L1MEd_5end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000777 |
|---|---|
| TE superfamily | L1 |
| TE class | LINE |
| Species | Eutheria |
| Length | 2224 |
| Kimura value | 31.29 |
| Tau index | 0.9542 |
| Description | 5' end of L1 retrotransposon, L1MEd_5end subfamily |
| Comment | 5' end of LINE elements with L1ME subfamily 3' ends ORF1 starts at pos. 682. ORF 684-1640 encodes a gag protein similar to those of other L1ME elements. ORF2 starts at position 2075 (standard first 150 nucleotides included). |
| Sequence |
CGGACTTCCGTTTCCGGCAATATGGCGGACTAGATAACCTGAAAACCCTCCCGCTACAAAACACCTAGAAATGCTGGATAAAATATAACAAACATCCTTTTAAATGCATAGCTGAGCTCGCAAGAAAGTAAGGGAAATCCCCAGGGGCCAAAAACGAAGAGGGAACTGAAAACCAGAGCGGTAAGCACGAGCTGAAGCTGCGGCTGCCCTGAGGGCATTTGCCGGTCTCGGTAACCNAGGGGCTTGGGTTTTAACGGCCACGCGGGGACAGGAGACGAGGCCTTGGGCCCGCGCAAGGCGGGGAGTTGGAACTGAGACCCCCGCATAAAGCCGGGACCCTCGAAGGGCTACACCCTCAGTGAAAGGGTGGACTAGAAAAAAATCCGCCCACCGGCACAGGGAGACGACAAGGAAACTTGTCTGTCTCGGCCTGGGCTCTGGGTGGAGAAAAAAAGTCTCCCCTGAGAATTCGTAACCACAGGCCTGCCCTCACGCGGGTTTGGGGTTCGAATTTACACTACCTGCGTGGTCCGGGAAACCCCAAGCCGAGAAATTAACTTAAAGTGGTCCCGGGCTGGTAGTACCCCTGGGGCGCCTGGCAGAAGCAAACGCAAANCCTCTCTGGAGGAACGCACCCTCAACCCAGGCCNCANAGGATTCCCACAGATAAAGCCCCGNCGAANATGAGCTCACAATCNAAAATTACAAAACACACGAGGAAACAANCCACCATGAGCGAGAGTCAGCAGAAACAACAAACAGCAGAATTAGACCCCCAAGAACTTCAGATANTGGAATTATCAGATANAGANTATAAAATAAGTATGTTTAAAATGNTTAAAGANATAAAAGAAGGAATTAAAAACATGAGNAAGGAACAAGANACTATNAAAAANGACCAGGCAGATTTGAAAAAGAACCAAATAGAACTTCTAGAAATGAAAAATATAGTCATTGAAATTAAAAACTCAATGGATGGGTTAAACAGCAGATTAGACACAGCTGAAGAGAGAATTAGTGAACTGGAAGATAGATCTGAAGAAATTACCCAGAATGCAGCACAGAGAGATAAAGAGATGGAAAATATGAAAGAGAGGTTAAGAGACATGGAGGATAGAATGAGAAGGTCTAACATACGTCTAATNGGAGTTCCAGAAGGAGAGAATAGAGAGAATGGGGGAGAGGCAATATTCGAAGAGATAATGGCTGAGAATTTTCCAGAATTGATGAAAGACATNAATCCTCAGATTCAGGAAGCNCAACGAATCCCAAGCAGGATAAATAAAAANAAATCCACACCTAGACACATCGTAGTGAAACTGCAGAACACCAAAGACAAAGAGAAGATCTTAAAAGCAGCCAGAGAGAAAAGACAGATTACCTACAAAGGAACGACAATTAGACTGACAGCNGACTTCTCAACAGCAACAATGGAAGCCAGAAGACAGTGGAATAATATCTTCAAAGTGCTGAGAGAAAATAACTGTCAACCTAGAATTCTATACCCAGCNAAACTATCNTTCAAGAATGAGGGCGAAATAAAGACATTTTCAGACAAACAAAAACTGAGAGAGTTTACCACCAACAGACCCTCACTAAAGGAACTNCTAAAGGATGTACTTCAGGAAGAAGGAAANTGANCCCAGAAGGAAGGNCTGAGATGCAAGAAGGAATGGTGAGCAAAGAAANTGGTAAACATGTGGGTAAATCTAAACAAACATTGACTGTATAAAACAATAATAATAATGNCTAATTTGNGGGGTATAAAAACAAGGTAGAACTAAAATACTGGACAACAATAACATGTAAGTCGGGAGGGGGGTGATCGGAGTTAAAGCGTTCTAAGGTCCTTGTATTGTTCGGGAGGAGGGTAAAGATATTGATTAACTTTAGACTTTGTTAAGTTAAGTATGCATGTTAAAATTTTAAGGGTAACCACTAAAAGAATAGAAATAGAATGTATAACTTCCAAACCAGTAGAGGGGAAAANAAAAAANAAAAANNNAATCAATCCAAAAGAAGGCAAGAAAGGAGAGAAAAAGAAACATAGAACAAATAGAAAGCACAAAATAAGATGGTAGAAATAAATCCAAATATATCAGTAATCACAATAAATGTAAATGGACTAAACTCNCCAGTTAAAAGACAGAGATTGTCAGATTGGATTAAAAAAACAAATCCAGCTATATGCTGTTTACAAGAGACACACCTAAAACATAAGGAC
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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 |
|---|---|---|---|---|---|---|
| L1MEd_5end | HSF1 | 1211 | 1223 | - | 16.13 | TTCTGGAAAATTC |
| L1MEd_5end | MAZ | 1813 | 1820 | - | 16.08 | CCCCTCCC |
| L1MEd_5end | HSF4 | 1211 | 1223 | - | 16.04 | TTCTGGAAAATTC |
| L1MEd_5end | SOX12 | 1855 | 1864 | - | 16.02 | CCCGAACAAT |
| L1MEd_5end | TCP4 | 564 | 571 | - | 15.98 | GGGACCAC |
| L1MEd_5end | SPL3A | 577 | 588 | - | 15.91 | AGGGGTACTACC |
| L1MEd_5end | HSF2 | 1211 | 1223 | - | 15.85 | TTCTGGAAAATTC |
| L1MEd_5end | HSFA1E | 1210 | 1223 | + | 15.82 | AGAATTTTCCAGAA |
| L1MEd_5end | FOXE1 | 1710 | 1721 | + | 15.81 | CTAAACAAACAT |
| L1MEd_5end | PK10344.1 | 564 | 571 | - | 15.74 | GGGACCAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
