L1M4b_5end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000248 |
|---|---|
| TE superfamily | L1 |
| TE class | LINE |
| Species | Eutheria |
| Length | 3237 |
| Kimura value | 22.68 |
| Tau index | 0.8323 |
| Description | 5' end of L1 retrotransposon, L1M4b_5end subfamily |
| Comment | gag ORF 1357-2340, pol ORF 3088-3237 (end) |
| Sequence |
AAGGAGTTCCACTTCCGGAATGGCGGCGTGAGGAGCTCCGCGGACCCGCTCCCCAGCGAAACAACCATAACTGGTGAAAATTATTTTAAAAAAACAACCATTTAAAGTCTCTGGAAATTGTCCTAAGGGCATACAGCAAATGAAGAAACATTTATTCAAGAAAATCTACTAAATCTCGGTAAGAACAGCGAGAGTCTGTGGCATTTGAGCCACGACCCGCTCCCTCCTCCCCCCTCCCCAGCTCAGCGTGACGGAAGCTCCACTCCGGGCGGGTGCGGCCAAGAANACGGGGCTCCCTCTCCCCCCAGCTCCCAGTCGAGGGCTACGGTATCTCCCCGGGAGGGGCAGGCCGCCAGCATTTCTCATCCCCCCCAGCTCCGTGTTGCAGAGGCTAAATTCCAGGCGAGTGCGGCCGAGAGGTCGGGGGCTCCCTTCCTCCACCCAGCCCCCACTCGTAGGGCGGAGGCTCTACCCCGGGCGCGGCAGGCCGAGAATACTGGGGCCCCGATCGCCCTCGCCCCAGCTCGCTCGTAGGGCGGAGGTTCCACGCCGGGAGAGGCAAGCCGAGAAGACCAGAGGCTACCGCCCCCGCCCAGCGCCCTGCTCNTAAAGCAGGGGTGTCACTCCGAGAGAAGCGGGCCACTGTCCCCGCCCCCAGCTCCGGAGCAGTGGCTCAGAGATTTTGCCCAGGGGGAGAGGCAGGCCATAAGAACAGAGAGCTCCGAAGCTCTCCCCAAAGGAACTGACTTTATTTGNAACAGAGTGTGGGGAAGTTCAAGCCTAAGGGCGCTCTCGAAAACAATGGAGATTTTGGTGGTAAGCAATTAAGAGGAGGCTGGTAGCTCCATGAGAGCAACAAGCTAAACCGTAGGCCAGCTAGTTTACCAGAGAGAACCAGGGAAAGAGACAGCTAAGAAGAGCCCTCCTGGGGTCAGAACAAACCTCAAAGACTGGCCTCAAAAACTACCCCTGCAAAGGGGCCCGAATTTAATTGGATCAGACTGTGGAGCAATTTATGCCCCAGGGCATTGTCGAAAACAATAGAGCAATCAGCCGGCAATTAGTGGAGCCTAACAGCTGGGTGTGATACCAACAGAGGCAGACAGCTTAACAGAGAGATCAGGGAAAGAGACAGTCAAAGAGAGCCCTGCTAAAACCACTGTCATCCCAGGGTGACTGTGCGCATGCCCAAGGCTGCGCCCTCTGAGGAGCGACATCAGAGGCTTCACACTGCGGGGGAAATAGACTTCACTAAAATAGTCCAGCCAAGTCACTAAACAAATAAACAAGCAAACAACAACAACAAGCCGGGGGAGGGGAATCAGTATCCAGAGTTGCTACAATATATTATCTAAAATGTCCAGTTTTCAACAAAAAATTATGAGACATGCAAAGAAACAGGAAAGTGTGACCCATACACAGGAAAAAAAGCAGGCAACAGAAACTGCCTGTGAGAGGGCCCAGATGTCGGATTTAGCAGACAAAGACTTCAAAGCAGCCATTATAAATATGTTCAAAGAACTAAAGGAAACCATGNTTAAAGAAGTAAAGGAAGGTATGATGACAATGTCTCATCAAATAGAGAATATCAATAAAGAGATAGAAATTATAAAAAAGAACCAAATGGAAATTCTGGAGTTGAAAAGTACAATAACTGAAATGAAAAATTCACTAGAGGGGCTCAACAGTAGATTTGAACTGGCAGAAGAAAGAATCAGCGAACTTGAAGATAGATCGATAGAGATTATGCAATCCGAAGAACAGAGAGAAAAAAGAATGAAGAAAAATGAACAGAGCCTCAGAGAAATGTGGGACACCATTAAGCGCACCAACATACGCGTAATGGGAGTACCAGAAGGAGAGGAGAGAGAGAAAGGAGCAGAAAAAATATTCGAAGAAATAATGGCTGAAAACTTCCCAAATTTGATGAAAAACATTAATCTACACATCCAAGAAGCTCAACGAACTCCAAGTAGGATAAACGCAAAGAGATCCACACCCAGACACATCATAGTAAAAATGCTGAAAGCCAAAGACAAAGAGAAAATCTTGAAAGCAGCAAGAGAAAAACGACTCATCACGTACAAGGGAACCCCAATAAGATTAACAGCTGACTTCTCATCAGAAACAATGGAGGCCAGAAGGCAGTGGGATGACATATTCAAAGTGCTGAAAGAAAAAAACTGTCAACCAAGAATCCTATATCCAGCAAAACTATCTTTCAAAAATGAAGGCGAAATAAAGACATTCCCAGATAAACAAAAACTGAGAGAATTTGTTGCTAGCAGACCCGCCTTACAAGAAATACTAAAGGAAGTTCTTCAGGCTGAAAGCAAGTGACCCCAGACGGTAATTCGAATCCACACGAAAAAACAAAGAGCACCGGTAAAGGTAATTATGTAATTATAAAAGACAGTATAAATGCATATTTCTTCTCCTTTCTTCTCTTAACTGATTTAAAAAGCAATTGTATAAAACAATATGTATATAATTGTATTGTTGGGCCTATAACATATAGAAATGTAATATATTTGACAATAACAGCACAAAGGAGGTGGGTGGGAGCAAAGCTGTATTGGAGTAAGGAAATGACACCAGATGGTAACTCGAATCCACAGGAACAAATGAAGAGAACCAGAAATGGTAAATAAGAAGGTTAATATAACAAACTCTATAAATATATACTTGCTCTCCTTTCTTCTCTCAGCTTCTTTAAAAGACATAAAATTATATAAAGTAATAATTATAACAATGTATTGTTGGGTTTGTAACATATATAGATGTAATATGTATAACAATAATAGCACAAAAAGGGGGAAAAGGGAATAGAGCTATATAGGAGTAACGTTTCTATATCTCACTGGAATTAAGTTAGTATAAATCTGAAGTNGATTCTGATAAGTTAAGATGTATATGGTAAGCCCTAGAGCAACCACTAAGAAAATAACTCAAAAAAATATAGTGAAAAAAATCATTAAAGGAATTAAAATGTTACACTAGAAAATATTCACTTAATGCAAAAGAAAGCAGTAAAGGAGGAATAGAGGAACAAAAAAGACATGAGACATATAGAAAACAAAAAGTAAAATGGCAGACGTAAATCCAACTATATCAATAATAACATTAAATGTGAATGGATTAAACAATCCAATCAAAAGGCAGAGATTGTCAGACTGGATTAAAAAACAAGATCCAACTATATGCTGTCTACAGGAGACACACTTTAGATTCAAAGAT
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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 |
|---|---|---|---|---|---|---|
| L1M4b_5end | TFAP2C | 1018 | 1028 | + | 16.61 | GCCCCAGGGCA |
| L1M4b_5end | PDR3 | 37 | 44 | + | 16.61 | TCCGCGGA |
| L1M4b_5end | PDR3 | 37 | 44 | - | 16.61 | TCCGCGGA |
| L1M4b_5end | CIN5 | 2395 | 2404 | - | 16.57 | ATTACATAAT |
| L1M4b_5end | TAL1::TCF3 | 2594 | 2603 | - | 16.51 | ACCATCTGGT |
| L1M4b_5end | FOXE1 | 86 | 97 | + | 16.40 | TTAAAAAAACAA |
| L1M4b_5end | FOXD3 | 1275 | 1288 | + | 16.38 | TAAACAAATAAACA |
| L1M4b_5end | SP9 | 647 | 656 | + | 16.33 | CCCCGCCCCC |
| L1M4b_5end | KLF15 | 587 | 594 | + | 16.27 | CCCCGCCC |
| L1M4b_5end | KLF15 | 647 | 654 | + | 16.27 | CCCCGCCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
