AmnSINE1
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000067 |
|---|---|
| TE superfamily | L2-end |
| TE class | SINE |
| Species | Amniota |
| Length | 575 |
| Kimura value | 34.39 |
| Tau index | 0.8527 |
| Description | Amniota SINE1 |
| Comment | Derived from both chicken and human sequence. Reference coords 1-114: 5S-RNA, 168-328: Deu-core, 508-575: LINE2-like tail. |
| Sequence |
GCCTGCAGCCATACCACCTCGGGCTGTGATCTCGTCAGATCTCACAAGCTAAGCAGGGTCGGGCCTGGTCAGTACTTGGATGGGAGACCTCCAAGGAAACCCAGGTGCTGCAGGAAGTGGTGCTGGTGATTCAGTAGGTGGCACTCTTCCCTCTGAGTCAGTACTGAACCAGTGCCCCAGCGTGGTGTTAGGGGGCACTGTGCTGCTGGAGGTGCCGTCTTTCGGATGAGACGTAAAACCGAGGTCCTGACCACTTGTGGTCATTAAAGATCCCATGGCACTTTTCGCAAGAGTAGGGGTGTTAACCCCGGTGTCCTGGCCAAATTCCAATTTGGGTAATTACATTCTGCCTACCTAAATTCCCCCTGCAGTTTCAATTGGATACGGTATTCTTCACTTCCTGTCCTAAACTGTTGTGTAGTGTTGCTGTGCGCTGTTAAACAGCTGCCGCGTTCCACCCCAGAGGTGGCTGCATTTCAGTGGTGGGTGAAGTGATCCCTGTATGTAGCTTGTAAAGCGCTTTGGGATCCTTCGGGATGAAAGGCGCTATATAAATGCAAGGTATTATTATTATT
|
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 |
|---|---|---|---|---|---|---|
| AmnSINE1 | ZBTB11 | 395 | 403 | + | 14.03 | CACTTCCTG |
| AmnSINE1 | Rhox11 | 432 | 440 | + | 13.96 | CGCTGTTAA |
| AmnSINE1 | bHLH112 | 251 | 257 | + | 13.92 | CCACTTG |
| AmnSINE1 | OsFBH1 | 251 | 257 | + | 13.92 | CCACTTG |
| AmnSINE1 | sc | 440 | 449 | + | 13.89 | AACAGCTGCC |
| AmnSINE1 | Ascl2 | 440 | 449 | - | 13.87 | GGCAGCTGTT |
| AmnSINE1 | ZNF175 | 110 | 118 | + | 13.86 | GCAGGAAGT |
| AmnSINE1 | MYB63 | 480 | 490 | - | 13.86 | TCACCCACCAC |
| AmnSINE1 | fos-1 | 154 | 160 | - | 13.76 | TGACTCA |
| AmnSINE1 | sc | 440 | 449 | - | 13.69 | GGCAGCTGTT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
