L1MD2_3end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000287 |
|---|---|
| TE superfamily | L1 |
| TE class | LINE |
| Species | Eutheria |
| Length | 1106 |
| Kimura value | 22.37 |
| Tau index | 0.8586 |
| Description | 3' end of L1 retrotransposon, L1MD2_3end subfamily |
| Comment | ORF2 ends at bp ~675 |
| Sequence |
CTNGTATCTAGAATATATAAAGAACTCTCAAAACTCAACAGTAAAAAAACAAACAATCCAATTAGAAAATGGGCAAAAGACATGAACAGACATTTCACCGAAGAGGATATACAGATGGCAAATAAGCACATGAAAAGATGTTCAACATCATTAGCCATTAGGGAAATGCAAATTAAAACCACAATGAGATATCACTACACACCTATCAGAATGGCTAAAATAAAAAATAGTGACAACACCAAATGCTGGCGAGGATGCGGAGAAACTGGATCACTCATACATTGCTGGTGGGAATGTAAAATGGTACAGCCACTCTGGAAAACAGTTTGGCAGTTTCTTATAAAACTAAACATGCANTTACCATACGACCCAGCAATTGCACTCTTGGGCATTTATCCCAGAGAAATGAAAACTTATGTTCACACAAAAACCTGTACACGAATGTTCATAGCAGCTTTATTCGTAATAGCCAAAAACTGGAAACAACCCAAATGTCCTTCAACGGGTGAATGGTTAAACAAACTGTGGTACATCCATACCATGGAATACTACTCAGCAATAAAAAGGAACGAACTATTGATACACGCAACAACTTGGATGGATCTCAAGGGAATTATGCTGAGTGAAAAAAGCCAATCTCAAAAGGTTACATACTGTATGATTCCATTTATATAACATTCTTGAAATGACAAAATTATAGAGATGGAGAACAGATTAGTGGTTGCCAGGGGTTAGGGATGGGGGTGGNGNGGGGGAAGGGAGGTGGGTGTGGCTATAAAAGGGCAGCACGAGGGATCCTTGTGGTGATGGAACNGTTCTGTATCTTGACTGTGGTGGTGGNTACACGAATCTACACATGTGATAAAATTGCATAGAACTAAATACACACACACACACATGAGTACANGTAAAACTGGNGAAATCTGAATAAGATCGGTGGATTGTATCAATGTCAATTTCCTGGTTNTGATATTGTACTATAGTTNTGCAAGATGTTACCATTGGGGGAAACTGGGTGAAGGGTACACGGGATCTCTCTGTATTATTTCTTACAACTNCATGTGAATCTACAATTATCTCAAAATAAAAAGTTTAATTTAAAAAAA
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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 |
|---|---|---|---|---|---|---|
| L1MD2_3end | RXRG | 503 | 516 | + | 0.26 | CGGGTGAATGGTTA |
| L1MD2_3end | CG4360 | 38 | 50 | + | -1.21 | ACAGTAAAAAAAC |
| L1MD2_3end | Rarb | 634 | 649 | + | -2.09 | CAATCTCAAAAGGTTA |
| L1MD2_3end | TRP1 | 422 | 442 | + | -3.60 | ACACAAAAACCTGTACACGAA |
| L1MD2_3end | EWSR1-FLI1 | 754 | 771 | + | -9.68 | GGAAGGGAGGTGGGTGTG |
| L1MD2_3end | BCL6B | 719 | 735 | + | -17.90 | TGGTTGCCAGGGGTTAG |
| L1MD2_3end | BPC5 | 64 | 93 | + | -41.35 | AGAAAATGGGCAAAAGACATGAACAGACAT |
| L1MD2_3end | BPC5 | 697 | 726 | + | -45.20 | ATAGAGATGGAGAACAGATTAGTGGTTGCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
