CR1-3_Croc
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001325 |
|---|---|
| TE superfamily | CR1 |
| TE class | LINE |
| Species | Amniota |
| Length | 3605 |
| Kimura value | 33.02 |
| Tau index | 0.0000 |
| Description | CR1 (Chicken Repeat 1) retrotransposon, CR1-3_Croc subfamily |
| Comment | - |
| Sequence |
GGGATCCATCTGACGAGAACGGGGAAGAGCATCTTTGGGCGTCGTCTGGCCAACCTAGTAAGGAGGGCTTTAAACTAGGTTCCACGGGGATGGTGATCAAAACCCTCCAGCAACAGAGCACACAGTCCAGAGGGGAAAGGACTCGAAGAAGCAACTCAACTCTGGGAAAGGGCCAGAGAGCTACAGGACTGCAACAAGTGGCCAAAAGGAAGCGAGTAGGTCAAAATGCAAAATACGTCCGATGCATGTATACAAATGCGAGAAGTATGGGGAATAAACAAGATGAGCTGGAAGCTGCAGCCTGTGAAAAGAACTATGATCTGATTGGCATCACAGAGACCTGGTGGGACAGCTCTTATGACTGGAATGTCAACATCGAGGGTTACACTCTGTTTCGGAAGGACAGGGTTGGGAGAAAAGGTGGTGGTGTTGCCTTGTATGTCAAAAACACATACACTTGTTCCCTGGTTCAGGAGGAAGAAGACAGCAAAGCAGAATGCATTTGGGTGAAGATGAAAGGTGAAAGATGCAGCACCGATATAATGGTGGGGATTTATTATAGGCCACCAAATCAGGAAGAGGAGGTGGATGAGGCACTCTTCAAGCAGGTGACAAATCTATCCAAAAGCTATGGGATGGTACTGATGGGAGACTTCAATTTTCCGGACATCTGCTGGAAGAACAATGCAGCCAAACATAAAATGTCAAGCCGGTTCCTAACTTGTGTGGAGGACAACTTTCTGTTCCAGAAAGTGGAGGATACAACTAGGGGATCATCTATCTTGGATCTTGTCCTGACCAACAGGGAAGAACTGGTGGAGGATGTGAAGGTGATGGGTAACTTGGGAGGAAGCGATCACGATATGATAGAATTCCAGATCCTGAGACGGGGAAAGCATGAGGTCAGCAAAATTAGGACGCTAGATTTCAAAAAGGCGGATTTCATCCGACTCAAGGAGTTAATAGGCATGGTGCCATGGGAGGACAGACTGAAGGATAAAGGCGCCCAGGAGGGCTGGGAGCTTCTAAAGGGCACAGTATTGGAAGCCCAACAAGAAACTGTCCCGACACGATGGAAGCACAAGAAGAATGGCAAGAGACCAATGTGGCTGCACAAGGAGCTTCTAAAATGCCTCAAATGCAAAAGGAAAGCATACAGGCAATGGAAGAATGGGCAGGTCACCAAGGAAGCGTACCAGGAAATAGCAAGAACCTGCAGGGACAAAATCAGGAAGGCAAAGATAAAGAACGAGCTGCACCTGGCGAAGGAGGTTAAGGACAACAAGAAGAGGTTCTATAAGTATGTTGGCCAGAAAAGAAGGACCAAGGAAGCTGTGGGTCCNCTGTTAACAAGCCAGGGGGAACTCCTAACNGAAGATGCAAAGAAGGCGGAGCTACTCAACAGCTACTTTGCCTCAGTCTTCACAAAAAAATTAAGCTGCAGCCAGACACCTAATAAGGATTATCTGGATAAGGAAGGGGGCAAGCTGAGGGANGAGATAACAAAAGAGACGGTCAGAGAGCTTTTGNTGGGTCTGAATGAATTCAAGTCAGCAGGGCCGGATGAACTTCATCCCAGGGTACTGAAGGAACTGGCAGAGGAGATCTCGGAGCCCTTGGCAATGATCTTCATGAAGTCGTGGGAGACGGGCCAGGTACCAGAGGACTGGAAAAGGGCCAACGTAGTGCCCCTCTTTAAAAAAGGCAAAAAGGAGGACCCGGGGAACTACAGACCGGTTAGCCTCACCTCAATACCTGGGAAGTTACTGGAGCATATCCTAAGGAAGGCCATTTGCAAGCATCTGGAGGAGGAAAGGCTGATCACAAGCAGCCAGCATGGATTTACGAAAAACAAATCGTGTCAAACAAACTTGATCTCCTTCTTTGACAAAGTAACTACTTGGGTGGATGAAGGGAATGCTGTGGATATAGTGTATCTGGACTTCAGCAAGGCTTTTGACAAGGTCCCGCATGACCTTCTCATAAACAAATTGGAGAAATGTGGGCTGGACAAAACTACTACAAGGTGGATAGATAACTGGCTCAATAGCCGCAAGCAAAGGGTAATTATTAACGGGTCCATGTCAGAATGGCAGGAGGTTTCGAGTGGAGTCCCACAGGGGTCTGTCCTGGGCCCGGTGCTGTTCAACGTGTTTATTAATGATTTGGATGCTGGCATAGAAAGCTTCTTGAGCAAGTTTGCAGACGACACGAAACTGGGAAGGATTGCGAACACGTTGGAGGACGNGAGCGCAATTCAGAAGGATCTCGACAGATTGGAAAGCTGGGCTAGAGCTAACAGGATGAAGTTCAATGCGGACAAATGCAAGGTGCTACACCTCGGGAGGAATAATCAAAAACACAAATACAAAATGGGTGACACCTGGCTGGATGGCAGCACTATGGAAAAGGACCTGGGAGTCTTGGTAGATCACAGACTCAATATGAGTCTGCAGTGTGATGCAGCCGCACAAAAGGCGAATGCGGTTTTGGGATGCATCAATAGAAGCATTAGGTGCAAGACACGGGAGGTGATAGTGCCTCTCTACTCGGCACTGGTTAGGCCTCATCTGGAGTACTGTGTGCAGTTCTGGGCTCCACATTTTAAAAAGGACGTGGAGAAGTTAGAGAGGGTCCAGAGGCGGGCAACAAAGATGATAAAGGGCTTGGAAGGCAAGTCATACGAGGAGAGGCTGAAGGAGCTAGGCATGTTCAGCTTGCGGAAAAGGCGCTTAAGAGGGGACATGATAGCAGTCTTCAAATACTTGAAGGGCTGCCATAAAGAAGAGGGAAAGCACCTTTTCTCTCTTGCTGCAGAGAGGAGGACGCGGACCAATGGCTTGAAGTTGCAGCAAAGTAGGTTTAGATTGGATATCCGGAAAAACTTCTTCACTGTTAGAACAGTGAGGCAGTGGAATAGACTGCCTAGGGAAGTTGTGGACTCTCCATCACTGGAGGTGTTCAAGAAGAGGTTGGACAGCCACTGGTCGGGGATGATCTAGGCGTAGCTATGCCTATGTTCTACTATGGGTATTTCCCATGCTTCTGGGCTTTGCTGGTTGCCCCCGCCTCCCCCCCCCCCCCTTTCTGCTACATGTGTCAGGGTGTTTTTAAGCCTTCCTCAGAGGCATTGGGTGTTGGCTGCAGCCAAGGCTGGGGACTTTGACTGGGGTGTGCCAATGCTCCTGCTGGGACCAAAGCCGGAGGTTCCTGGCTAGAGGGTCTTGCCCCTCCGCTCAGGGTCAGACCGATCGCCATATTTGGGGTCAGGAAGGAATTTTACCCCATGGTCAGATTGGTACGGACTGTGGGGGTTTTTGCCTTCCTCTGTAGCGGGGGGCGTGGCCCTCTACCCGGGATCTCTTGAGCATATATTGACAACATTTCATAGAAGCAGGACATTGGCTGCCGTGGTTCCCCTGCTTTACCTGTGGCAGGTTAGGGTGTTAGGTCTGTGTTGTGTCAGGGTTGACGGTAGTCTTACGTAGAGTTTAGATTATGGTTGTATGGGATGGTTTGGATAGGGATGATCCTGCCTCAGGCAGGGGGTTGGACTAGATGACCTCTGGAGGTCCCTTCCAGCCCTACTTCTCTATGATTCTATG
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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 |
|---|---|---|---|---|---|---|
| CR1-3_Croc | THI2 | 1199 | 1213 | + | -7.59 | GGAAATAGCAAGAAC |
| CR1-3_Croc | DAL81 | 2473 | 2491 | + | -39.70 | AAAAGGCGAATGCGGTTTT |
| CR1-3_Croc | BPC5 | 1220 | 1249 | + | -43.54 | GGACAAAATCAGGAAGGCAAAGATAAAGAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
