LTR108a_Mam
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000384 |
|---|---|
| TE superfamily | ERV3 |
| TE class | LTR |
| Species | Eutheria |
| Length | 511 |
| Kimura value | 24.95 |
| Tau index | 0.0000 |
| Description | LTR108a_Mam (Long Terminal Repeat) for ERVL endogenous retrovirus |
| Comment | LTR108a_Mam has 5 bp TSDs, with a preference for GNNNC. The substitution level found in the Laurasiatherian reconstruction is ~21%. |
| Sequence |
TGTGTAGGATAGAGTTGATTTACAGCTGGACTGGGAAAGCTCTATCTTTATCTCTGGGGACGCCTGGATGTCTGGCTTTGACTCTTGGCCAAGATAAGGGCAGTGGGATTTATGATGTGCTGTTTAAAGTCCGAAACTCCCCTGGCGACCCCCAGGGTCAGTTTGTTTACTGATGGTTTTCANCTGGCNTAACCGGTTAGACAGCCTGGCTTGACTACGTGACCAGAGGGGCATAAAAGACCCCGCTGGGAACTTCTGCCTTGAGCTCTCCCGAAGCCAAGATTCCTCGCACAGATCTTGGTGGTTCAATCCGGAGACGAAGCGCGTCCTGTGTGCGAATAAGGACCCTGGGGAGCTTGCGCCTGGATGTCTCTCGGACCCCCAATGCTTGCCTGCACTCTCTTTCTCTTGCTGCACCGTATCCTTTGCCTTTAAATAAAAGCCTTACGTGAGTATGCTCTGTGGAGTCTGGTGAGTCCTTTCAAATATCCGAACTTGNGAAATCTTTGCA
|
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 |
|---|---|---|---|---|---|---|
| LTR108a_Mam | BPC1 | 397 | 420 | - | -1.58 | ACGGTGCAGCAAGAGAAAGAGAGT |
| LTR108a_Mam | ZNF410 | 108 | 123 | - | -1.96 | ACAGCACATCATAAAT |
| LTR108a_Mam | BPC6 | 392 | 412 | + | -2.58 | CCTGCACTCTCTTTCTCTTGC |
| LTR108a_Mam | BPC6 | 390 | 410 | + | -2.84 | TGCCTGCACTCTCTTTCTCTT |
| LTR108a_Mam | BPC5 | 394 | 423 | - | -48.04 | GATACGGTGCAGCAAGAGAAAGAGAGTGCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
