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 | ERF082 | 698 | 706 | + | 14.91 | TCGCCGCCG |
| MER50 | Pparg::Rxra | 480 | 492 | + | 14.84 | AAGTCAAAGGTCA |
| MER50 | ERF112 | 698 | 706 | + | 14.83 | TCGCCGCCG |
| MER50 | THAP1 | 30 | 37 | + | 14.80 | GCAGGGCA |
| MER50 | NR4A1 | 485 | 492 | + | 14.66 | AAAGGTCA |
| MER50 | PPARD | 479 | 492 | + | 14.65 | CAAGTCAAAGGTCA |
| MER50 | ATHB-40 | 122 | 132 | - | 14.62 | ACCAATTATTA |
| MER50 | SREBF1 | 80 | 89 | + | 14.60 | ATCAGGTGAT |
| MER50 | ERF15 | 699 | 706 | + | 14.58 | CGCCGCCG |
| MER50 | GSM1 | 447 | 456 | + | 14.56 | AAACCCCGGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
