AmnSINE2
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000068 |
|---|---|
| TE superfamily | Unknown_LINE-dependent |
| TE order | SINE |
| Species | Amniota |
| Length | 358 |
| Kimura value | 34.72 |
| Tau index | 0.0000 |
| Description | Aminiota SINE2 |
| Comment | The copy number ranges from ~100 in the human genome to ~178 in the chicken genome. 45% of human copies are in highly conserved regions. Shows distant similarity to Leu tRNA. Tentatively classified as SINE element. Inverted from UCON3 original. Reference coords 1-78:tRNA-Leu- TTG, 137-264:Deu core, remainder must match an as yet unknown LINE. |
| Sequence |
GCCGGAGGGGATGGCTTAGTGGTCTAAGCATCAGGTTTGAAATACCTAGACTCCCTGGAACCACAGGTTCAAATCCCAGCAGGGTCGACTCAGCCCTTCATCCTTCCGAGGTAGATAAATTGAGTNCCACGCAGTTTACTGTGTGNGGGTCTTTCGGATGAGACCTTAAAAACCAAAGCCCTGTCTGCTCTGCGTGGACATTAAAGATCCCGTGGCGCTTTTCGTAAGAGTAGGGGTTTGCCCCGGTGCCCTTGGCCGAATTTCTGGAACCCGGCTGAAANCCCGGGGAAACCGAGAGCCTGGCTTATCCCTATAGGGTATTAGNCACCCTATAAAAGTTAAATTTATTTATTTATTT
|
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 |
|---|---|---|---|---|---|---|
| AmnSINE2 | STB4 | 104 | 110 | - | 12.55 | CTCGGAA |
| AmnSINE2 | FOXD3 | 342 | 355 | - | 12.53 | TAAATAAATAAATT |
| AmnSINE2 | FOXC2 | 345 | 355 | - | 12.51 | TAAATAAATAA |
| AmnSINE2 | AT5G04760 | 304 | 310 | + | 12.51 | CTTATCC |
| AmnSINE2 | ZSCAN29 | 190 | 200 | - | 12.51 | TGTCCACGCAG |
| AmnSINE2 | ZNF148 | 1 | 10 | - | 12.50 | CCCCTCCGGC |
| AmnSINE2 | HOXB13 | 329 | 337 | + | 12.44 | CCTATAAAA |
| AmnSINE2 | fd59A | 346 | 355 | - | 12.32 | TAAATAAATA |
| AmnSINE2 | FOXC1 | 345 | 355 | - | 12.26 | TAAATAAATAA |
| AmnSINE2 | abi4 | 244 | 253 | + | 12.13 | CGGTGCCCTT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
