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 | Fer1 | 438 | 450 | + | 1.54 | TAAACAGCTGCCG |
| AmnSINE1 | Rarg | 165 | 179 | - | -2.40 | TGGGGCACTGGTTCA |
| AmnSINE1 | Rarg | 55 | 71 | + | -3.60 | AGGGTCGGGCCTGGTCA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
