X9_LINE
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001122 |
|---|---|
| TE superfamily | L1 |
| TE class | LINE |
| Species | Amniota |
| Length | 936 |
| Kimura value | 35.38 |
| Tau index | 0.0000 |
| Description | L1 retrotransposon, X9_LINE subfamily |
| Comment | X9_LINE is found in both human and chicken at low copy number. |
| Sequence |
TAATTTTTTATGATANTAGTTCTTGGAAGATAAAGATACCNTACAATGCCTAAAAATAAACCTGGATCCGCTAAAGATTCGGCATTTTGCTCCCAAGCTTCCGCTAGCCGGGAGACGGGCCTGTCTGCTTTCGGTTTCACACCATCGGGAGGTACAGATTTGACTTATCAAACGATGTCGGATTTACTTAGTAAGAACTCGGCGGATATTAGTAAAAGGTTGGACGCGATTCAGGCTACAATGGCTGCAACGGATAAGAAGTTTGAAAGCTTTGGTTCAAGACTGCAGGAGGCTGAGAGGAAAATTGAAGACACGGAGATAACGATCGATGGACACGACGCTATTCTAACTGAGAATACCAAAGACTGTAAAGCGCTGAGAAATCGAATTGATGACCTGGAAAACAAGCTCAGATTAAGAAATGTCAGGTTGGTAGGGGTTCCTGAAGGCGCGGAGACGAGAGAAGCTGAGATATTTTTTTCGCAATGGATTATGAAGGTGCTGGGGATGGATAATTTTGAACTCCCTCTACAATGCGTCGTGGCGCGTCATATCCCTGGGAAGGCCAATCAGGCAACACCCCGCACGGTNCTTGCGGAATGTGCAGCTCTTGGAACGAGGAACAACGTTTTGAAATTGGCACGTAAATCTGAGTCCAGTTTTCAGGGTTCAAGAATCTTATTTTATCCGGATTACAGTCCTGTTCTTCTTCGGCGTCGGAAGGCGTTTGTGACTGTTAAAACGAGAATGAAAAATATGGGCCTGGAATACGCGTTGCTTTATCCTGCCAGGCTGAGGGTTCGCTGTGGAGGCCAGACATATGTCTTTCTTTCTCCCACGGATGCTACAGCGTTTCTGGATAAGAAGGAGGCAGACTGCGCCCGAACGGTGGAAGAAATGGCTTCGGAGGACTCCGGCACGAAGAGCGTATTCTTT
|
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 |
|---|---|---|---|---|---|---|
| X9_LINE | IME1 | 198 | 205 | - | 15.91 | CCGCCGAG |
| X9_LINE | Stat5a | 20 | 28 | - | 15.91 | TTCCAAGAA |
| X9_LINE | NEUROG1 | 816 | 825 | + | 15.87 | GACATATGTC |
| X9_LINE | NEUROG1 | 816 | 825 | - | 15.87 | GACATATGTC |
| X9_LINE | LHY | 470 | 478 | + | 15.86 | AGATATTTT |
| X9_LINE | RVE1 | 470 | 478 | - | 15.59 | AAAATATCT |
| X9_LINE | RVE7L | 470 | 478 | - | 15.47 | AAAATATCT |
| X9_LINE | HAP3 | 564 | 572 | - | 15.14 | TGATTGGCC |
| X9_LINE | Stat5a::Stat5b | 20 | 28 | - | 15.04 | TTCCAAGAA |
| X9_LINE | Irf1 | 129 | 139 | - | 14.84 | TGAAACCGAAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
