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 | FKH1 | 162 | 174 | - | 14.18 | ATCAGTAAACAAA |
| LTR108a_Mam | slp2 | 163 | 170 | - | 14.11 | GTAAACAA |
| LTR108a_Mam | HHO2 | 279 | 286 | + | 14.10 | AAGATTCC |
| LTR108a_Mam | eor-1 | 397 | 409 | - | 13.97 | AGAGAAAGAGAGT |
| LTR108a_Mam | FOXG1 | 163 | 170 | - | 13.80 | GTAAACAA |
| LTR108a_Mam | WRKY46 | 76 | 85 | + | 13.72 | CTTTGACTCT |
| LTR108a_Mam | let-381 | 163 | 170 | - | 13.69 | GTAAACAA |
| LTR108a_Mam | BZIP69 | 20 | 30 | + | 13.56 | TTACAGCTGGA |
| LTR108a_Mam | hif-1 | 215 | 223 | + | 13.44 | CTACGTGAC |
| LTR108a_Mam | FKH2 | 164 | 170 | - | 13.43 | GTAAACA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
