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 | REST | 1036 | 1055 | + | 16.16 | CCAGGACCCAGGCCAGCCCT |
| L1M3e_5end | ZNF213 | 214 | 225 | + | 16.15 | CCCCAGGCAGCA |
| L1M3e_5end | MAZ | 202 | 209 | + | 16.08 | CCCCTCCC |
| L1M3e_5end | SP1 | 202 | 210 | - | 16.06 | GGGGAGGGG |
| L1M3e_5end | opa | 1799 | 1810 | + | 15.99 | GCCCGCCCGCGG |
| L1M3e_5end | ZNF454 | 1485 | 1501 | + | 15.96 | GGCTCCAGGCCCGTCCC |
| L1M3e_5end | KLF5 | 881 | 890 | + | 15.96 | GCCCCACCCT |
| L1M3e_5end | SP4 | 202 | 210 | - | 15.85 | GGGGAGGGG |
| L1M3e_5end | ZKSCAN5 | 266 | 274 | + | 15.83 | GGAAGTGAG |
| L1M3e_5end | ZNF454 | 1158 | 1174 | + | 15.76 | GGCTCCAGGCACCAGGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
