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 | BPC5 | 672 | 701 | - | -38.15 | GAGGAGAGAGAGAGAGACAGCTTACGCCAT |
| LTR13 | DAL81 | 504 | 522 | - | -38.87 | GATAACTGCGGGCGGGCCT |
| LTR13 | BPC5 | 674 | 703 | - | -40.17 | GAGAGGAGAGAGAGAGAGACAGCTTACGCC |
| LTR13 | BPC5 | 902 | 931 | - | -44.39 | CAAGACAAAGAGATAAAAGAAAAGACAGCT |
| LTR13 | BPC5 | 904 | 933 | - | -45.16 | CACAAGACAAAGAGATAAAAGAAAAGACAG |
| LTR13 | BPC5 | 900 | 929 | - | -45.33 | AGACAAAGAGATAAAAGAAAAGACAGCTGG |
| LTR13 | BPC5 | 676 | 705 | - | -45.39 | GAGAGAGGAGAGAGAGAGAGACAGCTTACG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
