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 | At3g11280 | 197 | 210 | - | 11.92 | TACATTATCTCATT |
| MIRc | AT5G05790 | 197 | 210 | - | 11.89 | TACATTATCTCATT |
| MIRc | AT3G10580 | 144 | 157 | + | 11.82 | ATGGGGATAATAAT |
| MIRc | AG | 128 | 143 | + | 11.79 | TTTCCTCATCTGTAAA |
| MIRc | MYB83 | 180 | 187 | - | 11.77 | CAACAACC |
| MIRc | nhr-142 | 87 | 94 | - | 11.70 | GGTCACAC |
| MIRc | PI | 127 | 140 | - | 11.67 | ACAGATGAGGAAAC |
| MIRc | HNF4A | 31 | 39 | - | 11.53 | CCAAGTCCA |
| MIRc | HNF4G | 31 | 39 | - | 11.40 | CCAAGTCCA |
| MIRc | M1BP | 85 | 95 | - | 11.37 | AGGTCACACAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
