HAL1
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000154 |
|---|---|
| TE superfamily | L1 |
| TE class | 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 | ZNF675 | 1873 | 1891 | + | 20.37 | GGAGCAGGAGGACAGAAGG |
| HAL1 | ZNF281 | 385 | 394 | - | 20.07 | GGGGGAGGGG |
| HAL1 | ZNF281 | 418 | 427 | - | 20.07 | GGGGGAGGGG |
| HAL1 | ZNF136 | 1575 | 1589 | - | 19.52 | GAATTCTAGGTTGGA |
| HAL1 | IDD4 | 1150 | 1164 | + | 19.35 | ACAAAAAGACAAAGA |
| HAL1 | ZNF148 | 385 | 394 | + | 18.97 | CCCCTCCCCC |
| HAL1 | ZNF148 | 418 | 427 | + | 18.97 | CCCCTCCCCC |
| HAL1 | IDD6 | 1149 | 1164 | - | 18.96 | TCTTTGTCTTTTTGTT |
| HAL1 | IDD6 | 1149 | 1164 | - | 18.93 | TCTTTGTCTTTTTGTT |
| HAL1 | STAT1::STAT2 | 1912 | 1924 | - | 18.73 | AGTTTCATTTTCT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
