MIRc
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000976 |
|---|---|
| TE superfamily | L2-end |
| TE class | SINE |
| Species | Mammalia |
| Length | 268 |
| Kimura value | 35.35 |
| Tau index | 0.9012 |
| Description | MIRc (Mammalian-wide Interspersed Repeat - variant c) |
| Comment | MIRc is a pan-mammalian SINE with a 5' end derived from a tRNA, a central deeply-conserved CORE region (shared with other MIRs), and a 3' terminal ~55bp related to an L2 LINE. |
| Sequence |
CGAGGCAGTGTGGTGCAGTGGAAAGAGCACTGGACTTGGAGTCAGGAAGACCTGGGTTCGAGTCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTCACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTGCCCTGCCTACCTCACAGGGTTGTTGTGAGGATCAAATGAGATAATGTATGTGAAAGCGCTTTGTAAACTGTAAAGTGCTATACAAATGTAAGGNGTTATTATTATT
|
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 |
|---|---|---|---|---|---|---|
| MIRc | NR5A1 | 90 | 101 | - | 13.84 | TGCCCAAGGTCA |
| MIRc | sex-1 | 89 | 96 | - | 13.51 | AAGGTCAC |
| MIRc | Prdm15 | 46 | 56 | + | 13.39 | GAAGACCTGGG |
| MIRc | NR2F2 | 90 | 96 | - | 13.14 | AAGGTCA |
| MIRc | AGL16 | 128 | 142 | + | 13.12 | TTTCCTCATCTGTAA |
| MIRc | nhr-25 | 90 | 97 | - | 13.07 | CAAGGTCA |
| MIRc | AT5G05790 | 144 | 157 | - | 13.02 | ATTATTATCCCCAT |
| MIRc | Nr5A2 | 90 | 98 | + | 12.96 | TGACCTTGG |
| MIRc | bap | 105 | 111 | - | 12.93 | TTAAGTG |
| MIRc | ZNF331 | 66 | 75 | - | 12.91 | GGCAGAGCCG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
