HAL1b
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000155 |
|---|---|
| TE superfamily | L1 |
| TE class | LINE |
| Species | Eutheria |
| Length | 2421 |
| Kimura value | 30.63 |
| Tau index | 0.9553 |
| Description | L1 retrotransposon, HAL1b subfamily |
| Comment | The 'ORF1-like' coding region ends somewhere around bp 660. gag ORF from 715-1686. |
| Sequence |
AAAAATTCACCAGCAGCAACCAAACAAGGAAAGGGGTACAACCTCATGCCATAAACTTCGAAAAGTGGCGGCCAAGGAAAGAAACAGAAGATTCTGGCGCGGTNTAGCATGGCTCCTAACCCCGCCCCCACCCCCCAGAAGCGGTACTGAGGAAAGAAGGTGAGTCGACAAAATCCTGAGAATTCTCACTAATACCCTCCAATTTGGAGAGAAGCGGACTGAGGGGGTGAGTAGGCAGCCCNGGGAAAAGTCAAGGAAAAACCCTCGAGAGTAGAAGCCCCTACGTACCACCGCGGGACCTCGGCAGAGGCAGGAAGGGCCGCCAGGGCTTGCCATCTTCCAGGGCNCCGCGCTGAATTGGGGGAATGANCCGAAGCCCACGGGAGTGGGATACGCCCCCGGCTAGGTGGAGTGAGCCCTGGTACAGGACATTTAACGAAATCTCAGAAGAGAGAGCAGAGCCCAGGTCCTCCAACAAAGGCTGCACNCAGCCCCAGCCGAGCTCTCCCCCCTTCCCCCATCCCCGCGCCCTCAGGCTACAGAAAAGTGGATAGAAAGCAATACCCAGCCCTCAAACTGTAGCTCAGAGGGGAAGACAAACAGGTCTCAGATAAGGTGGGAAGGGNGTCAAGGAGAATTCACCCACACTATATCAGAGCAAATAGAAGGTCTGGACAGAGCTGCCCACGTTAAGCATGAGCAAGATGAAAAGAAATGGCATGGCAACTATGCAAACATACTACAGCAAAGAAGAGAGAGNGAAAGGAAGAAAGGAGACANAGCATGCAAAAGACAGACGAAGAACCCAGTCTGGAAGAAAACATAACCCAAGGAACAGAAGAAAATTCCCCGCGAGTGCTTCGCGCTATAGAANAACTTAATAAGAACATGAATTCAATAAAACAAGAGCTCAAAGACGAGATGATAAAACAACAGAATGAGATGAAAAGGGAGATTGCAGAGCTAAGGAAACAAATTGAGGACCAAAACAACACCATTACAGAACTAATAAATAAATTAGAAACAGCAAGGAACAGAATAGACACGGCTGAAAATCGAATTACTGACATAGAGGAAAGGCTTGAGATAATCACAGTGAATGCAGAAGGAAAAGACAAAGAGATTAAAGCAATTAGAGAGAAGATAATAGATATGGAGGACAGACAAAGACGATCCAACATAAGGATAATTGGTGTCCCTGAAGTAGAGAACCCAACAAATGGAACAGAAAAAGTATTCAAAGATATAATACAAGAAAATTTCCCTGAAATGAAGGAAGAACTGAATCTGCAGATCGAAAGGGCACACCGTGTTCCAGGAAAAATTGATACAGAACGATCGACACCGAGACATATCCTGGTTAAGTTATTGAACTTCAAGGATAAAGAAAGAATTCTTCAGGCATCCAGGCAGAAAAAGCAAGTCACCTACAAGGGGGAAAAAATCAGGCTGGCCTCAGACTTCTCCACAGCAACATTCAATGCCAGAAGACAATGGAGCAATGTCTACAAAGTTCTGAGGGAAAGAAAGTGTGACCCAAGAATNTTATACCCAGCCAAGTTGTCGTTCAAGTATAAAGGCAACAGGCAGACATTCTCAAACATGAAAGAACTCAGGGAATATAGCACCCATGAGCCCTTCTTGAAAAAACTACTTGACGATGAAATCCAGCCAACCAAGAGATGAATCAAAATAAAGAACTCAGGAATGGAGAAGCCGTGGTAAAAGGACTGGTGGTGAGCACTGAATCCATTTAAATATAGAACTAAGACTAAACAACTGTGGGAATTATGGTTACAGAACAGAATGTAAATGTTATAAACCTTGACAANGTAAAAATAATATAANTAACAAAAATCGGGAGGTGGGAGAGGAGAGGTGGGAGGAAGTGTAAGAGTGCTAATTTCCTCATCTTTCATAGCAGGGAGTCAATCGATACTGTCTAAAATTGAAACATGTAGTTTAAAAANATAATGACTCCAACCTCTTAATGTTTTTCATAATCTTTTTTCTTAACCTTAGAGGGATCTTTTAGGAANTAATATCTCTTGTGGTGAAGAAACATTTATCTGAAGTTCAGCAATTCCTTCAGTTTCACTTCAGTTTCTTTTTCTTCTGTTAAATTCAAGTAAAATTAAATTTAATACTTTTNATTTAAAATAGCATGTATAGTATGATCCCATTTTTATAAAATTATTTCTATCTATCCATCCATCCATCCATCTATCCTTCTATCTGTATATATGCATAGAAAGATGTCTGGAATGATGTTCACCAAATGTTAACGATGGTTATTTCTGGGTGGTGGGATTTNGGGTGATTTNTTGCTTTCTTCTTTGTACTTTTCTGTATTGCTTGAATTTTTTATAATGAGCATGTATCATTTTTATAAAAACAATAAAGTNATTATTTTTTTAAAAA
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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 |
|---|---|---|---|---|---|---|
| HAL1b | ZNF148 | 120 | 129 | + | 15.95 | CCCCGCCCCC |
| HAL1b | Stat4 | 1313 | 1322 | + | 15.84 | TTCCAGGAAA |
| HAL1b | PRDM9 | 1870 | 1889 | + | 15.82 | AGAGGAGAGGTGGGAGGAAG |
| HAL1b | KLF7 | 120 | 127 | - | 15.72 | GGGCGGGG |
| HAL1b | ZNF331 | 455 | 464 | + | 15.68 | AGCAGAGCCC |
| HAL1b | Klf15 | 122 | 143 | + | 15.67 | CCGCCCCCACCCCCCAGAAGCG |
| HAL1b | Trl | 448 | 456 | + | 15.63 | AAGAGAGAG |
| HAL1b | Trl | 751 | 759 | + | 15.63 | AAGAGAGAG |
| HAL1b | STAT1 | 1313 | 1321 | + | 15.62 | TTCCAGGAA |
| HAL1b | btd | 121 | 129 | - | 15.62 | GGGGGCGGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
