LTR10C
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000394 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Catarrhini |
| Length | 591 |
| Kimura value | 4.93 |
| Tau index | 0.9412 |
| Description | LTR10C (Long Terminal Repeat) for HERVI endogenous retrovirus |
| Comment | LTR10C is a long terminal repeat that appears to be associated with HERVI. |
| Sequence |
TGTAAAAAGTAAAGTAGAGGTTCCTCTTCAAAGACTTTCCTCCCCGTCTAATTAGGAATAAATAGTAACTTCTCTTAGAAGCAAAATTTATTCAAAGACCTGTGCTAACATTCTTAAATATCTGCTAGCCGTAATAAAGAAATCAATGTACTTTATGTTCTTAGCTCCCACAATTTAGCCTAAATATTTGCCCTGGCATGCTTATACTGGTCCAAGCAAGCATTAGGTCATAGCCTGTTCCTCTTCCTTATTTGAAGGTGTTTTTACCTTTCTCAGCATTCCACAAGTTACTTCCTCCTTCCTTTGTTCTCCTCTGCCTTTGCCTCTTTTAAAAAGTTCTAAGTTGCTAGCCAATCGGGACAAATACAGAATGTGAGGTCCCGTTCCAGCCAATGGAAACCGGACACAGCAGTAGGGTGGACGCGTCAGGTTATAAATGACCCTGTCTCCTTTGTTCGGTGTACTCTCGTGGCAAAACTGCTGGCGAGTGTACCCTTTCTGCAGAAAGTANAAAAATGGCCTTGCTGAGGAAATTAAATTTATGTTCAAGTGCTATTTCTTTACGGCACCGGGGAACAAGCATTTCAAACA
|
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 |
|---|---|---|---|---|---|---|
| LTR10C | ZIC1 | 408 | 421 | - | 5.85 | TCCACCCTACTGCT |
| LTR10C | TP53 | 195 | 212 | + | 5.49 | GGCATGCTTATACTGGTC |
| LTR10C | TFAP4::FLI1 | 399 | 412 | + | 3.71 | ACCGGACACAGCAG |
| LTR10C | Rarb | 438 | 453 | - | 1.86 | AAAGGAGACAGGGTCA |
| LTR10C | Rarg | 438 | 452 | - | -1.74 | AAGGAGACAGGGTCA |
| LTR10C | EWSR1-FLI1 | 293 | 310 | - | -5.24 | AGAACAAAGGAAGGAGGA |
| LTR10C | EWSR1-FLI1 | 297 | 314 | - | -14.30 | GAGGAGAACAAAGGAAGG |
| LTR10C | AT4G12670 | 529 | 557 | - | -17.06 | AATAGCACTTGAACATAAATTTAATTTCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
