Helitron1Nb_Mam
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000158 |
|---|---|
| TE superfamily | Helitron-1 |
| TE class | RC |
| Species | Eutheria |
| Length | 1116 |
| Kimura value | 28.27 |
| Tau index | 0.0000 |
| Description | Helitron DNA transposon, Helitron1Nb_Mam subfamily |
| Comment | Helitrons are thought to transpose with a rolling circle mechanism, and represent a distinct class of DNA transposon. Helitron1Nb_Mam represents a non-autonomous helitron fossil found broadly in mammals. Helitron1Nb_Mam is identical to Helitron1Na_Mam except over the region 696-913 in "1Nb" and 696-859 in "1Na", where they are unrelated. |
| Sequence |
TCTATCTATATAAAACACTTAGGTATGTTTCCCCAAGGTTCAGCTGGGCGTGGTTTTCACGTGATCACTCCAGCCAATGAACGCGCAAGCATCCAGTGATCACGTGAAAACCACGCCTGTTAATTTATAAATGTTGACACTGACAGGTGACAGGTAGGTAGTGACTGTTTATAAGAATTGTATGCATTTCTGAGCATTTATTTACTTAATCTTTTTAAAATTAAGCTTAGAATTTCTACAACGTGTAACGTTAAACATGTGTCACCTATTTTGAACTTAATACAGTGCATAAAAGTATTTATAAGAATTGTATGCATTTCTGAGCATTTATTTACTTAATCAAAAATTTTATGCGTTTTGAGCATTTATTTACTTAATCAAAGGTTTAAAAGTTTTAAGAAGTATAAAAATGGCTGAACCATGTGTAAGAACTCTGAGAAACCATAGAAGAAATGCTAATGAAACATTAGAGGAGAGATCAAATAGACTACGAGACCGAAATGAAACTCTACGATGACGAAGACGGACAGAGAACACTGAAGAAAGAGAAGAACGATTGGAAATGAGAAGAAAAAGAGCGAAACGCCTAGGACTAATCAAATAGAAGTACCGGATGCGAATAATCAACAAGCTGTAATCAANTGTGGAAGAGCATAACATAGGAAATATGTGTTACAACTGTGAGCACTGCAATGCAAGATATTGGGGACAAGAGTTAAACACATCGAATAAATACACTAAATGCTGTCACGATGGAAAGGTTTCACTCGACCCACTGTCTGAGACACCTACTCTATTATAAGAGCTGCTTNCAGGGAATACATGCGAAGAAACAAAAAACTCACAGAGAACATATACGAGAGCGNAACTCAGCAATGGCGTTCACATCAGTGGGCGCNGAGATTAAATCACTGCCNGTATTTAGTCACGGACAACTATATGTTGCTCTCTCAAGAGTTCGATCATTGGACTCATTAAGTGTTGTATCTGAGAAGAATAAGATTGTTAATTGTGTTTACAATGAAATATATGAATAAATAAATAAAATGCGTTAATATTTTATTAATAACTATTAAGATCTGCTAGAACGGCGTATGTTACGCCGGGTACAGCTAG
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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 |
|---|---|---|---|---|---|---|
| Helitron1Nb_Mam | LRL2 | 101 | 115 | - | 19.31 | CGTGGTTTTCACGTG |
| Helitron1Nb_Mam | LRL2 | 49 | 63 | + | 19.31 | CGTGGTTTTCACGTG |
| Helitron1Nb_Mam | FoxA-a | 197 | 209 | - | 17.36 | TTAAGTAAATAAA |
| Helitron1Nb_Mam | FoxA-a | 327 | 339 | - | 17.36 | TTAAGTAAATAAA |
| Helitron1Nb_Mam | FoxA-a | 365 | 377 | - | 17.36 | TTAAGTAAATAAA |
| Helitron1Nb_Mam | AS2 | 1089 | 1106 | + | 17.23 | CGGCGTATGTTACGCCGG |
| Helitron1Nb_Mam | TGIF2 | 141 | 152 | + | 17.11 | TGACAGGTGACA |
| Helitron1Nb_Mam | GFI1 | 906 | 916 | + | 16.98 | AAATCACTGCC |
| Helitron1Nb_Mam | TGIF2LX | 141 | 152 | - | 16.48 | TGTCACCTGTCA |
| Helitron1Nb_Mam | TGIF2LX | 141 | 152 | + | 16.42 | TGACAGGTGACA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
