DIRS-1b_Amnio
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0006272 |
|---|---|
| TE superfamily | DIRS |
| TE class | 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 | Spps | 104 | 114 | + | 18.44 | GCCACGCCCCC |
| DIRS-1b_Amnio | Spps | 5336 | 5346 | - | 18.44 | GCCACGCCCCC |
| DIRS-1b_Amnio | MAFF | 5190 | 5200 | + | 18.24 | GTCAGCATTTT |
| DIRS-1b_Amnio | CDF5 | 973 | 993 | - | 18.20 | TGTACTTTTTCTTCCCCTTTT |
| DIRS-1b_Amnio | Bteb2 | 104 | 116 | + | 18.08 | GCCACGCCCCCTT |
| DIRS-1b_Amnio | Bteb2 | 5334 | 5346 | - | 18.08 | GCCACGCCCCCTT |
| DIRS-1b_Amnio | SP8 | 105 | 115 | + | 17.99 | CCACGCCCCCT |
| DIRS-1b_Amnio | SP8 | 5335 | 5345 | - | 17.99 | CCACGCCCCCT |
| DIRS-1b_Amnio | KLF11 | 105 | 114 | + | 17.92 | CCACGCCCCC |
| DIRS-1b_Amnio | KLF11 | 5336 | 5345 | - | 17.92 | CCACGCCCCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
