LTR12C
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000402 |
|---|---|
| TE superfamily | ERV1 |
| TE class | LTR |
| Species | Hominoidea |
| Length | 1579 |
| Kimura value | 6.12 |
| Tau index | 0.9672 |
| Description | LTR12C (Long Terminal Repeat) for HERV9 endogenous retrovirus |
| Comment | This sequence is a hybrid between PTR5 and LTR12. |
| Sequence |
TGTGAGAGGTGACAGCGTGCTGGCAGTCCTCACAGCCCTCGCTCGCTCTCGGCGCCTCCTCTGCCTGGGCTCCCACTTTGGCGGCACTTGAGGAGCCCTTCAGCCCGCCGCTGCACTGTGGGAGCCCCTTTCTGGGCTGGCCAAGGCCGGAGCCGGCTCCCTCAGCTTGCGGGGAGGTGTGGAGGGAGAGGCGCGAGCGGGAACCGGGGCTGCGCGCGGCGCTTGCGGGCCAGCTGGAGTTCCGGGTGGGCGTGGGCTCGGCGGGCCCCGCACTCGGAGCGGCCGGCCGGCCCGCCGGCCCCGGGCAGTGAGGGGCTTAGCACCCGGGCCAGCGGCTGCGGAGGGTGTACTGGGTCCCCCAGCAGTGCCGGCCCACCGGCGCTGCGCTCGATTTCTCGCCGGGCCTTAGCTGCCTTCCCGCGGGGCAGGGCTCGGGACCTGCAGCCCGCCATGCCTGAGCCTCCCCCCCCCNTCCGTGGGCTCCTGTGCGGCCCGAGCCTCCCCGACGAGCGCCGCCCCCTGCTCCACGGCGCCCAGTCCCATCGACCACCCAAGGGCTGAGGAGTGCGGGCGCACGGCGCGGGACTGGCAGGCAGCTCCACCTGCGGCCCCGGTGCGGGATCCACTGGGTGAAGCCAGCTGGGCTCCTGAGTCTGGTGGGGACNTGGAGAACCTTTATGTCTAGCTCAGGGATTGTAAATACACCAATCGGCACTCTGTATCTAGCTCAAGGTTTGTAAACACACCAATCAGCACCCTGTGTCTAGCTCAGGGTTTGTGAATGCACCAATCGACACTCTGTNATCTAGCTACTCTGGTGGGGNCTTGGAGAACCTTTATGTCTAGCTNAGGGATTGTAAATACACCAATCGGCACTCTGTATCTAGCTCAAGGTTTGTAAACGCACCAATCAGCACCCTGTGTCTAGCTCAGGGTTTGTGAATGCACCAATCGACACTCTGTATCTAGCTAATCTGGTGGGGACGTGGAGAACCTTTGTGTCTAGCTCAGGGATTGTAAACGCACCAATCAGCGCCCTGTCAAAACGGACCANTCGGCNCTCTGNNNNNNAGACCANTCGGCTCTCCGNNNNNTGGACCAATCAGCAGGATGTGGGTGGGGCCAGATAAGAGAATAAAAGCAGGCTGCCCGAGCCAGCAGTGGCAACCCGCTCGGGTCCCCTTCCACACTGTGGAAGCTTTGTTCTTTCGCTCTTTGCAATAAATCTTGCTGCTGCTCACTCTTTGGGTCCACACTGCCTTTATGAGCTGTAACACTCACCGCGAAGGTCTGCAGCTTCACTCCTGAAGCCAGCGAGACCACGAGCCCACCGGGAGGAACGAACAACTCCAGACGCGCCGCCTTAAGAGCTGTAACACTCACCGCGAAGGTCTGCAGCTTCACTCCTGAGCCAGCGAGACCACGAACCCACCAGAAGGAAGAAACTCCGAACACATCCGAACATCAGAAGGAACAAACTCCGGACGCGCCGCCTTTAAGAGCTGTAACACTCACCGCGAGGGTCCGCGGCTTCATTCTTGAAGTCAGTGAGACCAAGAACCCACCAATTCCGGACACA
|
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 |
|---|---|---|---|---|---|---|
| LTR12C | REST | 317 | 336 | + | 20.33 | TTAGCACCCGGGCCAGCGGC |
| LTR12C | HAP5 | 1025 | 1038 | - | 18.78 | GGGCGCTGATTGGT |
| LTR12C | HAP5 | 745 | 758 | - | 17.96 | GGGTGCTGATTGGT |
| LTR12C | HAP5 | 906 | 919 | - | 17.96 | GGGTGCTGATTGGT |
| LTR12C | KLF11 | 246 | 255 | - | 17.79 | CCACGCCCAC |
| LTR12C | SP8 | 245 | 255 | - | 17.55 | CCACGCCCACC |
| LTR12C | Gli2 | 545 | 553 | + | 17.12 | GACCACCCA |
| LTR12C | dar1 | 1113 | 1123 | - | 17.08 | GCCCCACCCAC |
| LTR12C | KLF9 | 1113 | 1123 | - | 17.03 | GCCCCACCCAC |
| LTR12C | Clamp | 35 | 48 | - | 17.02 | GAGCGAGCGAGGGC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
