L1PB1_3end
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000347 |
|---|---|
| TE superfamily | L1 |
| TE class | LINE |
| Species | Simiiformes |
| Length | 898 |
| Kimura value | 8.88 |
| Tau index | 0.9952 |
| Description | 3' end of L1 retrotransposon, L1PB1_3end subfamily |
| Comment | ORF2 ends at bp ~684 |
| Sequence |
CTAATATCCAGAATCTACAANGAACTCAAACAAATCAGCAAGAAAAAAACAAACAATCCCATCAAAAAGTGGGCTAAGGACATGAATAGACAATTCTCAAAAGAAGATATACAAATGGCCAACAAACATATGAAAAAATGCTCAACATCACTAATGATCAGGGAAATGCAAATCAAAACCACAATGCGATACCACCTTACTCCTGCAAGAATGGCCATAATCAAAAAATCAAAAAATAATAGATGTTGGCGTGGATGCGGTGAAAAGGGAACACTTCTACACTGCTGGTGGGAATGTAAACTAGTACAACCACTATGGAAAACAGTGTGGAGATTCCTTAAAGAACTAAAAGTAGAACTACCATTTGATCCAGCAATCCCACTACTGGGTATCTACCCAGAGGAAAAGAAGTCATTATACGAAAAAGATACTTGCACACGCATGTTTATAGCAGCACAATTCGCAATTGCAAAAATATGGAACCAGCCCAAATGCCCATCAATCAACGAGTGGATAAAGAAANTGTGGTATATATATACCATGGAATACTACTCAGCCATAAAAAGGAATGAANTAATGGCATTCGCAGCGACCTGGATGGAATTGGAGACTATTATTCTAAGTGAAGTAACTCAGGAATGGAAAACCAAACATCGTATGTTCTCACTCATAAGTGGGAGCTAAGCTATGAGGACGCAAAGGCATAAGAATGATACAATGGACTTTGGGGACTCGGGGGAAAGGGTGGGAGGGGGGTGAGGGATAAAAGACTACANATTGGGTACAGTGTACACTGCTCGGGTGATGGGTGCACCAAAATCTCANAAATCACCACTAAAGAACTTACTCATGTAACCAAACACCACCTGTTCCCCAAAAACCTATNGAAATAAAAAAA
|
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 |
|---|---|---|---|---|---|---|
| L1PB1_3end | IRF8 | 420 | 432 | + | 0.96 | CGAAAAAGATACT |
| L1PB1_3end | IRF9 | 418 | 432 | + | 0.53 | TACGAAAAAGATACT |
| L1PB1_3end | ZSCAN31 | 693 | 710 | - | 0.44 | TTCTTATGCCTTTGCGTC |
| L1PB1_3end | IRF4 | 420 | 433 | + | -0.42 | CGAAAAAGATACTT |
| L1PB1_3end | Rarb | 399 | 414 | + | -5.47 | AGAGGAAAAGAAGTCA |
| L1PB1_3end | EWSR1-FLI1 | 739 | 756 | + | -10.01 | GAAAGGGTGGGAGGGGGG |
| L1PB1_3end | EWSR1-FLI1 | 735 | 752 | + | -12.08 | GGGGGAAAGGGTGGGAGG |
| L1PB1_3end | BPC5 | 64 | 93 | + | -45.68 | AAAAAGTGGGCTAAGGACATGAATAGACAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
