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 | hlh-1 | 440 | 449 | + | 15.83 | AACAGCTGCC |
| AmnSINE1 | AGL16 | 324 | 338 | + | 15.82 | ATTCCAATTTGGGTA |
| AmnSINE1 | ETV1 | 396 | 404 | - | 15.81 | ACAGGAAGT |
| AmnSINE1 | GABPA | 110 | 119 | - | 15.79 | CACTTCCTGC |
| AmnSINE1 | ELF3 | 111 | 119 | - | 15.76 | CACTTCCTG |
| AmnSINE1 | ELF3 | 395 | 403 | + | 15.76 | CACTTCCTG |
| AmnSINE1 | EHF | 111 | 119 | - | 15.76 | CACTTCCTG |
| AmnSINE1 | EHF | 395 | 403 | + | 15.76 | CACTTCCTG |
| AmnSINE1 | ZNF175 | 396 | 404 | - | 15.73 | ACAGGAAGT |
| AmnSINE1 | SPIB | 394 | 406 | + | 15.54 | TCACTTCCTGTCC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
