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 | ZNF675 | 1103 | 1121 | + | 17.74 | AGACATGGAGGATAGAATG |
| L1MEd_5end | EBF1 | 138 | 148 | + | 17.72 | TCCCCAGGGGC |
| L1MEd_5end | NFKB2 | 132 | 142 | + | 17.53 | GGGAAATCCCC |
| L1MEd_5end | NFKB2 | 132 | 142 | - | 17.47 | GGGGATTTCCC |
| L1MEd_5end | Dif | 132 | 141 | - | 17.39 | GGGATTTCCC |
| L1MEd_5end | dl | 133 | 142 | - | 17.26 | GGGGATTTCC |
| L1MEd_5end | Dif | 132 | 141 | + | 17.21 | GGGAAATCCC |
| L1MEd_5end | ZNF354A | 2112 | 2131 | + | 17.09 | TAAATGTAAATGGACTAAAC |
| L1MEd_5end | RELA | 133 | 142 | - | 16.96 | GGGGATTTCC |
| L1MEd_5end | Ebf4 | 138 | 148 | + | 16.93 | TCCCCAGGGGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
