L1M3e_5end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000242 |
|---|---|
| TE superfamily | L1 |
| TE class | LINE |
| Species | Euarchontoglires |
| Length | 2113 |
| Kimura value | 24.19 |
| Tau index | 0.9892 |
| Description | 5' end of L1 retrotransposon, L1M3e_5end subfamily |
| Comment | Contains multiple ~30 bp tandem duplications in the promoter region. |
| Sequence |
GACGTCAGCAAGATGGCGGAATAGGACTTTCCAGCGCTCGTCCTCACAGAAACATCAATTTGAACAACTATCCACGCACGAAAATACCTTCACAAGAGCTAAGGAAACCAGGTGAGAGATTACAGCACCTGGGTGTAGCACAGAAATAAGAAAAGACGCATTGAAGAGGGTAGGAAGGACAGTTTTACATTACCCGCGTCACCCCTCCCCCAACCCCAGGCAGCACAGCGTGGAGAGAGATACCCTCCGCNTGGGGGAAGGAGAGGGAAGTGAGCACCGGACTTTGCCTCGGACCCCAANCACCGGGCCCGCCCCAGTAAAACCCAGCGCCGGGCAGGCCCCCACGGCCCCAGACTCCAGGCCGGTACCCGCGGACTGAGCCGCGCCAGATCCCACAGCCCAGGCTCCAGGCCTGCCCGGCGGACTCAGTCTCCAGGCCCGCCCCAGCGCCAGGCCGACCCCAGTGCCCCAGGCTCCAGACCGGCCCCAGCGCCAGGCCGGCCCCAGCGGCCCCAGGCTCCAGGCCGNCCCCAGCGCCAGGCCGGCCCCCGCGGCCCCAGGCTTCAGGCCCGCCCCAGCACCAGGCCGGCCCCCGCAGCCCTAGNCATCAGGCCAGCACCCGCGGACCCAGCCTCCAGGCCGGCCCCTGCGGACACAGGCTCCAGGCCTACCCAGCGCCAGGCCAGCCCCTGCGGCCCCAGGCTCCAGGCCCACCCCAGGTTCCAGACCAGCCCAGAGCCAGGTCGGCCCACGTAGCCCCAGGCTTCAGGCCCGCCCCAGCGCCAGGTCAGCACCCCTGGCCTCAGACCNCGNCCCGGTACCAGGCCGGCACCCGCGGACACAGGCTCCAGGCCTGCCCAGTGCCAGGCCGGTCCCTGCGGCCCCACCCTCCAGGNCCGGCCCCTGCGGCCCCACGCTCCAGCAGACCCAGGGTCCAGGCCCGTCCCAGTAGACCCCAGCGCTAGGCCGGCCCCCACGGACCCAGGCTCCAGGACCGCCCCTGTGGACCCAGGTCCCAGGCCGGCCCCCGCGGCCCCAGGACCCAGGCCAGCCCTCGNAGACCTAGCCTCCAGGCCAGCCCTGCAGACCCAGCCTCCAGGCCGGCNCCCGCGGACCCAGGCTCCAGGCCATCCCCCAGGCTCCAGGCCAGCCCCAGTGGCTCCAGGCACCAGGCCAGCNCCCGCGGACCCAGGCTCCAGACCGGCCCCACGCTACCCCAGCACCAGGCCAGCCCCAGGCTCCAGGCCGGTCCCCGTGGCCCAGGCTCCAGTGGACCCAGGGTCCAGGCCTGCTCCAGCAGACCCAGGGTCCAGGCCCACCCCAGTAGACCCCGGCGCCAGGCCGGCCCCCGCGGACCCAGGCTCCAGGACCACCCCTGCAGACCCAGGCTCCAGGCCAGCCCCCGCGGACCAGGATCCANGGCCCANNNCCNCAGNCGCAGGCTCCAGGCCCGCCCCAGCGCCAGGCCAGCCCCCATGGACTCAGGCTCCAGGCCCGTCCCAGTGGACCCAGGCNCCAGGCCCATCCCAGCGCCAGGCCGGCCCCTGCAGACTCAGGCTCAAGGCCCACCCCAGCGCCAGGTCAGCCCCTGTGGACCCAGGCTTCAGGCCGGCCCCCGCGGACNCAGGCTCCAGGCCCGCCCTCGTGGACCCAGGCTCCAGGCCCACCCCCGCGGACCCAATCAACAGGTCCACCCAGTGGATCCAGGCTCCAGGCCCAACCCCGCGGACCCAGGCGCCAGGCCCGCCACCTGCTGACCCAGGCACCAGGCCAGCCTGCCCGAGGACTCCAGCAGCAAGCCCGCCCGCGGACCACGCCAGACGGCCTGCCCAGAATCTCTGGATGACTGGTGAAGGGCTTTCCCNGACAAAGCCAGTCTGCAAAGACTGGAATAAGTNCCTACTTCTTCAAATGCGCAGACACCAACGCAAGGCCCAAGGATCACGAANAATCAGGGAAACATGACACCACCAAAGGAACAAAATAAAGCGCCAGTAACCGACCCTAAAGAAATGGAGATNTACGAACTGCCTGACAAAGAATTCAAAATAATCGTTTTAAGGAAGCTCAGTGAGCTNCAAGAGAACACAGATAAACAACTAAACGAAATCAG
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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 |
|---|---|---|---|---|---|---|
| L1M3e_5end | KLF4 | 882 | 889 | + | 15.48 | CCCCACCC |
| L1M3e_5end | ARALYDRAFT_495258 | 1203 | 1210 | + | 15.43 | GGCCCCAC |
| L1M3e_5end | ARALYDRAFT_495258 | 880 | 887 | + | 15.43 | GGCCCCAC |
| L1M3e_5end | ARALYDRAFT_495258 | 908 | 915 | + | 15.43 | GGCCCCAC |
| L1M3e_5end | ARALYDRAFT_484486 | 1203 | 1210 | + | 15.43 | GGCCCCAC |
| L1M3e_5end | ARALYDRAFT_484486 | 880 | 887 | + | 15.43 | GGCCCCAC |
| L1M3e_5end | ARALYDRAFT_484486 | 908 | 915 | + | 15.43 | GGCCCCAC |
| L1M3e_5end | dar1 | 881 | 891 | + | 15.38 | GCCCCACCCTC |
| L1M3e_5end | TCP16 | 1003 | 1010 | + | 15.32 | GTGGACCC |
| L1M3e_5end | TCP16 | 1270 | 1277 | + | 15.32 | GTGGACCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
