LTR86C
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000610 |
|---|---|
| TE superfamily | ERV3 |
| TE class | LTR |
| Species | Eutheria |
| Length | 621 |
| Kimura value | 33.83 |
| Tau index | 1.0000 |
| Description | LTR86C (Long Terminal Repeat) for ERVL endogenous retrovirus |
| Comment | 5 bp TSDs, with a bias for NNNNC. |
| Sequence |
TGCAGGATAGGCCCTATAGCTGGTCTAAGGGCCTGTTAGCATGACTCCCAGAGACGTCTGGGTAACTGACCCTTGTTCTAGTTCCGCAGCNCTGAGTTCAGGAATGTACTTGGACCAGGCTGTGTTAGCCTGGGGAGGCTGAGGGTGATAAATGAGGACTGTGTTCATGCCTGAGTGTACTGTACTGTACTGTGCTCTGCAGTCATATTGTATATTGTATAACTCCGAGATTGATGAGGTGCACCTGGCCCAGATGAGGTGGTCCCCGGCACATATCCAGACTAGCCTACGTGCAGAACTGCTCCAGCCTTATGTATATAAGGCTGGGCTTGGAGGGGGGCAGTTGAGCTTCCAGAAGGTCTGATGTGACCCTCACTCACTCAGACGTTATCATCCGCAACTGTGCGCCCCCTGGTGAGGATCTTGGGGTCCGGAAGCTTGCACCTCCGTCTGTCCTGGAGAATGTTGCTGATCTCTCTGCCGTGTATCCTGACTGCGCTGACTTCCTTCTGTATCCTTTAGATAAGTAAACCTTGTTTGATTTACCCAAGTGGTGTCTGTGTCTGGTCTTTCCGTCAATCTGAACCTACTATTGACATTTGTCAATACAGTGGTCGTGCA
|
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 |
|---|---|---|---|---|---|---|
| LTR86C | Ets21C | 431 | 438 | + | 14.07 | CCGGAAGC |
| LTR86C | bHLH112 | 548 | 554 | - | 13.92 | CCACTTG |
| LTR86C | OsFBH1 | 548 | 554 | - | 13.92 | CCACTTG |
| LTR86C | SUT2 | 220 | 229 | + | 13.84 | TAACTCCGAG |
| LTR86C | nhr-6 | 594 | 601 | - | 13.81 | AAATGTCA |
| LTR86C | Ets65A | 431 | 438 | + | 13.77 | CCGGAAGC |
| LTR86C | Ets96B | 430 | 438 | + | 13.72 | TCCGGAAGC |
| LTR86C | TEAD1 | 99 | 107 | - | 13.63 | ACATTCCTG |
| LTR86C | ZIC4 | 406 | 419 | + | 13.58 | CGCCCCCTGGTGAG |
| LTR86C | TCP16 | 259 | 266 | + | 13.49 | GTGGTCCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
