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 | ZNF740 | 46 | 55 | + | 19.43 | CCCCCCCCAC |
| MER50 | Nr2f6 | 480 | 492 | + | 18.09 | AAGTCAAAGGTCA |
| MER50 | Nrf1 | 360 | 371 | + | 17.60 | CTGCGCATGCGG |
| MER50 | Nrf1 | 396 | 407 | + | 17.60 | CTGCGCATGCGG |
| MER50 | phol | 257 | 266 | - | 17.57 | CGCCATTTTG |
| MER50 | TB1 | 43 | 51 | + | 17.38 | GGGCCCCCC |
| MER50 | SREBF1 | 80 | 89 | - | 17.14 | ATCACCTGAT |
| MER50 | NR2F1 | 480 | 492 | + | 16.85 | AAGTCAAAGGTCA |
| MER50 | Ebf2 | 417 | 425 | + | 16.79 | CCCAAGGGA |
| MER50 | TB1 | 44 | 52 | + | 16.64 | GGCCCCCCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
