L1MEb_5end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000774 |
|---|---|
| TE superfamily | L1 |
| TE class | LINE |
| Species | Eutheria |
| Length | 1089 |
| Kimura value | 28.63 |
| Tau index | 0.9360 |
| Description | Partial 5' end of L1 retrotransposon, L1MEb_5end subfamily |
| Comment | 5' end of L1ME1 or L1ME2 LINE1. Average divergence from consensus is 26%. L1MEB_5 is 70% similar to L1MDA_5 sequence. |
| Sequence |
CAGANTTCCGCTTCCGGTAATGGCGGAGTAAGCTCCTATCGGACCAACCCTCCCGCAGATAACAACTATAAACTCTGGACAAAATACAAAAAACAACTACCTGAAGGCACTGGAGAGCGACCAAAAGCAGGCAGANACTGGAGGGGAGTCGACACTTGGAAGAAGGGAACGGCACNGGGTGAGTTCCCATTTTTACGGCTTTTNGCCTGAGGGCAGGCCNCAGTCGGTGCGNCGTACAGGTGGCTAAAACTCCAGTAGAAAACCCGCAGTCTTNCTGGCTTGAAGAACCAGAGGACAGAGTTCGGGGCAACCACAGCCGCTGGAAAGTGAGGGGGAAATCCCGGAAAGGAGAGAGCCAGAGAGAGGAGCCCCAAATTCTGCGTATAAACTCTGCCCAAATCTCTGGCTGACCCCTGAACCACGCATGCGCGGGGCAGACTCCAAGCAGCCCAGCTAAAGATAAAAGAACTGAACTGAGATTTNAGCTGCCGCCCAAGAGACAGAGTTTGNAGTTTGAGTCCAGCCAAGTTAACTGCCTGCTAAAACAAAANAANCAACACTCTTCAGAGGAANATAACAGAATCCAGAGTCTCTACAACGTANCATTCACAATGTCCAGGATACAATCCNAAAATTATNCNAGATANGAAGAAACAGGAAAAATGTGACCCATNCTCAAGAGAAAAGAAAATAGAAACCGACCCCGAGATGACCCAGATGTTGGAATTAGCAGACAAGGACTTTAAAGCAGCTATTATAAATATGTTCAANGANNTAAAGGAAAATATGCTCATAATGAATGAAAAGATAGGAAATCTCAGCAGAGAAATAGAAACTATAAAAAGAACCAAATGGAAATTCTAGAACTGAAAAATACAATATCTGAAATAAAAAATTCACTGGATGGGCTTAACAGCAGANTGGAGATGACAGAGGAAAGAGTCAGTGAACTTGAAGATAGATCAATAGAAATTATCCAATCTGAAGAACAGAGAGAAAAAANATTTAAAAAAAAAGAGCAGAGCCTCAGNGACCTGTGGGACAATATCAAAAGGTCTAACATACGTGTAATTGGAGTCCCAGAAGGAG
|
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 |
|---|---|---|---|---|---|---|
| L1MEb_5end | EWSR1-FLI1 | 343 | 360 | + | -9.84 | GGAAAGGAGAGAGCCAGA |
| L1MEb_5end | BCL6B | 334 | 350 | - | -11.83 | TCCTTTCCGGGATTTCC |
| L1MEb_5end | BPC5 | 334 | 363 | + | -40.15 | GGAAATCCCGGAAAGGAGAGAGCCAGAGAG |
| L1MEb_5end | BPC5 | 336 | 365 | + | -42.66 | AAATCCCGGAAAGGAGAGAGCCAGAGAGAG |
| L1MEb_5end | BPC5 | 324 | 353 | + | -46.49 | AAAGTGAGGGGGAAATCCCGGAAAGGAGAG |
| L1MEb_5end | BPC5 | 344 | 373 | + | -47.67 | GAAAGGAGAGAGCCAGAGAGAGGAGCCCCA |
| L1MEb_5end | BPC5 | 332 | 361 | + | -47.79 | GGGGAAATCCCGGAAAGGAGAGAGCCAGAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
