LTR13
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000406 |
|---|---|
| TE superfamily | ERV2 |
| TE class | LTR |
| Species | Hominoidea |
| Length | 1007 |
| Kimura value | 4.52 |
| Tau index | 0.7187 |
| Description | LTR13 (Long Terminal Repeat) for HERVK13 endogenous retrovirus |
| Comment | LTR of class II endogenous retrovirus HERVK13. 6 bp target site dups. The tandem duplication at pos 313-368 and 366-422 is absent in some copies and tripled in others. |
| Sequence |
TGTGGGCGGCAAGCCACCCAGGCGCCGAGGCAAGAGACCGAGGGCACGAGCTGTTCCAGTATAATAAAATATATAAAACAAGAATAGTTATACCAGATATAGATCTTAGATATGATTATATATGAATATCATTAATCATTAGTTTGTAGCAATTACTCTTTATTCCAATATTATAATAATCCTCGCTCTATAATCATAACCTAGGAAAAACCAGGCCATACAGAGATAGGAGCTGAGGGGACATAGTGAGGAGTGACCAGAAGACAAGAGTGCGAGCCTTCTGTTATGCCCGGACAGGGCCACCAGAGGGCTCCTTGGTCTAGCGGTAACGCCAGCGTCTGGGAAGACGCCCGTTGCCAGGCGGACCGTGGTCTAGCGGTAGCGTNAGTGTCAAGGAAAAACACCCGCTACTTAGCAGACCGGGAAAGGGAGTCTCCCTTTCCCCGGGGGAGTTTAGAGAAGACTCTGCTCCTCCACCTCTTGTGGAGGGCCTGACATCAGTCAGGCCCGCCCGCAGTTATCCGGAGGCCTAACCGTCTCCCTGTGATGCTGTGCTTCAGTGGTCACGCTCCTAGTCCGCCTTCATGTTCCATCCTGTACACCTGGCTCTGCCTTCTAGATAGCAGTAGCAAATTAGTGAAAGTACTAAAAGTCTCTGATATGCAGAAATAATGGCGTAAGCTGTCTCTCTCTCTCTCCTCTCTCTCTCTGCCTCGGCTGCCAGGCAGGGAAGGGCCCCCTGTCCAGTGGACACGTGACCCACGTGACCTTACCTATCATTGGAGATGGCTCACACTCCTTACCCTGCCCCTTTGCCTTGTATCCAATAAATANCAGCGCAGCCNGGCATTCGGGGCCACTACCGGTCTCCGCGCCTTGGTGGTAGTGGTCCCCCGGGCCCAGCTGTCTTTTCTTTTATCTCTTTGTCTTGTGTCTTTATTTCTACACTCTCTCGTCTCCGCACACGGGGAGAAAANCCCACCGACCCTGTGGGGCTGGTCCCTACA
|
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 |
|---|---|---|---|---|---|---|
| LTR13 | ARALYDRAFT_897773 | 886 | 894 | - | 16.39 | GGGGACCAC |
| LTR13 | BPC6 | 682 | 702 | + | 16.36 | CTGTCTCTCTCTCTCTCCTCT |
| LTR13 | eor-1 | 698 | 710 | - | 16.24 | AGAGAGAGAGAGG |
| LTR13 | TCP3 | 886 | 893 | - | 16.23 | GGGACCAC |
| LTR13 | TCP24 | 886 | 893 | - | 16.21 | GGGACCAC |
| LTR13 | Usf | 759 | 768 | + | 16.16 | CCCACGTGAC |
| LTR13 | TCP5 | 886 | 893 | - | 16.15 | GGGACCAC |
| LTR13 | eor-1 | 687 | 699 | - | 16.15 | GGAGAGAGAGAGA |
| LTR13 | Ebf4 | 441 | 451 | - | 16.04 | TCCCCCGGGGA |
| LTR13 | Ebf4 | 441 | 451 | + | 16.04 | TCCCCGGGGGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
