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 | Klf15 | 412 | 433 | + | 17.06 | CGACTGCCCCTCCCCCACCCCG |
| HAL1 | FEV | 2 | 10 | - | 17.06 | ACCGGAAGT |
| HAL1 | KLF9 | 774 | 784 | + | 17.03 | GCCCCACCCAC |
| HAL1 | ELK1 | 2 | 10 | - | 17.02 | ACCGGAAGT |
| HAL1 | ETV5 | 2 | 10 | - | 17.00 | ACCGGAAGT |
| HAL1 | klu | 777 | 787 | + | 16.93 | CCACCCACGCG |
| HAL1 | ZNF281 | 2200 | 2209 | + | 16.91 | GGGGGATGGG |
| HAL1 | ELK3 | 2 | 10 | - | 16.80 | ACCGGAAGT |
| HAL1 | PATZ1 | 423 | 433 | - | 16.72 | CGGGGTGGGGG |
| HAL1 | Ets96B | 2 | 10 | - | 16.57 | ACCGGAAGT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
