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 | Hand1::Tcf3 | 70 | 78 | + | 13.24 | GTCTGGCTT |
| LTR108a_Mam | sma-4 | 69 | 75 | + | 13.18 | TGTCTGG |
| LTR108a_Mam | FOXF2 | 163 | 171 | - | 13.14 | AGTAAACAA |
| LTR108a_Mam | srp | 92 | 99 | + | 13.11 | AGATAAGG |
| LTR108a_Mam | BZIP18 | 20 | 29 | + | 13.00 | TTACAGCTGG |
| LTR108a_Mam | MYR2 | 279 | 286 | - | 12.98 | GGAATCTT |
| LTR108a_Mam | CAMTA1 | 320 | 328 | + | 12.98 | AAGCGCGTC |
| LTR108a_Mam | FOXO6 | 164 | 170 | - | 12.98 | GTAAACA |
| LTR108a_Mam | FOXD1 | 164 | 170 | - | 12.98 | GTAAACA |
| LTR108a_Mam | ZBTB6 | 259 | 267 | + | 12.96 | CCTTGAGCT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
