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 | Wt1 | 387 | 396 | + | 18.54 | CCTCCCCCAC |
| HAL1 | Wt1 | 420 | 429 | + | 18.54 | CCTCCCCCAC |
| HAL1 | PATZ1 | 417 | 427 | - | 18.42 | GGGGGAGGGGC |
| HAL1 | Dif | 1793 | 1802 | + | 18.13 | GGGAATTCCC |
| HAL1 | Dif | 1793 | 1802 | - | 18.13 | GGGAATTCCC |
| HAL1 | ets-7 | 2 | 11 | - | 17.82 | AACCGGAAGT |
| HAL1 | IDD7 | 1150 | 1163 | + | 17.64 | ACAAAAAGACAAAG |
| HAL1 | VIP1 | 1831 | 1840 | + | 17.08 | TGACAGCTGT |
| HAL1 | dar1 | 774 | 784 | + | 17.08 | GCCCCACCCAC |
| HAL1 | tll | 2461 | 2470 | - | 17.07 | AAAAGTCAAA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
