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 | CTCF | 281 | 313 | + | 26.61 | CTGTTATGCCCGGACAGGGCCACCAGAGGGCTC |
| LTR13 | RAMOSA1 | 685 | 698 | - | 25.64 | GAGAGAGAGAGAGA |
| LTR13 | RAMOSA1 | 687 | 700 | - | 20.96 | AGGAGAGAGAGAGA |
| LTR13 | RAMOSA1 | 683 | 696 | - | 20.84 | GAGAGAGAGAGACA |
| LTR13 | bHLH18 | 752 | 766 | + | 20.30 | CACGTGACCCACGTG |
| LTR13 | RAMOSA1 | 698 | 711 | - | 19.89 | CAGAGAGAGAGAGG |
| LTR13 | bHLH18 | 752 | 766 | - | 19.51 | CACGTGGGTCACGTG |
| LTR13 | RAMOSA1 | 700 | 713 | - | 19.21 | GGCAGAGAGAGAGA |
| LTR13 | BPC6 | 678 | 698 | + | 18.68 | TAAGCTGTCTCTCTCTCTCTC |
| LTR13 | Clamp | 685 | 698 | - | 18.41 | GAGAGAGAGAGAGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
