MIRc
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000976 |
|---|---|
| TE superfamily | L2-end |
| TE order | 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 | Ppara | 90 | 96 | - | 12.88 | AAGGTCA |
| MIRc | svp | 90 | 96 | - | 12.82 | AAGGTCA |
| MIRc | Nkx3-1 | 74 | 80 | + | 12.79 | CCACTTA |
| MIRc | At3g11280 | 144 | 157 | - | 12.44 | ATTATTATCCCCAT |
| MIRc | INO4 | 208 | 216 | + | 12.31 | GTATGTGAA |
| MIRc | ARG81 | 38 | 44 | - | 12.30 | TGACTCC |
| MIRc | AGL15 | 128 | 143 | + | 12.20 | TTTCCTCATCTGTAAA |
| MIRc | JUND | 197 | 207 | + | 12.13 | AATGAGATAAT |
| MIRc | ss | 86 | 93 | + | 12.10 | TGTGTGAC |
| MIRc | ESR2 | 39 | 53 | + | 12.00 | GAGTCAGGAAGACCT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
