAGTGAGCAAGGGGAGAGT |
| L2b_3end | Rxra | 210 | 223 | + | 3.91 | CAGCTCAAATGTCA |
| L2b_3end | dar1 | 236 | 246 | + | 3.15 | AGCCCTCCCTG |
| L2b_3end | RXRG | 210 | 223 | + | 0.62 | CAGCTCAAATGTCA |
| L2b_3end | NR1H2::RXRA | 209 | 225 | + | 0.55 | TCAGCTCAAATGTCACC |
| L2b_3end | TCP14 | 276 | 293 | - | 0.10 | AGGACTGGGGGGGCCCAG |
| L2b_3end | BPC6 | 326 | 346 | + | -0.39 | ACATGTCTGTCTCCCCCACTA |
| L2b_3end | GLIS1 | 245 | 259 | + | -2.96 | TGACCCCCCAGGCCG |
| L2b_3end | EWSR1-FLI1 | 23 | 40 | - | -16.12 | GGAGATGAGGCCGGAGAG |
| L2b_3end | BPC5 | 35 | 64 | - | -44.62 | AGAGTGAGCAAGGGGAGAGTGGTAGGAGAT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
