CR1-1_Amn
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001336 |
|---|---|
| TE superfamily | CR1 |
| TE class | LINE |
| Species | Amniota |
| Length | 813 |
| Kimura value | 30.90 |
| Tau index | 0.0000 |
| Description | CR1 (Chicken Repeat 1) retrotransposon, CR1-1_Amn subfamily |
| Comment | - |
| Sequence |
CGAGAAAGGACTTGGGGTNGTGGTGGATAAAACTCTAAAACCTTCGGCACAGTGCTTAACAGCAGTNAAAAAAGCAAACAAAATNCTGGGATGCATAAATAGAGGTATCGAATATAAGTCGGAGGAAATTATTCTAGCACTGTATAAGGGACTAGTGAGGCCACATTTGGAATACTGTGCGCAGTTCTGGTCACCTTATTATAAAAAGGATATTATAGAAATGGAGAAGGTACAGCGGAGGGCAACCAGAATGATACAGGGACTCGGGGATCTTAGTTATTCAGAAAGGTTAGAGAAACTAGGTCTGTATTCTTTGGAAAAGAGGAGATTAAGAGGGGACCTCACTGAGGTATACANAATTCTGAAGGGAATAGAGAGGATAGATGCTACAAGGCTATTTGAGCTAGTGTCAAATACAAGAACAAGGGGGCACGAACTNAAGCTAAGGAAGGGCCGGGCACTAAAGGAATTTAGGCGGAATTTCTTTACGCAGAGNATAGTTAATATATGGAACTCATTGCCACAGGANGTCGTGGAGGCNAGNANTATAACCGGGTTCAAAAGGGGACTGGATAAATTCATGGAGGATAGGTCCATTAGTGGCTATTAAACAGAACGGNTAAGGAATGNTGTCCCTAGCCTCTGNTTGTCGGAGGGTGGAGANGGATGGCAGGAGANAGATCACTTGATCATTACCTGTTAGGTTCACTCCCTCTGAAGCATCTGGTACTGGCCACTGTCGGNAGACAGGATACTGGGCTAGATGGACCNTTGGTCTGACCCAGTATGGCAGTTCTTATGTTCTTATGTTCT
|
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 |
|---|---|---|---|---|---|---|
| CR1-1_Amn | THAP1 | 237 | 244 | + | 12.95 | GGAGGGCA |
| CR1-1_Amn | MCM1 | 161 | 172 | + | 12.88 | CCACATTTGGAA |
| CR1-1_Amn | Zm00001d035604 | 699 | 705 | - | 12.82 | ACCTAAC |
| CR1-1_Amn | DOF5.1 | 317 | 335 | + | 12.79 | GAAAAGAGGAGATTAAGAG |
| CR1-1_Amn | DOF1.7 | 69 | 79 | + | 12.73 | AAAAAGCAAAC |
| CR1-1_Amn | Isl1 | 594 | 600 | + | 12.65 | CCATTAG |
| CR1-1_Amn | ZSCAN21 | 51 | 57 | - | 12.61 | AAGCACT |
| CR1-1_Amn | MYB92 | 699 | 705 | - | 12.52 | ACCTAAC |
| CR1-1_Amn | Rhox11 | 56 | 64 | - | 12.51 | TGCTGTTAA |
| CR1-1_Amn | RARG | 426 | 438 | - | 12.51 | AGTTCGTGCCCCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
