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 | BPC1 | 1864 | 1887 | + | 18.09 | GAGAGAGAGAAAGGAGCAGAAAAA |
| L1M4b_5end | KLF12 | 647 | 655 | - | 18.01 | GGGGCGGGG |
| L1M4b_5end | KLF10 | 647 | 655 | - | 17.88 | GGGGCGGGG |
| L1M4b_5end | ZNF677 | 178 | 189 | + | 17.87 | GGTAAGAACAGC |
| L1M4b_5end | SP1 | 647 | 655 | - | 17.80 | GGGGCGGGG |
| L1M4b_5end | PRDM9 | 223 | 242 | - | 17.79 | GCTGGGGAGGGGGGAGGAGG |
| L1M4b_5end | DOF3.2 | 3071 | 3086 | - | 17.74 | TTACTTTTTGTTTTCT |
| L1M4b_5end | RAMOSA1 | 1862 | 1875 | + | 17.69 | AGGAGAGAGAGAAA |
| L1M4b_5end | SP2 | 647 | 655 | - | 17.56 | GGGGCGGGG |
| L1M4b_5end | SP4 | 647 | 655 | - | 17.54 | GGGGCGGGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
