Helitron3Na_Mam
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000160 |
|---|---|
| TE superfamily | Helitron-1 |
| TE order | RC |
| Species | Eutheria |
| Length | 486 |
| Kimura value | 31.32 |
| Tau index | 0.8210 |
| Description | Helitron DNA transposon, Helitron3Na_Mam subfamily |
| Comment | Helitrons are thought to transpose with a rolling circle mechanism, and represent a distinct class of DNA transposon. Helitron3Na_Mam represents a non-autonomous helitron fossil also found in other mammals, though it is not clearly similar to the other human helitron models. |
| Sequence |
TCTATATAAATAAAATTAAGTTTCTGTCTGTTTGTCTGTTACCGCATCACGCGAAAATGGCTGGATGGATTTTCACCAAATTTGGAGGGTATGTTTGGGATGGTCTGACTTAAAATATAGGCTATGTGGCATACACGAAATTCACTTTGGGGGGCCCTGGGGGGCACCTCAAAGAGATAGGCAGTCATCCTCCAGAGCAGCTGAAACTGAGGTACAACGAGAGGCCCGTGTGACTGCCGATCGGGAGAGACATGCCATACGTATTAAGACGCCGTGGACAGAGAAAACAAACAGTGGTTTCAAATATGAGCCCCAAATCGAAAGTCACAAGGGCAGACGCTCCGAATTGCAGGCGTTGATTTGCGATCGAGCTGCTTCTCACATGGGCAACTCTATGTAGCGTGCTCCAGGGTGAGTAGCAGCAGGGATTTATTTATTTAACGATGGTTAATGATTCTCCCGAGCAACGCCGGGGAGGCCAGCTAG
|
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 |
|---|---|---|---|---|---|---|
| Helitron3Na_Mam | BAD1 | 149 | 160 | - | 13.66 | CCAGGGCCCCCC |
| Helitron3Na_Mam | nhr-142 | 323 | 330 | + | 13.66 | AGTCACAA |
| Helitron3Na_Mam | D1 | 434 | 441 | - | 13.38 | TTAAATAA |
| Helitron3Na_Mam | IDD4 | 21 | 35 | - | 13.29 | ACAAACAGACAGAAA |
| Helitron3Na_Mam | PLAGL2 | 149 | 156 | - | 13.18 | GGCCCCCC |
| Helitron3Na_Mam | TFAP2C | 153 | 165 | + | 13.16 | GGCCCTGGGGGGC |
| Helitron3Na_Mam | PIF5 | 379 | 386 | + | 13.10 | TCACATGG |
| Helitron3Na_Mam | TFAP2C | 153 | 165 | - | 13.09 | GCCCCCCAGGGCC |
| Helitron3Na_Mam | IDD6 | 29 | 44 | + | 13.09 | TGTTTGTCTGTTACCG |
| Helitron3Na_Mam | Crg-1 | 430 | 440 | - | 13.07 | TAAATAAATAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
