LTR7Y
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000589 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Hominidae |
| Length | 464 |
| Kimura value | 5.96 |
| Tau index | 0.9508 |
| Description | Long terminal repeat of an HERVH endogenous retrovirus |
| Comment | LTR of an HERVH element active 7-18 MYA, mostly in the common ancestor of gorilla, human and chimp. Updated from 2005 entry. Two copies are in the human hg38 genome are precisely absent from the chimpanzee genome: a solo LTR at chr11:49842787-49843262 with surprisingly many mutations, and a copy with a partial internal sequence at chr9:86586832-86589058. A 21-bp sequence starting at pos 174 is present in 1 or 2 tandem copies. |
| Sequence |
TGTCAGGCCTCTGAGCCCAGGCCAGGCCATCGCATCCCCTGTGACTTGCACGTATACATCCAGATGGCCTGAAGTAACTGAAGATCCACAAAAGAAGTAAAAACAGCCTTAACTGATGACATTCCACCATTGTGATTTGTTCCTGCCCCACCCTAACTGATCAATGTACTTTGTAATCTCCCCCACCCTTGCTTTGTAGTCTCCCCCACCCTTAAGAAGGTTCTTTGTAATTCTCCCCACCCTTGAGAATGTACTTTGTGAGATCCACCCCTGCCCACCAGAGAACAACCCCCTTTGACTGTAATTTTCCATTACCTTCCCAAATCCTATAAAACGGCCCCACCCCTATCTCCCTTCGCTGACTCTCTTTTCGGACTCAGCCCGCCTGCACCCAGGTGAAATAAACAGCCATGTTGCTCACACAAAGCCTGTTTGGTGGTCTCTTCACACGGACGCGCATGAAA
|
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 |
|---|---|---|---|---|---|---|
| LTR7Y | KLF1 | 146 | 153 | - | 14.64 | GGGTGGGG |
| LTR7Y | KLF1 | 181 | 188 | - | 14.64 | GGGTGGGG |
| LTR7Y | KLF1 | 204 | 211 | - | 14.64 | GGGTGGGG |
| LTR7Y | KLF1 | 235 | 242 | - | 14.64 | GGGTGGGG |
| LTR7Y | KLF1 | 338 | 345 | - | 14.64 | GGGTGGGG |
| LTR7Y | TEAD4 | 119 | 126 | + | 14.45 | ACATTCCA |
| LTR7Y | ZFP42 | 404 | 416 | - | 14.38 | CAACATGGCTGTT |
| LTR7Y | Glyma19g26560.1 | 336 | 343 | + | 14.23 | GGCCCCAC |
| LTR7Y | GLYMA19G26560 | 336 | 343 | + | 14.23 | GGCCCCAC |
| LTR7Y | Nfat5 | 305 | 312 | - | 14.18 | ATGGAAAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
