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 | ZNF558 | 1922 | 1950 | + | 37.48 | ATTTGATGAAAAACATTAATCTACACATC |
| L1M4b_5end | ZNF136 | 2186 | 2200 | - | 22.25 | GGATTCTTGGTTGAC |
| L1M4b_5end | CG4360 | 1297 | 1309 | + | 21.74 | ACAACAACAAGCC |
| L1M4b_5end | DOF3.6 | 3067 | 3087 | - | 20.14 | TTTACTTTTTGTTTTCTATAT |
| L1M4b_5end | ZNF281 | 1310 | 1319 | + | 20.07 | GGGGGAGGGG |
| L1M4b_5end | CDF5 | 3067 | 3087 | - | 19.76 | TTTACTTTTTGTTTTCTATAT |
| L1M4b_5end | Klf6-7-like | 582 | 601 | + | 19.49 | ACCGCCCCCGCCCAGCGCCC |
| L1M4b_5end | ZNF148 | 1310 | 1319 | - | 18.97 | CCCCTCCCCC |
| L1M4b_5end | DOF1.5 | 3073 | 3088 | + | 18.65 | AAAACAAAAAGTAAAA |
| L1M4b_5end | ZNF281 | 647 | 656 | - | 18.37 | GGGGGCGGGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
