CR1-L3B_Croc
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001327 |
|---|---|
| TE superfamily | CR1 |
| TE class | LINE |
| Species | Amniota |
| Length | 3277 |
| Kimura value | 38.62 |
| Tau index | 0.0000 |
| Description | CR1 (Chicken Repeat 1) retrotransposon, CR1-L3B_Croc subfamily |
| Comment | pol ORF 404-3151. |
| Sequence |
TAGAAAATCAGGGATCTTGGAAGAGAGCTGAAGAAGAGGAAAGTCCAAGTGATCTTCTCGGAGATCCTTCCGGTCCCGCGAGCAAGAGAAGACAGAAGCGGAAAATACTGGAGGTGAACCGTTGGCTGCACGACTGGTGTGAGTGAAGGTTTTGGTTTTGTGGAACGTTGGGCCACTTCCAGNGGAGAAGGGACTGTATGAATAGGACGGCCTGCATCTCAGCAGGGGGCGAANCANTNTTCTCGGCTGGNAGACTAGCTGGAGCAGCCAGGAGGACGTTAAACTAGCAACGCAAGGGGAGGGTGCTAAGAAGGCAAACGCGNTACAAACTCAAACTCAGCATGTCGCGAACAAATTGAACCGACGTGGCAAAGAATGTGAAGAGAAGANATTTTTCAATTGCTTATATACCAATGCTAGGAGTCTGGGTAACAAGCAAGAGGAACTGGAAATTCTCATTGATGAGAAGAAATTTGATATAATTGGCATTACTGAAACCTGGTGGGATGATTCGCATGACTGGAATGTTAAAATCNCTGGTTATAACCTGTTTAGGAAGGACAGAGCGGGTAAAAGAGGCGGGGGAGTGGCGCTCTACATTAAAGACACCATTACCTGTTTTAGAGTTATTGATAACTCAGAACCGCAGGATCTTGAATGCATATGGATCAATGTGCTAACTAACAAAGCCCAGGAGGGGGTACTGGTGGGGGTCTGTTACAGACCACCGAATCAAACCAGAGAACAGGATGAGTTACTCCTTAAGCACCTGTCTGTAATGTGTGGAAAGAAAAACTGTGTTGTTACGGGGGACTTCAGTTTGGGAGACATATGCTGGAGGTCTCATGCAGCCAGTAGTAAAACATCATTAGAGTTTCTAAAAATTATAGATGATAATTTTCTAACACAAAAGGTATTGCACCCAACACGAGGTAACTCTATTTTGGACCTCATTATGACGGATAAAGATGAATTAATCACTGGACTGGAAGTTGGTGGTTGCCTAGGGACCAGTGATCATGACCTGATTACATTCAATATGGGCAAACAGAGGACAGTCCCAACCAGTAATATATATACTTGGTGCTTCAAAAGGGCTAATTTCCCAAAGCTGAGGAAAATTATGAGCGAAATTGACTGGGAGGAAAAATTTAGACAGAAAAATGTGAATGAAAATTGGGAGTTCTTTAAGAAGAGTTTATTAGATGGCCAAAAAGCCACGATTCCACAATCAAGAAAGAGGACAACTTTGGCTAAAAGCCCATCCTGGTTCAGTGGCGAAGTGAAGGCAGCAATTAGAAATAAAAAAGCAATATATAACAAATGGGAAAAAGGGGAAATAGATAGCAATCGATATAAATTAGAAGTTATGAAGTGTAGAAAATTGATAAGGGAAGCTAAAGACATCAGGGAAAAATCCATGGCTGGCAGGGCTAAGGACAATAAGAAGGAATTTTTNAAGTATATTAGGAACAAAAGAAATCCTAGCAATGGTATAGGCCCATTACTAGATGGAGATGGTAAAATTGTTAATAATGATGCAGAAAAGGCAGAAGTGTTCAATAAATATTTCTGTTCTGTATTTGGAAAGAAGCAGGATGATGTACTCGTATCACATGAGGATGATGAAGTACTTTCCAGTCCATTAGTAACTAAGGAGGATGTTAAACAACATCTACTAGGGATAAACATTTTTAAATCAGCAGGCCCGGATAACTTGCACCCAAGAGTCCTAAAAGAGCTGGCTGAGGAGATCTCTGGCCCGCTGATGTTAATTTTTAATAAATCTTGGAATACCGGGGAAATTCCAGAAGACTGGAAGAGTGCTAATGTTGTGCCAATATTCAAAAAGGGCAAGCGGGATGACCCGGGTAACTATAGGCCGGTTAGCCTGACATCAGTCCCGGGCAAAATAATGGAAAAGCTGATACGGGATTCAATTAATAAAGAATTAAAGGATAGGAATATAATTAATGCCAGTCAACATGGTTTTATGGAAAATAGGTCTTGTCAAACAAACCTGATTTCATTCTTTGATGAGATTACAAGTTTGGTTGATAAAGGTAACTGCGTAGATGTAATATACTTAGACTTTTGTAAGGCGTTTGACTTAGTACCGCACGACATTCTGATTAAAAAATTAGCACTATACAATATCAATAAAGCACACGTTAAATGGATTAAGAACTGGCTAACTGACAGATCTCAAAAAGTAGTCGTCAATGGGGAATCATCATCGAATGGGGGTGTTTCTAGTGGGGTTCCGCAGGGATCGGTACTAGGCCCGACGCTATTCAACATTTTCATCAATGATCTGGAAGTAAATATAAAATCACTGCTGATAAAATTTGCGGATGACACAAAGATTGGCGGAGTGGTAAATAACGATGAGGACAGGGCAGTCATACAGAGCGATCTGGATCGCTTGGTAAGCTGGGCCCATTCAAACAAAATGCGTTTTAATACAGCCAAATGCAAAGTTATACATCTAGGAACAAGGAATGCAGGCCATACCTACAGAATGGGGGACTGTATCCTGGAAAGCAGTGACTCTGAAAAGGATTTAGGGGTCATAGTGGACAAGCAACTCAACATGAGCTCCCAGTGCGATGCTGTGGCAAAAAGGGCTAATGCGATCCTTGGATGTATAAACAGGGGAGTAGCGAGTAGGAGTAGGGAGGTGATTTTACCTCTGTATACGGCATTGGTGAGACCGATACTGGAATACTGCGTNCAGTTCTGGTGTCCACATTTTAAAAAGGATGTTGAAAAATTGGAGAGGGTGCAGAAAAGAGCCACAAAAATGATTCGAGGGCTGGAGAAAATGCCTTACAGTGAGAGACTTAAAGAGCTCAATCTGTTTAGCTTATCAAAAAGAAGATTGAGAGGTGACTTGATTACAGTGTATAAGTACCTTCACGGGGAGAAAATACCGGGTACTAAAGGGCTCTTTAATCTAGCGGAGAAAGGCATAACAAGAACCAATGGCTGGAAGCTGAAGCCAGACAAATTCAAATTAGAAATAAGGCACANATTTTTAACAGTGAGGGTGATTAACCACTGGAACAAACTACCAAGGGAAGTGGTGGATTCTCCATCTCTTGATGTCTTCAAATCAAGACTGGATGCCTTTCTGGAAGATATGCTTTAGTCAAACACAAGTTATTGGGCTCAATACAGGGGTAACTGGGTGAAATTTAATGGCCTGTGNTATACAGGAGGTCAGACTAGATGATCTAATGGTCCCTTCTGGCCTTAAANTCTATGAATCTATGAA
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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-L3B_Croc | TCX3 | 3008 | 3019 | + | 17.89 | AAATTCAAATTA |
| CR1-L3B_Croc | ZIC1 | 218 | 231 | - | 17.74 | CGCCCCCTGCTGAG |
| CR1-L3B_Croc | BZIP16 | 362 | 371 | + | 17.05 | CGACGTGGCA |
| CR1-L3B_Croc | KLF16 | 581 | 591 | - | 16.98 | GCCACTCCCCC |
| CR1-L3B_Croc | AFT1 | 915 | 924 | + | 16.93 | TATTGCACCC |
| CR1-L3B_Croc | ZIC4 | 218 | 231 | - | 16.75 | CGCCCCCTGCTGAG |
| CR1-L3B_Croc | ZIC5 | 217 | 231 | - | 16.68 | CGCCCCCTGCTGAGA |
| CR1-L3B_Croc | lin-54 | 3006 | 3018 | + | 16.60 | ACAAATTCAAATT |
| CR1-L3B_Croc | BZIP68 | 362 | 371 | - | 16.36 | TGCCACGTCG |
| CR1-L3B_Croc | GFI1 | 2330 | 2340 | + | 16.36 | AAATCACTGCT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
