Helitron2Na_Mam
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000159 |
|---|---|
| TE superfamily | Helitron-1 |
| TE class | RC |
| Species | Theria_mammals |
| Length | 324 |
| Kimura value | 33.87 |
| Tau index | 1.0000 |
| Description | Helitron DNA transposon, Helitron2Na_Mam subfamily |
| Comment | Helitrons are thought to transpose with a rolling circle mechanism, and represent a distinct class of DNA transposon. While named a helitron, this 324bp TE model its classification is tentative. There is suggestive similarity to a non-autonomous helitron in the sea urchin S. purpuratus. |
| Sequence |
TTGACCGAACGAAGTGAGGTCTCTGTTTCAACTCGACCGCTTGGCATTTTGCATTTGTCTGTCTGTTTGTTCCATGATAACTTTCGAAGGAGTTGACTGATTTTGACCAAATTTGGTACACTACTAAAGGGTATCAAGATACACCTTAAGTTCGATTTGTGGTTCAGTCTGCCATCTTGAAACAAAATGGCAGCCGATAAAAGTTTTCAAATGGGCATATCTTCTGTAATTTTTAATAGATTTCAATGAAATTTGGTACGTGGGTAGAGGTTACAGAGATATGTGATTGCACTGAGTGAAGTCTGCAGTTCACAGAACCACTAG
|
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 |
|---|---|---|---|---|---|---|
| Helitron2Na_Mam | AGL3 | 107 | 116 | - | 12.23 | CCAAATTTGG |
| Helitron2Na_Mam | Stat2 | 20 | 29 | - | 12.19 | GAAACAGAGA |
| Helitron2Na_Mam | HSF1 | 69 | 75 | - | 12.13 | ATGGAAC |
| Helitron2Na_Mam | RUNX3 | 157 | 164 | - | 12.06 | AACCACAA |
| Helitron2Na_Mam | Prdm4 | 175 | 185 | + | 12.03 | TCTTGAAACAA |
| Helitron2Na_Mam | STE12 | 178 | 184 | + | 12.00 | TGAAACA |
| Helitron2Na_Mam | STE12 | 24 | 30 | - | 12.00 | TGAAACA |
| Helitron2Na_Mam | WRKY59 | 92 | 101 | - | 11.99 | ATCAGTCAAC |
| Helitron2Na_Mam | AG | 104 | 119 | + | 11.89 | TGACCAAATTTGGTAC |
| Helitron2Na_Mam | SPL8 | 110 | 125 | - | 11.81 | AGTAGTGTACCAAATT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
