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 | EBF3 | 417 | 425 | + | 16.59 | CCCAAGGGA |
| MER50 | MAZ | 372 | 379 | + | 16.08 | CCCCTCCC |
| MER50 | Zm00001d005892 | 699 | 706 | + | 15.92 | CGCCGCCG |
| MER50 | NFIB | 523 | 539 | - | 15.78 | CTTGGAAGAGGGCCAAG |
| MER50 | PLAGL2 | 43 | 50 | + | 15.67 | GGGCCCCC |
| MER50 | ZBTB14 | 495 | 502 | + | 15.55 | CCGCGCAC |
| MER50 | Os05g0497200 | 699 | 706 | + | 15.51 | CGCCGCCG |
| MER50 | THRB | 480 | 492 | + | 15.33 | AAGTCAAAGGTCA |
| MER50 | ZBTB6 | 233 | 241 | - | 15.31 | GCTTGAGCC |
| MER50 | KLF5 | 371 | 380 | + | 15.31 | GCCCCTCCCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
