L2
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000358 |
|---|---|
| TE superfamily | L2 |
| TE class | LINE |
| Species | Mammalia |
| Length | 3082 |
| Kimura value | 37.63 |
| Tau index | 0.7930 |
| Description | L2 (LINE2) retrotransposon |
| Comment | L2 (LINE2) spread before the mammalian radiation, and copies are only 65-75% similar to the consensus. The 5' end is probably incomplete. The 3' end is also incomplete, but this terminus is extended by three model variants: L2a_3end, L2b_3end, and L2c_3end. Note that, whereas L1 is A- and purine-rich in the coding strand, L2 is C- and pyrimidine-rich. |
| Sequence |
ACCTCCNAGCCTCCATCGGCAGGGGTCAAGAGGGAGCCCCATGCGCTCNGAGTAAGACCGCCCTCCCCNGGCCTCCACGCCNCCATCGGCAGGAGTNAAGAGAGGGCCCCAGAACTCTGCGTGCTCCTGGCAAGACTCCNACTCCCCACTTCCCCCTCAACACTCACAGCCTCGCCACCACTATCTGCCTTGAGACCATCAGGACTAATCTCATCATGCCCTTTATCCCTGTTTACGTCAGTCACCACAAGAAGCCCAAGACTCCCAGGTCATCCCTCATCCCCCGGACTCTNATCCCCATACGGCTCTGTACATCTCCTNTTCTGACCCCATCTCCCACCCCTCCCCAACTCCTGAAACCCTTCCACTGTGCCCTCTGGAACTCACGGTCCGTCATCAGCAAAATCCCCCGTATCCTCAACCTCTTCTCTGAACGTTCCCTTCACCTTCTTGCTCTAACNGAAACCTGGCTCTCCCCTGAGGACACTGCTTCCCCTGCAGCCCTCTCAAGTGGTGGCTGTTTTCTCTCCCACANCCCTCGTACCACTGGGCCTGGAGGTGGGGTAGGTGTCCTCCTTGCTCCTCATTGCCGCTTCCAGACCATTCTCCCTCCCTCCTCCCTAAAACACCCCAGCTTTGAATCTCATGTCATCAGACTATACCACCCGCTACCCCTCCTTGTTGCAGTCATCTACCGACCTCCGGGTCACTCCCCCTCATTCCTTGAAGATTTTAGCTCCTGGCTCACTGTCACTCTCTCCAACACTACTCCTGTCATAATTCTTGGTGATTTCAATATCCACGTAGATGATCCTTCCAATACCCTGGCCTCTCAGTTCCTTGACCTCCTCTCCTCCAATGATCTTGTCCTCCACCCTACCTCAGCCACTCACTCCCATGGTCATACCCTAGACCTTGTCATTACCAATAACTGCAACCCCTCCATAATCTCAATTTCAAGCATCCCACTCTCTGACCACCACCTCCTATCTTTCCAGCTCACTCCCTCTAGTACCCCGACTCCAACAATTCTTCGACCCCACCGGGACCTCCAATCCATTGATCCTACCACCTTTTCACTGTCCCTCACCCCCCTCATGTCCTCACTTCCCTCCTTACCCAGCTTAGATTCCATGGTCNATCATTATAATCACTCCCTTGCATATACCCTCAACTCCCTTGCCCCTCTCTCGCTTCGTCGTACTCGCCTGGCAAAACCNCAACCCTGGTTAAATCCAACTCTCCGCCTACTCCGCGCCTGCACCCGNGCAGCTGAACGTGGCTGGAGAAAAACACACAACCATGCTGACTGGTCTCACTTTAAATTCATGACCACNAACCTCAAGTGGGCCCTTAATGCTGCCCGGCAATCNTACTACATTTCCCTAGTCCATTCACTCTCCCACTCTCCTAGACGACTATTTCACACCTTCTCCTCTCTCCTCAAACCTCCAACACCTCCTCCCCTATCCTCACTCTCAGCTGATGACCTTGCTTCCTATTTCACTGAGAAAATAGAAGCAATCAGAAGAGAACTTCCACANNCTCCCACCACCACATCTACCCACCTACCTGCATCTGTGCCCACATACTCTGCCTTCCCTCCTGTTACTACGGATGAACTGTCCGTGCTCCTATCTAAGGCCAACCCCTCCACTTGTGCACTAGATCCCATCCCCTCTCGCCTACTCAAGGACATCGCTCCAGCAATTCTCCCCTCTCTCTCCTGCATCATCAATTTTTCCCTCTCTACTGGATCATTCCCATCAGCATACAAACATGCTGTNATTTCTCCCATCTTTAAAAAACAAAAATTCTCCCTTGACCCCACNTCCCCCTCCAGCTACCGCCCCATTTCTCTGCTCCCCTTTACAGCAAAACTCCTCGAAAGAGTTGTCTATACTCGCTGTCTCCAATTCCTCTCCTCCCATTCTCTCTTGAACCCACTCCAATCAGGCTTTCGTCCCCACCACTCCACCGAAACTGCTCTTGTCAAGGTCACCAATGACCTCCACGTTGCTAAATCCAATGGTCAATTCTCAGTCCTCATCTTACTTGACCTNTCAGCAGCATTTGACACAGTTGATCACTCCCTCCTTCTTGAAACACTTTCTTCACTTGGCTTCCAGGACACCACACTCTCCTGGTTTTCCTCCTACCTCACTGGCCGCTCCTTCTCAGTCTCCTTTGCTGGTTCCTCCTCATCTCCCCGACCTCTNAACGTTGGAGTGCCCCAGGGCTCAGTCCTTGGACCTCTTCTCTTCTCTATCTACACTCACTCCCTNGGTGATCTCATCCAGTCTCATGGCTTTAAATACCATCTATATGCTGATGACTCCCAAATTTATATCTCCAGCCCGGACCTCTCCCCTGAACTCCAGACTCGTATATCCAACTGCCTACTCGACATCTCCACTTGGATGTCTAATAGGCATCTCAAACTTAACATGTCCAAAACTGAACTCCTGATCTTCCCCCTCAAACCTGCTCCTCCCGCAGTCTTCCCCATCTCAGTNAATGGCAACTCCATCCTTCCAGTTGCTCAGGCCAAAAACCTTGGAGTCATCCTTGACTCCTCTCTTTCTCTCACACCCCACATCCAATCCATCAGCAAATCCTGTCGGCTCTACCTTCAAAATATATCCAGAATCCGACCACTTCTCACCACCTCCACTGCCACCACCCTGGTCCAAGCCACCATCATCTCTCGCCTGGATTACTGCAATAGCCTCCTAACTGGTCTCCCTGCTTCCACCCTTGCCCCCCTNCAGTCTATTCTCAACACAGCAGCCAGAGTGATCCTTTTAAAACGTAAGTCAGATCATGTCACTCCTCTGCTCAAAACCCTCCAATGGCTTCCCATCTCACTCAGAGTAAAAGCCAAAGTCCTTACAATGGCCTACAAGGCCCTACATGATCTGGTCCCCCGTTACCTCTCTGACCTCATCTCCTACCACTCTCCCCCTCGCTCACTCCGCTCCAGCCACACTGGCCTCCTTGCTGTTCCTCGAACACGCCAGGCACGCTCCCGCCTCAGGGCCTTTGCACTTGCTGTTCCCTCTGCCTGGAACGCTCTTCCCCC
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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 |
|---|---|---|---|---|---|---|
| L2 | BPC5 | 1380 | 1409 | - | -47.24 | AGAGTGGGAGAGTGAATGGACTAGGGAAAT |
| L2 | BPC5 | 987 | 1016 | - | -47.65 | GGTACTAGAGGGAGTGAGCTGGAAAGATAG |
| L2 | BPC5 | 1716 | 1745 | - | -48.30 | GGAAAAATTGATGATGCAGGAGAGAGAGGG |
| L2 | BPC5 | 1905 | 1934 | - | -48.48 | AGAATGGGAGGAGAGGAATTGGAGACAGCG |
| L2 | BPC5 | 1060 | 1089 | - | -48.96 | TGAGGGACAGTGAAAAGGTGGTAGGATCAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
