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 | Clamp | 49 | 62 | - | 15.28 | GAGCGAGGGGGAGA |
| L2a_3end | TFAP2A | 122 | 130 | + | 15.22 | GCCTCAGGG |
| L2a_3end | TFAP2C | 122 | 130 | - | 15.20 | CCCTGAGGC |
| L2a_3end | PRDM9 | 39 | 58 | - | 14.90 | GAGGGGGAGAGTGGTAGGAG |
| L2a_3end | IDD1 | 424 | 435 | + | 14.75 | TTTTGTCTGTTT |
| L2a_3end | NUC | 424 | 435 | + | 14.71 | TTTTGTCTGTTT |
| L2a_3end | cnd-1 | 336 | 343 | - | 14.66 | CAGATGGT |
| L2a_3end | ATF2 | 29 | 38 | - | 14.65 | ATGAGGTCAG |
| L2a_3end | ZNF768 | 23 | 31 | + | 14.62 | ACCTCTCTG |
| L2a_3end | MAC1 | 213 | 220 | + | 14.47 | TTTGCTCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
