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 | TBR1 | 1423 | 1431 | - | 16.00 | AGGTGTGAA |
| L2 | TFAP2B | 2230 | 2240 | - | 16.00 | GCCCTGGGGCA |
| L2 | Clamp | 2962 | 2975 | - | 15.95 | GAGTGAGCGAGGGG |
| L2 | TFAP2C | 2230 | 2240 | - | 15.93 | GCCCTGGGGCA |
| L2 | ERF9 | 2663 | 2681 | - | 15.88 | GGTGGCAGTGGAGGTGGTG |
| L2 | SP4 | 340 | 348 | - | 15.85 | GGGGAGGGG |
| L2 | Esrrg | 1993 | 2001 | + | 15.85 | TCAAGGTCA |
| L2 | ZKSCAN5 | 1103 | 1111 | - | 15.83 | GGAAGTGAG |
| L2 | PRDM9 | 2927 | 2946 | - | 15.83 | TGAGGTCAGAGAGGTAACGG |
| L2 | RAX3 | 1565 | 1576 | - | 15.78 | GCAGGTAGGTGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
