MER50
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000807 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Haplorrhini |
| Length | 734 |
| Kimura value | 11.50 |
| Tau index | 0.9594 |
| Description | MER50 Long Terminal Repeat for ERV1 endogenous retrovirus |
| Comment | MER50 has 4 bp TSDs. Note that MER stands for MEdium Reiteration frequency interspersed repeat. As such, MERs as a group are a grab bag of DNA transposons and retrotransposons. |
| Sequence |
TGTTACAGTAGGTAGCTAGTCAGACATGAGCAGGGCAGGAGAGGGCCCCCCCCACACACACCAGGAATGTCAGGCGACCATCAGGTGATGGTCAGGCGGTTGTTAAACTGTCTCTCTAAAATAATAATTGGTCGCAGCCGGCGCCAGGGAAAGGCAGTCTCCCAATAGATAGAAAACACCTGAAACTGGTGATCAGCAGCTTCCCGATAAGATCTCAGGAGTTGGGCGAGTGGGCTCAAGCATGCGCACTAAGAGGCAAAATGGCGGAGTTTAACTGGTATATGACCTTCCTCTAGGAACACTCGACTGGTAAGGGAAGAACGCCTCAAGTGAGCATGCGTACAACTCCAGTAAACACACTGCGCATGCGGCCCCTCCCAAGTGCTGGCAGGCCACTGCGCATGCGGACAGCCCACCCCAAGGGAAAATCAGGGGAGAAGGGACGCAAACCCCGGAAGCATGCCAACGTATAAAACCCCAAGTCAAAGGTCAAACCGCGCACTTGATCTCTCAAGTCGCCCGCTTGGCCCTCTTCCAAGTGTACTTTACTTCCTTTCGTTCCTGCTCTAAAGCTTTTTAATAAACTTTCACTCCTGCTCTAAAACTTGCCTCGGTCTCTCCCTCTGCCTTATGCCCCTCGGTCGAATTCTTTCTTCTGAGGAGGCAAGAATTGAGGTTGCTGCAGACCCGTACGGATTCGCCGCCGGTAACTCAGATACCTTCCACCGNTAACA
|
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 |
|---|---|---|---|---|---|---|
| MER50 | EWSR1-FLI1 | 605 | 622 | - | -14.51 | GGGAGAGACCGAGGCAAG |
| MER50 | EWSR1-FLI1 | 432 | 449 | + | -16.16 | GGGGAGAAGGGACGCAAA |
| MER50 | BPC5 | 606 | 635 | - | -32.30 | GGCATAAGGCAGAGGGAGAGACCGAGGCAA |
| MER50 | BPC5 | 14 | 43 | + | -44.35 | AGCTAGTCAGACATGAGCAGGGCAGGAGAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
