LTR85b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000604 |
|---|---|
| TE superfamily | Gypsy |
| TE class | LTR |
| Species | Eutheria |
| Length | 784 |
| Kimura value | 33.12 |
| Tau index | 0.9939 |
| Description | LTR85b (Long Terminal Repeat) with unclear association (possibly Gypsy) |
| Comment | 4 bp TSDs. |
| Sequence |
TGTAACAGAGAGGAAAAAATTGCTATTTAAAACCANAACTGACTGCAGCCGCTTCTGCCTCCTAAGGGAGTGGCANAATTCCTCTCCGGAGNAGATGGCTCTTTGTTTAGGAAAATACCTTGATAGGCCNCTTTGGGTGTGAAAGGTGAGGCCCCCAGGGCATGGTCTGGAAGGAGACAGTGAAACAAAGAGANAGCTAAACTGCTCTGCATAANAAAATGAACAGAATTTNGGGGANNTGGAGGGNNGGNAGGAGAGGGGAGAGGGAGNTGAGAGAGGGGAGACAGGGGCAAGCAACTGAGAGAAGTCAGGAGATATGGGAAGCCTGTGGAGAAAGGTGGCCAGTGAGAAATTCCCGGTGGCGGAGGTGGCCGAAGGACTTTTAAGAACAGGGATGTCTAATATTCAATTTTAAGTTGTTTGCGTTGCTGTGATGTAACCCCCTCCGTCNCCCCAAACCTTCAGTAAAGTCTGCTACACACACAAATGCCTTGTGTGAGTGGTGTTTTGGGGAAATCAAGGAAAGGGGCTGNGTTCCACGTCTGGGTCGGCGCGGAGCAGAGAGAAGAGAACAGCCACGGGAGGTGAGACGCGAGTGAGATCGAGAGTTCAGCGGAAGCAGGAANTCGGAGCCAGAGGTGACCATGAGAACGTAAGCCCCCCGGGAATTCGCAGAAATCTTGGGGAGGGCATTGGACTTCCCACAGGATGTGGGATGGGGGTTTGAGCCAATTTTATTTAAATCTCAAAGGACAGGGTGACCTCAGCTGACATCTGGGTTACA
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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 |
|---|---|---|---|---|---|---|
| LTR85b | ESR2 | 750 | 764 | - | 20.02 | AGGTCACCCTGTCCT |
| LTR85b | ERF5 | 357 | 371 | - | 19.79 | CCACCTCCGCCACCG |
| LTR85b | ERF057 | 358 | 371 | - | 18.79 | CCACCTCCGCCACC |
| LTR85b | THRA | 758 | 775 | + | 18.49 | GTGACCTCAGCTGACATC |
| LTR85b | TFAP2C | 150 | 162 | - | 17.67 | TGCCCTGGGGGCC |
| LTR85b | TFAP2A | 150 | 162 | - | 17.67 | TGCCCTGGGGGCC |
| LTR85b | TFAP2C | 150 | 162 | + | 17.53 | GGCCCCCAGGGCA |
| LTR85b | TFAP2A | 150 | 162 | + | 17.48 | GGCCCCCAGGGCA |
| LTR85b | TFAP2B | 150 | 162 | - | 17.20 | TGCCCTGGGGGCC |
| LTR85b | TFAP2B | 150 | 162 | + | 17.07 | GGCCCCCAGGGCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
