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 | Klf3/8/12 | 3338 | 3346 | - | 16.60 | GCCACGCCC |
| CR1-3_Croc | TFAP2C | 3535 | 3543 | - | 16.57 | GCCTGAGGC |
| CR1-3_Croc | TFAP2A | 3535 | 3543 | + | 16.42 | GCCTCAGGC |
| CR1-3_Croc | NAC075 | 2183 | 2202 | - | 16.27 | CAAACTTGCTCAAGAAGCTT |
| CR1-3_Croc | TEAD1 | 362 | 370 | - | 16.23 | ACATTCCAG |
| CR1-3_Croc | KLF9 | 3336 | 3346 | - | 16.16 | GCCACGCCCCC |
| CR1-3_Croc | KLF10 | 3337 | 3345 | + | 16.15 | GGGGCGTGG |
| CR1-3_Croc | TFAP2B | 3535 | 3543 | + | 16.07 | GCCTCAGGC |
| CR1-3_Croc | phol | 3253 | 3262 | + | 16.02 | CGCCATATTT |
| CR1-3_Croc | DOF3.6 | 1696 | 1716 | - | 15.83 | CCTCCTTTTTGCCTTTTTTAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
