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 | ZNF530 | 391 | 404 | - | 16.60 | GAAAGGGAAGGGGA |
| MER4D1 | ZNF740 | 665 | 674 | + | 16.45 | CCCCCCCCTC |
| MER4D1 | PBX1 | 728 | 736 | - | 15.97 | ATCAATCAA |
| MER4D1 | REF6 | 184 | 192 | + | 15.93 | AAAACAGAG |
| MER4D1 | MEIS1 | 729 | 737 | - | 15.29 | CATCAATCA |
| MER4D1 | USF1 | 263 | 272 | - | 15.14 | GTCATGTGAT |
| MER4D1 | ceh-60 | 623 | 631 | - | 14.71 | TGATTGGCA |
| MER4D1 | NFYA | 625 | 632 | + | 14.54 | CCAATCAG |
| MER4D1 | elt-3 | 463 | 470 | - | 14.52 | TCTTATCA |
| MER4D1 | elt-3 | 524 | 531 | - | 14.52 | TCTTATCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
