LTR19B
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000432 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Haplorrhini |
| Length | 580 |
| Kimura value | 7.55 |
| Tau index | 1.0000 |
| Description | LTR19B (Long Terminal Repeat) for ERV1 endogenous retrovirus |
| Comment | LTR19 elements are flanked by 5 bp target site duplication. |
| Sequence |
TGACAGAGCAGGAGCACCGTCATCTCGGACAAACACCGCCACTTTAAGTTCCAGCTCCCTTTCTAGCCTCATGCATTTCAAGGAAATCACTTCTCTTCTAACTACAAGCAGCCAGAAAGAGCAGACAGTAAAACACAGATAAGACAGCTCGGGCACAGAGGGAGGTGGGGGGAAAGTCTCTTGGGTAACTGCCAAACTTCACCCTCATACAATGGGCCCCAGTAAAACAGTGGGCCTTAATAAGCACATTCCTTTCCCTTCAGGTGCACTAAGATAGGGAAGCTAAAAGCAGACTCGGGGNNNCGNCGGGGGGTATGCCTGCAGCTGCAGAAAGATGTATGGGAACAGACACACAACTCTCCCTCCCAGATAAGCACAACAAAGAGACACAGAAGCAGTCCAAGCCTCTGATAAACTCTCCCACCCTGAATCCTTAAAAACTCTTAGTCTGTAAGAGAGTGTGCCTCTGACCTAACTCGGCCAGAAGCCCCTCTCAGGTTTGTTTTCTCTAAAATAAACCTGTCTTTGNCGACTGTCGAGCCACCTTTCGTGTTTCTTTCCTCTTTCTTTAATTCTTACA
|
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 |
|---|---|---|---|---|---|---|
| LTR19B | MYB108 | 190 | 199 | + | 13.12 | TGCCAAACTT |
| LTR19B | ERF010 | 34 | 41 | + | 13.03 | CACCGCCA |
| LTR19B | TEAD2 | 246 | 252 | + | 13.03 | ACATTCC |
| LTR19B | ERF015 | 34 | 41 | + | 12.93 | CACCGCCA |
| LTR19B | DOF3.6 | 552 | 572 | + | 12.92 | GTTTCTTTCCTCTTTCTTTAA |
| LTR19B | RAP2-1 | 34 | 41 | + | 12.90 | CACCGCCA |
| LTR19B | DOF5.1 | 554 | 572 | - | 12.86 | TTAAAGAAAGAGGAAAGAA |
| LTR19B | DREB2C | 34 | 41 | + | 12.84 | CACCGCCA |
| LTR19B | GRF4 | 321 | 328 | + | 12.83 | GCAGCTGC |
| LTR19B | GRF4 | 321 | 328 | - | 12.83 | GCAGCTGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
