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 | Gfi1B | 813 | 822 | + | 15.95 | AAATCTCAGC |
| L1MEb_5end | ZBTB18 | 712 | 722 | + | 15.93 | ACCCAGATGTT |
| L1MEb_5end | Ets96B | 10 | 18 | - | 15.85 | ACCGGAAGC |
| L1MEb_5end | eor-1 | 350 | 362 | + | 15.79 | AGAGAGCCAGAGA |
| L1MEb_5end | THRB | 408 | 420 | - | 15.58 | GGTTCAGGGGTCA |
| L1MEb_5end | Ets97D | 10 | 18 | - | 15.54 | ACCGGAAGC |
| L1MEb_5end | Zbtb2 | 9 | 18 | - | 15.52 | ACCGGAAGCG |
| L1MEb_5end | RELA | 334 | 343 | - | 15.51 | CGGGATTTCC |
| L1MEb_5end | TFAP2A | 205 | 215 | - | 15.45 | TGCCCTCAGGC |
| L1MEb_5end | USV1 | 409 | 418 | + | 15.43 | GACCCCTGAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
