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 | MCM1 | 547 | 558 | + | 15.24 | CCTGTTTAGGAA |
| CR1-L3B_Croc | ZNF418 | 1392 | 1406 | + | 15.24 | GGGAAGCTAAAGACA |
| CR1-L3B_Croc | CDF5 | 1294 | 1314 | - | 15.20 | ATTGCTTTTTTATTTCTAATT |
| CR1-L3B_Croc | Spi1 | 437 | 449 | + | 15.20 | CAAGAGGAACTGG |
| CR1-L3B_Croc | RELA | 1801 | 1810 | - | 15.18 | TGGAATTTCC |
| CR1-L3B_Croc | OsbZIP69 | 360 | 371 | + | 15.16 | ACCGACGTGGCA |
| CR1-L3B_Croc | Ddit3::Cebpa | 913 | 922 | - | 15.13 | GTGCAATACC |
| CR1-L3B_Croc | ATMYB31 | 988 | 1002 | - | 15.13 | CAACCACCAACTTCC |
| CR1-L3B_Croc | MYB31 | 988 | 1002 | - | 15.13 | CAACCACCAACTTCC |
| CR1-L3B_Croc | SNAI2 | 766 | 773 | + | 15.10 | GCACCTGT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
