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 | ZNF16 | 338 | 358 | - | 3.31 | CGAAGGGAGATAGGGGTGGGG |
| LTR7Y | IRF3 | 305 | 321 | - | 2.83 | GGGAAGGTAATGGAAAA |
| LTR7Y | E2FC | 400 | 414 | + | 1.98 | AATAAACAGCCATGT |
| LTR7Y | TCP14 | 251 | 268 | + | -2.80 | GTACTTTGTGAGATCCAC |
| LTR7Y | BCL6B | 320 | 336 | - | -15.03 | CGTTTTATAGGATTTGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
