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 | usp | 3596 | 3604 | + | 17.04 | GGGGTCACG |
| CR1-L3A_Croc | HSFA4A | 1123 | 1136 | + | 17.02 | AGAAGATTCTGGAA |
| CR1-L3A_Croc | HSF4 | 1124 | 1136 | - | 17.00 | TTCCAGAATCTTC |
| CR1-L3A_Croc | KLF16 | 1613 | 1623 | - | 16.98 | GCCACTCCCCC |
| CR1-L3A_Croc | ZNF449 | 742 | 751 | + | 16.93 | CAGCCCAACC |
| CR1-L3A_Croc | ZNF816 | 1271 | 1285 | + | 16.85 | AGGGGACAGGCTGGC |
| CR1-L3A_Croc | ZNF257 | 523 | 532 | + | 16.56 | GAGGCAAGAG |
| CR1-L3A_Croc | RVE4 | 670 | 678 | - | 16.53 | AGATATTTT |
| CR1-L3A_Croc | erm | 1483 | 1493 | + | 16.48 | ATTGCTCATTT |
| CR1-L3A_Croc | PATZ1 | 1607 | 1617 | + | 16.43 | AGGGGAGGGGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
