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 | kn | 724 | 733 | - | 17.83 | TCCCCAGGGA |
| DIRS-1b_Amnio | E2F4 | 937 | 949 | - | 17.71 | TTTTGGCGCGCTT |
| DIRS-1b_Amnio | SP9 | 105 | 114 | + | 17.16 | CCACGCCCCC |
| DIRS-1b_Amnio | SP9 | 5336 | 5345 | - | 17.16 | CCACGCCCCC |
| DIRS-1b_Amnio | ZNF281 | 801 | 810 | - | 16.91 | GGGGGATGGG |
| DIRS-1b_Amnio | SPIC | 973 | 985 | + | 16.85 | AAAAGGGGAAGAA |
| DIRS-1b_Amnio | ZNF740 | 694 | 703 | + | 16.79 | CCCCCCCCAA |
| DIRS-1b_Amnio | Mad | 920 | 934 | - | 16.72 | CAGGCGTCGCCGCCC |
| DIRS-1b_Amnio | Klf3/8/12 | 104 | 112 | + | 16.60 | GCCACGCCC |
| DIRS-1b_Amnio | Klf3/8/12 | 5338 | 5346 | - | 16.60 | GCCACGCCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
