MER4D1
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000803 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Haplorrhini |
| Length | 900 |
| Kimura value | 12.09 |
| Tau index | 0.9731 |
| Description | MER4D1 Long Terminal Repeat for ERV1 endogenous retrovirus |
| Comment | MER4D1 LTR is a ~90% identical variant of MER4D, which itself is a ~192 bp insertion variant with respect to MER4B. 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 |
TGTAAACCAAAAATAAAATTCTAAGCCCCCCAACCGACTGAATGGACCCCTCCTCTCGGCCAAGGGCATTCCAAAGTAAACCTGAAAAACTAGTTCAGGCCATGATGGGAAGGGGGGGTCGGACATGCCTCATTATACCCTCCTCCCTTTGGAATTCAGGCACAACTGACCAGCATTAACATTAAAACAGAGATCTTAAGACTGACAAAACAGACTCTTTGTAGCAATAAGATACCAAATTCCAACCTGACTCTAGTATAGCATCACATGACAGATAGCAGGCCCTGAAAGAAATCGAAGTATTTTACCCCAAAATATATTTCTTTGACATATTTTGAAATGGCCCTGCAAAGCTGTCTCTTGTGGGGAAAATCTACATTCTGTAGAGAATCCCCTTCCCTTTCCAGGTCTTTTTCCTGATCCAGGAGAGAATTAACTAAGAGTCTGGCACCTTTTTAAGTCTGATAAGAAACATTTACAATCTATTCTCTCTGAAGCCTGCTACCTGGAGGCTTCATCTGCATGATAAGAACCTTGGTCTCCACAACCCCTTATCTTAACCCAGACACTCCTTTCTATTGATTCCAGGTCTTTAGATAATAACTNAACTCTTTCAACCAATTGCCAATCAGAAAATCTTTGAATCCACCGTATGACCTGGAAGCCCCCCCCTCCACTTCGAGTTGTCCCGCCTTTCCGGACCGAACCAATGTACATCTTACATGTATTGATTGATGTCTTATGTCTCCCTAAAATGTATAAAACCAAGCTGTAGCCCGACCACCTTGGGCACATGTTCTCAGGATCTCCTGGGGCTGTGTCACGGGCCATGGTCACTCATATTTGGCTCAGAATAAATCTCTTCAAATATTTTACAGAGTTTGACTCTTTTCGTCGACA
|
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 |
|---|---|---|---|---|---|---|
| MER4D1 | Usf | 263 | 272 | + | 13.34 | ATCACATGAC |
| MER4D1 | UGA3 | 687 | 693 | - | 13.34 | GGCGGGA |
| MER4D1 | RME1 | 144 | 153 | - | 13.33 | TCCAAAGGGA |
| MER4D1 | Ebf4 | 806 | 816 | - | 13.28 | GCCCCAGGAGA |
| MER4D1 | Prdm15 | 403 | 413 | - | 13.21 | AAAGACCTGGA |
| MER4D1 | Prdm15 | 584 | 594 | - | 13.21 | AAAGACCTGGA |
| MER4D1 | sma-4 | 562 | 568 | - | 13.18 | TGTCTGG |
| MER4D1 | ONECUT1 | 577 | 585 | - | 13.16 | GAATCAATA |
| MER4D1 | srp | 550 | 557 | - | 13.11 | AGATAAGG |
| MER4D1 | vfl | 502 | 508 | - | 13.07 | CAGGTAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
