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 | Stat5b | 20 | 28 | - | 14.16 | TTCCAAGAA |
| X9_LINE | nhr-70 | 233 | 241 | - | 14.15 | TTGTAGCCT |
| X9_LINE | LBD13 | 886 | 893 | - | 14.12 | TCCACCGT |
| X9_LINE | STAT3 | 20 | 28 | + | 14.10 | TTCTTGGAA |
| X9_LINE | MEF2A | 50 | 59 | + | 14.10 | CTAAAAATAA |
| X9_LINE | YRR1 | 313 | 322 | - | 14.04 | TTATCTCCGT |
| X9_LINE | HHO3 | 673 | 680 | - | 14.00 | AAGATTCT |
| X9_LINE | Tbx6 | 136 | 144 | - | 13.94 | TGGTGTGAA |
| X9_LINE | HHO5 | 73 | 80 | + | 13.94 | AAAGATTC |
| X9_LINE | nfya-1 | 564 | 573 | + | 13.92 | GGCCAATCAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
