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 | ZNF136 | 1486 | 1500 | - | 22.15 | GAATTCTAGGTTGAC |
| L1MEd_5end | TFAP2C | 205 | 217 | + | 20.03 | TGCCCTGAGGGCA |
| L1MEd_5end | TFAP2C | 205 | 217 | - | 20.02 | TGCCCTCAGGGCA |
| L1MEd_5end | TFAP2A | 205 | 217 | + | 19.98 | TGCCCTGAGGGCA |
| L1MEd_5end | TFAP2B | 205 | 217 | + | 19.93 | TGCCCTGAGGGCA |
| L1MEd_5end | TFAP2A | 205 | 217 | - | 19.87 | TGCCCTCAGGGCA |
| L1MEd_5end | TFAP2B | 205 | 217 | - | 19.75 | TGCCCTCAGGGCA |
| L1MEd_5end | ZNF76 | 1047 | 1063 | + | 19.14 | ACCCAGAATGCAGCACA |
| L1MEd_5end | DOF3.6 | 2026 | 2046 | - | 17.97 | GTTTCTTTTTCTCTCCTTTCT |
| L1MEd_5end | phol | 18 | 27 | - | 17.89 | CGCCATATTG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
