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
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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 | ELK4 | 9 | 17 | + | 15.33 | CGCTTCCGG |
| L1MEb_5end | sens | 813 | 822 | + | 15.25 | AAATCTCAGC |
| L1MEb_5end | FLI1::FOXI1 | 651 | 661 | + | 15.10 | GAAACAGGAAA |
| L1MEb_5end | EcR::usp | 939 | 953 | - | 15.08 | AAGTTCACTGACTCT |
| L1MEb_5end | ZBTB7A | 9 | 17 | - | 14.98 | CCGGAAGCG |
| L1MEb_5end | TFAP2A | 205 | 213 | - | 14.96 | CCCTCAGGC |
| L1MEb_5end | FEV | 10 | 18 | - | 14.90 | ACCGGAAGC |
| L1MEb_5end | ZNF257 | 933 | 942 | + | 14.87 | GAGGAAAGAG |
| L1MEb_5end | FLI1 | 10 | 18 | - | 14.82 | ACCGGAAGC |
| L1MEb_5end | ZNF317 | 913 | 920 | + | 14.80 | ACAGCAGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
