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
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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 | ATHB-15 | 133 | 145 | - | 16.01 | AAACTAATGATTA |
| LTR13 | TCP4 | 886 | 893 | - | 15.98 | GGGACCAC |
| LTR13 | TFEC | 752 | 759 | + | 15.88 | CACGTGAC |
| LTR13 | TFEC | 761 | 768 | + | 15.88 | CACGTGAC |
| LTR13 | PK10344.1 | 886 | 893 | - | 15.74 | GGGACCAC |
| LTR13 | CTCFL | 735 | 742 | - | 15.72 | CAGGGGGC |
| LTR13 | EBF1 | 441 | 451 | + | 15.70 | TCCCCGGGGGA |
| LTR13 | EBF1 | 441 | 451 | - | 15.70 | TCCCCCGGGGA |
| LTR13 | PLAGL2 | 733 | 740 | + | 15.67 | GGGCCCCC |
| LTR13 | Mad | 19 | 33 | + | 15.44 | CAGGCGCCGAGGCAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
