CR1-L3A_Croc
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001326 |
|---|---|
| TE superfamily | CR1 |
| TE class | LINE |
| Species | Amniota |
| Length | 4288 |
| Kimura value | 35.65 |
| Tau index | 0.0000 |
| Description | CR1 (Chicken Repeat 1) retrotransposon, CR1-L3A_Croc subfamily |
| Comment | - |
| Sequence |
CTGTGACCCTTGGGTCTNTGATCAGCCCTGGTGTTTGAAGTCTCTGAGTAGTTAATCCCTCCCTGATTAGCGAGGGGGTGGAGCTGAGCAGCGAGGCTTAGTAGTAAAGTCAGTTGCCAGGCGAACTCNTGAGCAGCGGAAAACGAGAGCGTTTTGGAGGGAGTTTGGAGGGGAGTGTGNGAAGCTTTCTTTCTAGGTACAGTTCTACGCTCAATACCGTGATGGCCAGCGATGGANCAGTGGTTGTGACCTGCAACGGATGCGCCACGTTTTCTTTCCTGCCTGAAGCCAGAAGGGACTTCCTGTGTATGAAGTGCAAGTTGGTGGCTGTGCTGGAAGAAAAGATTCGTGGTTTGGAAGGACAAGTACTGACGCTGCGGAGCATCAGAGAGGCTGAGGAGTTCTTGGACAACCAGATTCGGGAAGCATCACCACCCCAGATTCAAGAAAGAAAGGAACTGGCCACCAAGGAACCAGAAAGAGAGGAAACCAGAGAGGAGGCTTGGCAGTTCGTAACCACCAGAGGCAAGAGGACGAGGCGGCATTCTACACGGCTGGAGGCAGANGAGGATGGGCAGGCTGTGACCACCAGAGAGAAGAGGACCAGGAGGAATTCCACACAGCTAGAAGTATCCAATCGTTACCAGGTTCTCAGCGTGGAAACTGCAGAAAATATCTCTGAAGATCCAGCTGGTCGAATGGAACGGAGAGCTGTACGGGACATACCTGTGGATGGCTGCTCAGCCCAACCCGCAAGACGATCAAGCGTGCCCACAAAGAGATCTCCAACCATCCAAGGAAGACAGACGATCCTTGTCGGGGATTCTATACTAAGAAGAATGGAAAGAACGTTCTGCAAGGGACAGGCGGACAACAGGACGGTGTGCTGTCTTCCCGGAGCCAAGACACGAGATGCGACTCTAAGACTGGATAGGCTTCTGAAGTCGGCGGGCAAGGATCCACTGGTGATGGTGCATATCGGCACTAATGACACTGCTTCGCGNGATACCTCACAGATTATAGACGACTTCAGGGAACTCGGAAGGGTGCTGAAGGAGAAGAATGTCCAAGTGATCTTCTCGGAGATCCTTCCTGTCCCACGAGCGAAGGAAGACAGAAGGCAGAAGATTCTGGAAGTGAACCGCTGGCTAGGTAAGTGGTGTAAGGTAGAGGGTTTTGGTTTTGTGGAACACTGGTCCACCTTCTATGGGGAGAAGGGGCTGTACAGTTTGGATGGCCTCCATCTCAGTAGAAGGGGAACCAGTCTTCTAGGGGACAGGCTGGCTAGACTAGTCAGGAGGGCGTTAAACTAACAACAAAAGGAGGGAGTGAAAGAGGGAAACAAATGAGCACTCATTTAGCACAAAATCAAGATGTCGAGAACAAAATTAATCAAGGCACCAAGGGACGTGAAGAGAAGAAATTCTTTAATTGCCTATACACCAATGCTAGGAGCCTGGGTAATAAACAAGAGGAATTGGAATTGCTCATTTATGAGCATAAATTCGACCTAGTTGGTATTACTGAAACCTGGTGGGAAGATTCGCATGACTGGAATGTTAAAATCAATGGTTATAACCTATTTAGGAAGGATCGAGTGGGCAAAAGGGGAGGGGGAGTGGCACTCTATGTCAAAAATGGCATTACCTGTTTCCGAGTCACTGACAACTCGGAAGCAAATGATCTTGAATGCTTATGGATCAATGTTCTAACAGATAAAGCACAAGATGGGGTACTAGTTGGTGTCTGCTACAGACCACCAAATCACACTAGAGAACAGGATGACCGGCTCCTTAAGCACCTATCTATAATGTGTAGGGGAAAAAGCTGCGTTATCACGGGGGACTTCAATCTGAGTGACATATGCTGGAGGTCTCATGCTGCCAGTACTAAAACGTCCTCGGAATTTCTAAAAATTATAGATGACAATTTCCTAACTCAAAAAGTGTTGCATCCAACACGGGGGAATTCTATATTAGACCTCATCTTGACAGATAAAGAGGAATTGATCACAGAACTAAAAATTAGTGGTTGCTTAGGTGCAAGTGATCATGACTTGATTACATTTGTTATGTGCAAACAGAATAAAGTCCAAACCAGTAATATATATACTTGGTGCTTTAAAAGGGCCAGTTTCACAAAGCTGAAAACAATTATGAGCCAAATCAGCTGGGAGAAAGAATTTAAACAGAAAAATGTGAATGATAATTGGGAACTGTTTAAGAACATTTTACTAGATGCCCAAAAAGCCACAATCCCACAATCGAGAAAGAAGGCTACGCTGGTTAAAAAACCAGCCTGGCTTAGAGGGGAAGTGAAAGCAGCTATAAAAAATAAAAAAGCAATATATAACAAATGGAAAAAAGGGGAAGTTGATAGCAATGAATATAAATTAGAAGCTAGGAATTGTAGAAAATTGATAAGGGAAGCAAAAGGACACAAGGAGAAATCTATGGCCAGCAGAGTTAAGGACAATAAGAAGGAGTTTTTNAAGTATATTAGGAACAAAAGGAATCCTAACAATGGTATTGGTCCATTACTAGATGGAAATGGTAGAATTGTCAATAATAATGCAGAAAAGGCAGAAGTGTTCAATAAATATTTCTGTTCTGTATTTGGGAAAAAGCCAGATGATGTANTCGTATCACATGATGATGATGAAATACTTTCCATTCCAACAGTAACTAAGGAGGATGTTAAACAGCAGCTACTAAAGTTAGACATTTTTAAATCAGCAGGTCCGGATAACTTGCATCCAAGAGTTTTAAAAGAGCTGGCCGAGGAGCTCTCTGGACCGTTAATGTTGATTTTCAATAAGTCTTGGAACACTGGGGAAGTTCCAGAGGACTGGAAGAAAGCTAATGTTGTGCCAATATTTAAAAAGGGTAAACGGGATGACCCGGGTAATTATAGGCCTGTCAGCCTGACATCGATCCCGGGCAAAATAATGGAACGGCTGATACGGGACTCGATTAATAAAGAATTAAAGGAGGGTAATATAATTAATGCCAATCAACATGGGTTTATGGAAAATAGATCTTGTCAAACTAACTTGATATCTTTTGATGAGATTACAAGTTTGGTTGATAAAGGTAATAGCGTTGATGTAATATACTTAGACTTCTGTAAGGCATTTGACTTGGTACCGCACGACATTTTGATTAAGAAACTAGAACGATACAAAATCAACATGGCACACATTAAATGGATTAAAAACTGGCTAACTGATAGGTCTCAAAATGTAATTGTAAATGGGGAATCATCATCGAGCGGGCGTGTTTCTAGTGGGGTCCCGCAGGGATCGGTTCTTGGCCCTACGCTATTTAACATTTTTATCAATGACCTGGAAGAAAACATAAAATCATTACTGATAAAGTTTGCAGATGACACAAAGATTGGGGGAGTGGTAAATAATGAAGAGGACAGGTCACTGATACAGAGCGATCTGGATCGCTTGGTAAGCTGGGCGCAAGCAAACAATATGCGTTTCAATACGGCCAAATGTAAAGTCATACATCTAGGAACAAAGAATGCAGGCCATACTTACAGGATGGGGGACTCTATCCTGGGAAGCAGCGACTCTGAAAAGGACTTGGGGGTCACGGTGGATAATCAGCTGAACATGAGCTCCCAGTGCGACGCTGTGGCCAAAAGGGCTAATGCGATCCTTGGATGTATAAACAGGGGAATNTCGAGTAGGAGTAGGGAGGTTATATTACCTCTGTATTTGGCACTGGTGCGACCGCTACTGGAATACTGTGTCCAGTTCTGGTGTCCACANTTCAAGAAGGATGTTGANAAATTGGAGAGGGTTCAGAGAAGAGCCACGAGAATGATTAAAGGACTGGAAAACATGCCTTATAGTGAGAGACTCAAGGAGCTCAATCTATTTAGCTTATCAAAGAGAAGGTTAAGGGGTGACTTGATCGCAGTCTATAAGTACCTACACGGGGAACAGAAATTTGATAATAGAGGGCTCTTCAGTCTAGCAGACAAAGGTATAACAAGATCCAATGGCTGGAAGTTGAAGCTAGACAAATTCAGACTAGAAATAAGGNGCAANTTTTTAACAGTGAGGGTAATTAACCACTGGAACAACTTACCAAGGGNTGTGGTGGATTCTCCATCACTGGAAATTTTTAAATCAAGATTGGATGTTTTTCTAAAAGATATGCTCTAGTTCAAACAGGAATTAATTCGGGGAAGTCCTATGGCCTGCGTTAGCAGGAGGTCGGACTAGATGATCTACAGNGGTCCCTTCCGGCCTTANAATCTATGAATCTATGAA
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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-L3A_Croc | RVE7 | 670 | 678 | + | 16.38 | AAAATATCT |
| CR1-L3A_Croc | SPIC | 2362 | 2374 | + | 16.37 | AAAAGGGGAAGTT |
| CR1-L3A_Croc | ANL2 | 3000 | 3009 | - | 16.30 | GCATTAATTA |
| CR1-L3A_Croc | FOXO1::ELF1 | 298 | 310 | - | 16.25 | ATACACAGGAAGT |
| CR1-L3A_Croc | TEAD1 | 1552 | 1560 | - | 16.23 | ACATTCCAG |
| CR1-L3A_Croc | RVE6 | 670 | 678 | - | 16.23 | AGATATTTT |
| CR1-L3A_Croc | RVE5 | 670 | 678 | - | 16.21 | AGATATTTT |
| CR1-L3A_Croc | DOF3.2 | 2330 | 2345 | - | 16.21 | TTGCTTTTTTATTTTT |
| CR1-L3A_Croc | CDF5 | 2326 | 2346 | - | 16.20 | ATTGCTTTTTTATTTTTTATA |
| CR1-L3A_Croc | ZNF148 | 1607 | 1616 | - | 16.10 | CCCCTCCCCT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
