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 | eor-1 | 685 | 697 | - | 18.35 | AGAGAGAGAGAGA |
| LTR13 | CTCF | 299 | 313 | + | 18.07 | GCCACCAGAGGGCTC |
| LTR13 | RAMOSA1 | 696 | 709 | - | 17.94 | GAGAGAGAGAGGAG |
| LTR13 | RAMOSA1 | 702 | 715 | - | 17.60 | GAGGCAGAGAGAGA |
| LTR13 | eor-1 | 683 | 695 | - | 17.34 | AGAGAGAGAGACA |
| LTR13 | BAD1 | 893 | 904 | + | 17.16 | CCCGGGCCCAGC |
| LTR13 | DOF3.6 | 909 | 929 | + | 17.14 | TTTTCTTTTATCTCTTTGTCT |
| LTR13 | Clamp | 683 | 696 | - | 16.83 | GAGAGAGAGAGACA |
| LTR13 | ZNF257 | 27 | 36 | + | 16.56 | GAGGCAAGAG |
| LTR13 | ARALYDRAFT_496250 | 886 | 893 | - | 16.55 | GGGACCAC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
