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 | NR3C1 | 1302 | 1316 | - | 17.71 | GGAACACGGTGTGCC |
| HAL1b | PATZ1 | 125 | 135 | - | 17.64 | GGGGGTGGGGG |
| HAL1b | SP2 | 120 | 128 | - | 17.56 | GGGGCGGGG |
| HAL1b | SP4 | 120 | 128 | - | 17.54 | GGGGCGGGG |
| HAL1b | STAT1::STAT2 | 2102 | 2114 | + | 17.36 | AGTTTCTTTTTCT |
| HAL1b | NR3C2 | 1302 | 1316 | + | 17.30 | GGCACACCGTGTTCC |
| HAL1b | KLF14 | 120 | 128 | - | 17.26 | GGGGCGGGG |
| HAL1b | NR3C1 | 1302 | 1316 | + | 17.20 | GGCACACCGTGTTCC |
| HAL1b | ZNF281 | 126 | 135 | - | 17.16 | GGGGGTGGGG |
| HAL1b | ZNF281 | 510 | 519 | - | 17.12 | GGGGGAAGGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
