HAL1
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000154 |
|---|---|
| TE superfamily | L1 |
| TE order | LINE |
| Species | Eutheria |
| Length | 2507 |
| Kimura value | 31.19 |
| Tau index | 0.7715 |
| Description | L1 retrotransposon, HAL1 subfamily |
| Comment | HAL1 resembles half of a LINE1 element, as it encoded a protein closely related to LINE1 ORF1, but has no similarity to ORF2. The HAL1 3' end (position ~2300-2510) matches 3' UTRs of the oldest L1 subfamilies. The precise relationship between HAL1 and L1's is unresolved. |
| Sequence |
GACTTCCGGTTAAAGATGGCGGATTGAACACACGCATTTANTTTCGCTCCCTCCCGAAACCCCACTAAAATGACAGTAAAGGAATTTTTTAANAAAGGCATAAACCCACAAGGACAAAGAGAACGGGAGAGGAGACAACAGCAACAAAATTTTGGAAGCTGGAAAGCAGATGGACGAGTGGTAACTGACTTAGCAGACCCGAGAAAGCTGAATCCTAAGCCGGCAGTGGGGAAAGCCGAGAAGCAACCCGATTTACACCGCAGAATCCCCAAAAGGCTCAGGAATTGGCGGCACCAGGTACCTCTGGAAGTGGGGGTGAAGGTGGGGCTAAAAACAGGGAGGATTGGTTGAAAGTCTGTTTAAGAAGCAGTTAGACCCCCAGATCCCCTCCCCCACTCTATNGCAGCCAGGCGACTGCCCCTCCCCCACCCCGGCAGAAGACTGGAGGTTTATTCTCTGGAGAGGGTAAAACAGAGGGTCTCTGGACTGGGGGACACCAGGCACAGTTGAGGGCAGAGGGGTACCGTACTGAAAACAGGGGGATTAAGTGAAAGTNTACATACTGAATGNCGAGAGACCCCCAGCCCTCTTCCCCCACTCGGCTCCCAGAACGCTGGCAGCCAGGCCTATACCCTCCAGGCAGGAGATTGGAAGANTCTTCTCTGGGGAATCTGACCAGCCCAAGAGGAAAGACCTAAAGATACTGACATTNGGGGTTCCCCAAGCGAAATAGCCCAGCCAGATCACCCTACAGTGAAGCCCACAGTCGACAAGCCCCACCCACGCGCNCAGAGCTTCCAATCAGCTTTTTAGTGCCTCACTCTTAAATATGAGCAGACAGCCAAGGATCACCAGACATCTGAGGAAAGCCTCTAACATGAAAGANAGAGACCAAAACAAACAGAAAAAAAAAGCAACTTGGAGGAAACAGAAGACATGCAGAGAGAAGAAAACNTCTTTAAAAANATNATTAATATCCTCAGAGAGATAAGAGAAGATATTGCATCCATGAAACAAGAACAGGATGCTATAAAAAGGAACATTCAGAGAACAAAAAGAAGCTCTTGGAAATTAAAAATATGATAGCAGAAATNAAAACTCAATAGAAGGGTTGGAAGATAAAGTTGAGGAAATCTCCCAGAAAGTAGAACAAAAAGACAAAGAGATGGAAAATAGGAGAGAAAAGATAAGAAAATTAGAGGATCAGTCCAGGAGGTCCAACATCCGANTAATAGGAGTTCCAGAAAGAGAGAACAGAGAAAANGANGGAAGAGAAATTATCAAAGAAATAATNCAAGAAAATTTCCCAGAACTGAAGGACATGAGTTTCCAGATTGAAAGGGCCCACCGAGTGCCCAGCACAATGAATGAAAAAAATAGACCCACACCAAGGCACATCATCGTGAAATTTCAGAACACCGGGGATAAAGAGAAGATCCTAAAAGCTTCCAGAGAGAAAAAACAGGTCACATACAAAGGATCAGGAATCAGAATGGCATCGGACTTCTCAACAGCAACACTGGAAGCTAGAAGACAATGGAGCAATGCCTTCAAAATTCTGAGGGAAAATNATTTCCAACCTAGAATTCTATACCCAGCCAAACTATCAATCAAGTGTGAGGGTAGAATAAAGACATTTTCAGACATGCAAGGTCTCAAAAAATTTACCTCCCATGCACCCTTTCTCAGGAAGCTACTGGAGGATGTGCTCCACCAAAACGAGGGAGTAAACCAAGAAAGAGGAAGACATGGGATCCAGGAAACAGGGGATCCAACACAGGAGAGAGGCGAAGGGAATTCCCAGGATGATGGTGAAGGGAAGTCCCAGGATGACAGCTGTGCAGCAGGCCTAGAGAGCAACCAGTCCAGATTGGAGCAGGAGGACAGAAGGCTCCAGGAGAGATNTCTCCAAGAAAATGAAACTGATAGANTACCTGATGTGTTTGAACATATTGAGAGGAGATTTANACAATTGGCGGAGAGTTTGGGGATGAATTAGTGATAAGTACATAGAAAACTAAGCAAATGAAAAACGAGACAATTATTAACTCCAGGGAAAACAAAAAGTTGTACAAGAAAGGAAANGTAATCATAGTACACTACATGGCTCAGCTGTGAATAATATTTACATAGTCATAATAATGTAAACACTGAATATTGATTTAACCAAAATTATGATATAACTATATTGGGAGGATGGGGGGATGGGAAGTGTGTGTGTGNTGAGGGGGAGGTGTGAAAGAAGAGCTAAATCCTCATCTTCCATAGTAGGAAGTCAATAGATAATGCCTAAAATTGAAAAATCAAGAAATAGCAATATAAGCATGTTATTTAGAAATATGGAGGTAAATACCAGAAGAAACAGCTAAAAGAGTTGAAAGTGGTTGCCTCTGGGGAGGGAGTGAAGATGGAAGAGGGNAGGGATGGGGACTGCTTTTCGTNATAAGCCTTGTAGNACTATTTGACTTTTTAAACTATGTGCATGTATNACTTTGATAAAAATAAAA
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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 |
|---|---|---|---|---|---|---|
| HAL1 | phol | 12 | 21 | - | 16.57 | CGCCATCTTT |
| HAL1 | FOXB1 | 2122 | 2132 | - | 16.46 | TATGTAAATAT |
| HAL1 | WRKY50 | 2462 | 2470 | + | 16.45 | TTGACTTTT |
| HAL1 | cg | 2211 | 2221 | - | 16.45 | ACACACACACT |
| HAL1 | WRKY45 | 2461 | 2470 | - | 16.38 | AAAAGTCAAA |
| HAL1 | TCP23 | 1341 | 1348 | + | 16.36 | GGGCCCAC |
| HAL1 | Stat5b | 1304 | 1312 | + | 16.36 | TTCCCAGAA |
| HAL1 | ERF | 2 | 10 | - | 16.29 | ACCGGAAGT |
| HAL1 | Stat6 | 1683 | 1692 | - | 16.28 | TTCCTGAGAA |
| HAL1 | TBX20 | 2231 | 2241 | + | 16.26 | GAGGTGTGAAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
