MIRb
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000975 |
|---|---|
| TE superfamily | L2-end |
| TE class | SINE |
| Species | Mammalia |
| Length | 268 |
| Kimura value | 34.09 |
| Tau index | 0.8426 |
| Description | MIRb (Mammalian-wide Interspersed Repeat - variant b) |
| Comment | MIRb 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 |
CAGAGGGGCAGCGTGGTGCAGTGGAAAGAGCACGGGCTTTGGAGTCAGACAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTTGGGCAAGTTACTTAACCTCTCTGAGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATACCTACCTCGCAGGGTTGTTGTGAGGATTAAATGAGATAATGCATGTAAAGCGCTTAGCACAGTGCCTGGCACATAGTAAGCGCTCAATAAATGGTAGCTCTATTATT
|
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 |
|---|---|---|---|---|---|---|
| MIRb | svp | 93 | 99 | - | 12.82 | AAGGTCA |
| MIRb | Nkx3-1 | 77 | 83 | + | 12.79 | CCACTTA |
| MIRb | ESR2 | 42 | 56 | + | 12.79 | GAGTCAGACAGACCT |
| MIRb | Hoxd13 | 246 | 252 | + | 12.73 | CAATAAA |
| MIRb | NAC103 | 103 | 109 | + | 12.64 | CAAGTTA |
| MIRb | MYB67 | 160 | 167 | + | 12.61 | TACCTACC |
| MIRb | NAC062 | 107 | 113 | - | 12.45 | TAAGTAA |
| MIRb | At3g11280 | 147 | 160 | - | 12.44 | ATTATTATCCCCAT |
| MIRb | PITX2 | 184 | 191 | - | 12.42 | TTAATCCT |
| MIRb | PK21166.1 | 160 | 167 | + | 12.37 | TACCTACC |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
