MER39
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000758 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Euarchontoglires |
| Length | 707 |
| Kimura value | 19.31 |
| Tau index | 0.8174 |
| Description | MER39 Long Terminal Repeat for ERV1 endogenous retrovirus |
| Comment | MER39 has 4 bp TSDs, and is a member of a closely interrelated group of LTRs including MER21, MER34, LTR29, LTR48 and LTR49. Original orientation has been changed. 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 |
TGTTGGGGCTCAGAANACGATACCCCAAAGTATGGCGCCTTGGCATGCTGAGTACTTTGAACTGAAGGAGATTGGAAGGCCTCAGAAGCAGCCTCAGAAGCAAAGTCTCTCTCTGACCTTCTCCCGCCCTCCTGTCTCCCGCCCCCGTTCTCTCCTCCCCGAAGCGAGTCATAGAAACCAGAATTCCTCTTCCCCAAGGCGGGTCATAGAAACTAGAACCCCTCTCCCCCAAAGCAAGCCATAAAACCTAGAAANGTCACTCTGACCTTCCCCCGCCTTTCTGTNTNGGAGCNGGCCATAAAGAAATTCTCTGACCTNCCTTGTCTGANAGTAGGTCATAAGACCCTCATTCCAGAAGGGGTCCTGCCCTATACCCGGGAGGAAGGAATGCTACACAGAGAGGCCAAGAAGAATCTGAACAGACAGGCCTTGCTGGGTTTCCCCNCTCAGTTTATTACCATTAGATCATACCCCTTTTGTCCAATCACATTTCTNCACGACTGTCCATTCTTCATCGAACCTAAGCATAAAAATANAGTTTTCCCTGNGTCTTTGGGTCTTCATTTCTGAAGGCTCCCGTGTCACGTAAAACTTTGATTAAATAAATTTGTTATGCTTTTCTCTTGTTAATCTGTCTTTTGTTATAGGGGTGTCGGCCGTGANCCTTGCGATGGGTAGGAAAGGTATCACACCTTTCTNCCCCTACA
|
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 |
|---|---|---|---|---|---|---|
| MER39 | ZNF680 | 404 | 414 | + | 19.50 | CCAAGAAGAAT |
| MER39 | PRDM9 | 136 | 155 | - | 17.07 | GGAGAGAACGGGGGCGGGAG |
| MER39 | cad | 237 | 247 | + | 15.90 | AGCCATAAAAC |
| MER39 | SP2 | 137 | 145 | - | 15.71 | GGGGCGGGA |
| MER39 | btd | 138 | 146 | - | 15.62 | GGGGGCGGG |
| MER39 | TBX15 | 687 | 694 | - | 15.44 | AGGTGTGA |
| MER39 | ZNF768 | 396 | 404 | - | 15.25 | GCCTCTCTG |
| MER39 | snpc-4 | 650 | 661 | + | 15.19 | GTGTCGGCCGTG |
| MER39 | TBX1 | 687 | 694 | - | 15.16 | AGGTGTGA |
| MER39 | PATZ1 | 136 | 146 | - | 15.16 | GGGGGCGGGAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
