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
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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 |
|---|---|---|---|---|---|---|
| X9_LINE | IRF4 | 126 | 139 | - | 18.61 | TGAAACCGAAAGCA |
| X9_LINE | IRF8 | 127 | 139 | - | 17.44 | TGAAACCGAAAGC |
| X9_LINE | RVE4 | 470 | 478 | + | 16.53 | AGATATTTT |
| X9_LINE | NEUROG2 | 816 | 825 | + | 16.45 | GACATATGTC |
| X9_LINE | NEUROG2 | 816 | 825 | - | 16.45 | GACATATGTC |
| X9_LINE | RVE7 | 470 | 478 | - | 16.38 | AAAATATCT |
| X9_LINE | RVE6 | 470 | 478 | + | 16.23 | AGATATTTT |
| X9_LINE | RVE5 | 470 | 478 | + | 16.21 | AGATATTTT |
| X9_LINE | RVE8 | 470 | 478 | + | 16.08 | AGATATTTT |
| X9_LINE | sta-1 | 20 | 28 | - | 16.04 | TTCCAAGAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
