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 | ZNF418 | 115 | 129 | + | 14.80 | GAGCGACCAAAAGCA |
| L1MEb_5end | ETV5 | 10 | 18 | - | 14.71 | ACCGGAAGC |
| L1MEb_5end | ELK3 | 10 | 18 | - | 14.69 | ACCGGAAGC |
| L1MEb_5end | TFAP2C | 205 | 215 | + | 14.66 | GCCTGAGGGCA |
| L1MEb_5end | ERF::FOXO1 | 650 | 661 | + | 14.61 | AGAAACAGGAAA |
| L1MEb_5end | Kah | 235 | 244 | - | 14.61 | GCCACCTGTA |
| L1MEb_5end | NFkb | 332 | 342 | + | 14.57 | GGGGAAATCCC |
| L1MEb_5end | TWIST1 | 714 | 721 | + | 14.54 | CCAGATGT |
| L1MEb_5end | dl | 334 | 343 | - | 14.48 | CGGGATTTCC |
| L1MEb_5end | TFAP2B | 205 | 215 | + | 14.47 | GCCTGAGGGCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
