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 | PK19717.1 | 43 | 51 | + | 15.24 | GGGCCCCCC |
| MER50 | ZKSCAN1 | 5 | 13 | + | 15.18 | ACAGTAGGT |
| MER50 | ewg | 362 | 371 | - | 15.13 | CCGCATGCGC |
| MER50 | ewg | 362 | 371 | + | 15.13 | GCGCATGCGG |
| MER50 | ewg | 398 | 407 | - | 15.13 | CCGCATGCGC |
| MER50 | ewg | 398 | 407 | + | 15.13 | GCGCATGCGG |
| MER50 | NFIB | 523 | 539 | + | 15.13 | CTTGGCCCTCTTCCAAG |
| MER50 | ZNF530 | 34 | 47 | + | 15.12 | GGCAGGAGAGGGCC |
| MER50 | nhr-6 | 485 | 492 | + | 15.08 | AAAGGTCA |
| MER50 | Zm00001d020595 | 699 | 708 | - | 14.94 | ACCGGCGGCG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
