DIRS-1b_Amnio
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0006272 |
|---|---|
| TE superfamily | DIRS |
| TE order | LTR |
| Species | Amniota |
| Length | 5479 |
| Kimura value | None |
| Tau index | 0.0000 |
| Description | Long Terminal Repeat for an DIRS endogenous retrovirus |
| Comment | 20% subst outside CGs in painted turtle. CDSs with some frameshifts.Probably Amniota-wide |
| Sequence |
TTTCTGCAGCCCAGCGTCTCCCACAATTCTGATACGTATGGGCTATTCCCCTCCTGTCTGCAGTTTCCGGAGGCAGTTCAAAGCTGCAGCACAGCCCGTGCTAGCCACGCCCCCTTCTCCGGCTTGCTGCCAGATCTTCTGCCTCCGCGGCAGCAGTCAAGTGGCGGTTCNCTTTGCTCCCGACCTTTCCTTTNCGNCTTTATTTTTTTAGCCGTTTTTCGGGCAGTAGCGAGCAGCTCTTTCTTTCGTTTTCTCCCTCCTCCTGGACCGGGTATTGAGCAGCGCGGTGGTCGCAGCCACCCGGAGCCNCCGCTGCAGCGCCTCCCTGCCGAGCTCCTCTGCCCCCTTTCAGGCATGGCAGAGCAGCCGCGCAAGCACCGGGCTAAATCCAAACGGTGCTCCGTCTGCGAGGCAGCTTTNACAGGCTCTGCAGAGGGTAAATTATGCCCTGCCTGTTCTCAGCCAGCCGACCCTNGCNCTGCTAGGGCACGGGGCTCTGAGTCGGACAGGCATGTTGGGNCCCCTANCCCCCCAAGAAGCCGCGACTCCACCACAGAAAAGCCCGACCAGGAGACACAGAGCAGAACAGGGAGAGGCTCTAAGGACGAGGAGGACTTCATCCAGCCGGCCCAGGGGGTAAGTCCTGGGGCAACACAGGACCATAAAGATAAGACCCTTNCGGGGCTNCCGGTCCCCCCCCCAAGTCCTGAAATGGGTCCTAAGTCCCTGGGGAGAGAAGCAGGGCTCNTANNCAGCCCCCCTTCCTCCCAGCTTGAGTCAGGGAACTCTGGCAATGAGNCCCCATCCCCCGNCCTGGGGGAGTGGGACCCTGNAGGGGAGGACTCCGAGGGAGAAATTTCTAGAGGGCTCAAGGCCCTGCGCAAGGCNAGCCGCAAAAGACCACGTCCTGGCCACAGCCGGGCGGCGACGCCTGCAAAGCGCGCCAAAAAGCTAAAAAAGTCCAAAAAGAGCAAAAGGGGAAGAAAAAGTACAAAAAGCCCAAAAGGTATTTGTCCTCTGACTCAGACACCTCCTCCTCTACCGAGGAAGGAGAGCTATCAGACTCTGATTCTGAGCAGGACACGGACAAAATGCAACAAAGGTTTTNTTCCCCCTGAGAAGTTTGAAACCGTGTGCAAAAAGGTTGTATCCACGATCCAGATCCAACCTGAGCAGGCCCTCGAGGACAAGCCTCAGAGCAAATACCTCCCTTCCAAATCCTCNCCCGAGGCAGCGATTCCCCTGCACCCATCCTTTGAGGANGTAATCAGGGAGGAGTGGGAATCTCCTGANAAGGGTAAACACATTAACAGGCATGTTCTCAGATTCTACAAGCTGCAAGAGCCAAAGAATGCTCTCACTGATGTGCCTAAGGTCGATGCTGCCGTAGCATCTCTAGCAAAGGATATGGTTATTCCATCCGAAGGGGACTTCTTCCCCAAGGATCCAACGGATAGGAAGGTGGAAGCCACCCTCAGAAGGGACTTCGGTGCTTCCTCAGCCACCCTCAGAGCGTCTCTGGCAGCCACGTGCTTTGCTCGAGCCACAGTGTCCTGGCTGGAGGACTTTAAAGCCCTTAAGGGCAGAGACCAANCCGACTTCAAGTCTATACTTAAGAAAATCTCCCTAGCAACAGCATTCGTGGCAGATGCTTCAATGGATGCTATGAGGTTTTCTGCCAGGGCCATGGCATCCAGCTCAGCGGCCAGGAGACACATATGGCTTCGTCCCTGGAAGGTAGATACTCACTCCAAACAAGTCCTGTGCTCCTCTAAATTCACAGGATCTCTCCTCTTTGGAGAAAAATTGGACAAGATAGTGGCTGAAAACGCTGCCAAACCTAAACAGTCCCTCCCCTCTCCACTTAGTGCTCTAAGAAGGGACTACAAACCCACTNCCAGACAGAGACGCTCCTTTCGTCCATCTTCCTCACAGAGGTTCCAGAGGAAAGATAACAGATATGTCAAGGGAAAACCTTGGAACCGAGGAGCGAGCGGAAAACCTAGAGGTGCTCCCGCAACCTCCAAGAGCCCATTATGACAACGAGCGAATGTGCCTCCGCCCAGACCTGAGCTTGGGAGGCAGGATTTCCCACTTTCCAGATGAATGGTTTGCTTCGACCACAGACAAGCGGGTGCGAGAGANAGCGCGTCAGGGATACTCCCTCGAGCTAAGGGCTCCACCCCATCCCTTCTTCATCCAGTCTCCCGTCACCAGCGACCCCGCCAAGCGCAAGCTNGTCCGGAACGAGATCTCCCATCTCCTGGACATGGGAGCGATAGAAGGAGTTCCCCCAGAAGAAAGGTTCTCAGGGTTTTACTCCATCTTCTTCATTGTTCAGAAGCGCACTGGGGGAGTCAGGGCCATCCTCGACCTCAGAAGGCTCAACAAATNNATGAAGAAAACAAAGTTCCGGATGGNCACCCTAGCNTCGATAGTGACATCCCTGTNTCAAGGGGACTTCCTAACCTCAGTGGATCTGGCAGACGCATACCTCCACGTTCCAATGCGCCCGTGCCACCGCAGGCTTCTGAGATTTGCTTACGGCACGGATCACTACCAGTACCGAACGCTCCCNTTCGGCCTCTCGTCGGCCCCCAGGGTCTTTACGAAGATGCTGGCGGTGATCGTAGCCAGACTCAGGTCCCAGGGTATTCACCTGTACCCCTTTCTGGACGACTTCCTAATCAGAGCCCCGNCCCAGGCCGCGGCACGCAGTGCCACGATCCGGACTCTGGATCNCCTNCAAGCGCATGGCTTCGCAATAACACCAAGAAAAGCTCCCTGATTCCCTCGACAAGNATNATTCACCTGGGAGCGGAGATAGACACTTCGGCGGCANAGATCTACCCATCACTAGACAGATTCCAGAAGATCCAGGATCTGATATCCATGCTGGNCAAGTGCATGAGGCCAACCATAGCTCAGTGTCTCCAGCCACTGGGCCTCCTGGTCTCGCGCATAGGGGTCNCCCCATGGGCGAGGTCACACATCAGGTGCCTCCAGGCCTTTCTTCTGAGAGTATGGGACCATTCCCCGGAGCGAATGCAAGACCAGGTACTGGTCCCGAACCAGGTGCTNGACTCCCTGAGATGGTGGACAGTCCCGGAGAACGTCCGCAGGGGTCTTCCCATATGCCTTCCAGGCCTNCAGGTTCTCACAACAGACGCCAGTCTGAAGGGATGGGGAGCACNTCTGGGACCCAGAACGGCGCAGGGTATCTGGAGCTCCGGGGAAAGGAACCGCAGCATCAATCTCTTGGAGCTCAGAGCTGTCAAACTAGCTCTNCTGAGATTCCAGAGCTACCTAGAGGGCAATCACGTCTTGGTCCAGCCAGACAACACGACCACGGTTGCGTACATAAACAACCAAGGGGGAACAAGGAGCGTAGCTCTACGTGCAGAAGCGATGGAGACAATGGAATGGGCAGACAAGACTCTCCCTTCCCTAAAGGCGATNCACATAAAAGGGGAGCTGAACCAAAAGGCAGACTGGCTCAGCAGACGCAAAGTCAACNACTCGGAATGATGCCTGAACCAGGAAGTCTTCACTCTGATCTCGCAGACGTTCGGTCTCCCCTCAGTCGACCTGTTTGCCAATCGCAAGAATGCAAAACGGCCGAAATNCTTCACCNGGGAAGCAGACCCCAAGTCCATGGGGACAGATGCTCTGTCGCACAGATGGCCNCAAGGCCTGCTATACGCGTTCCCGCCCTTCCCTCTCCTAGGGAAGGTGATCCAAAAGATAAGGCGAGAAGAAGCAAGGGTGATAGTGCTAACTCCGCACCGGCCAAGGAGACCCTGGTTCTCTGATCTGATAGAACTAAAGCTGGAACCACCGTTGCAGCTNCCGGCGAGACCAGACATCCTTTACCAAGGCCCATTCCTCCATCCGGACCCAGACCGTCTTCATCTGACAGCCTGGCTATTGAAAGGGAAGCGTTAGCCGCGCTCGGCCTGTCTTCCAAAGTGATCGGGACTCTGCTCTCNTCCAGGAGAGTTTCCACGCTAAAAGCCTACTCCTCCATCTGGACCAAGTTCAGTNTTTGGTGCCAAGAGCACAGCGCAAATCCAAGGGATCCTGGGATTCCGGCTACTCTGGACTTCCTTCAGGAAGGTGCGGATAAGGGNCTTCAGCCNAGCACCGTAGCGCGCCAGGTGTCAGCCCTCAGTAGTGTACTGTTCGCAGGATCCTCGGGCTCCCTGGCCGAGAACCCTCAGGTATCCAGGTTCCTCAGAGCAGTCAGACTGGCCAGACCAGCGGTCAGACCGATCTTCCCTAAGTGGGACCTACCACTGGTGTTGAAAGCCCTAACCACCCATCCCTTTGAGCCTCTGACNTCTGTATCACCATTTTACCTCTCCATCAAAACCTGTTTTCTGGTGCCATCACGTCCGCCAGTGAGTTTCAGATGGAGCCTTATCCATGCAGGAACCTTACTGCGTGTTCCATGATGCAAGGTGGTGCTAAGACTCCAGAAACGTTCTTGCCTAAGGTGAACTCTCCTTTCCATGCCTCGCAGGAGATTGTCCTCCCTTCATTCTGTCCAAAGCCACAGCACCCGACTGAGAAGCNGTGGCACACCCTGGATGTCAGAAGAGCACTAAAGACTTATATCAAGCGTACAGAATCCACAAGGAGATCGGGCTCCCTGTTCGTTTCCTTTCACCCGAGGTGCCAAGGGCTTAGAGTATCCAAGCTATCCCTTGCCAGATGGATCAGACTATGCATCGTTGAGGCATACAAGCCATCCGGCGCGCCTGTTCCAGAAGGAATCAAGGCGCATTCCACAAGATCCATGGCAACCTCGTGGGCCGAAAGAGCGTGCGCTTCCACCGCAGAGATCTGCAGAGCAGCCACATGGTCATCGGCTAACGCCTCTATCAGACACTATAGGGTGGACTTTCTGTCTTCCGCAGAGGCCTCCTTTGGCAGGAAGGTGCTGCAGGCGGTGGTCCAGTAATAACCTTGCCGTTTGAGCAATTCGAAAGGGAGGGGTTCCTTTCCTGTTTCTTATGTTCGTTCTCCTATCCCTCCCTACTCCTGTTCACTGCTCGCTACTTCCCATACGTATCAGAATTGTGGGAGACGCTGGGCTGCAGAATGGAAAATTTCTTACCCGGTAATTTCCTTTCTGCTAGCAGCATCTCCCACAATTCTACCCACCCTGGACGGCTTCACAGCCGAGGGTCAGCATTTTATTTGGATAGTTACCGTATAGGCAGTGGCCTACTGTACATAGTTANTTGGTTGGCACTGGAATTATTGTTACTAATTATTTTCTACGAGTTTTTNCACAGCTTTGGAATGAATCATCTGGCAGCAAGCNGGAGAAGGGGGCGTGGCTAGCACAGGCTGTGCTGCAGCTTTGAACCGCCTCCGGAAACTGCAGACAGGAGGGGAATAGCCCATACGTATCAGAATTGTGGGAGACGCTGCTAGCAGAAAGGAAATTATCGGGTAAGAAATTTTCCATTCT
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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 |
|---|---|---|---|---|---|---|
| DIRS-1b_Amnio | PRDM9 | 3703 | 3722 | - | 16.58 | AGAGGGAAGGGCGGGAACGC |
| DIRS-1b_Amnio | TCP15 | 4283 | 4293 | + | 16.56 | GTGGGACCTAC |
| DIRS-1b_Amnio | TCP22 | 4283 | 4293 | + | 16.56 | GTGGGACCTAC |
| DIRS-1b_Amnio | HSFA1E | 852 | 865 | + | 16.48 | AGAAATTTCTAGAG |
| DIRS-1b_Amnio | TCP21 | 4283 | 4293 | + | 16.36 | GTGGGACCTAC |
| DIRS-1b_Amnio | Zfx | 2703 | 2712 | - | 16.33 | GCCGCGGCCT |
| DIRS-1b_Amnio | Rfx6 | 1626 | 1634 | + | 16.32 | CCTAGCAAC |
| DIRS-1b_Amnio | MAX::MYC | 1525 | 1534 | - | 16.31 | AGCACGTGGC |
| DIRS-1b_Amnio | TCP20 | 4283 | 4293 | + | 16.28 | GTGGGACCTAC |
| DIRS-1b_Amnio | ZBTB6 | 866 | 874 | - | 16.28 | CCTTGAGCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
