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 | Ar | 1301 | 1316 | + | 21.95 | GGGCACACCGTGTTCC |
| HAL1b | Klf6-7-like | 115 | 134 | + | 20.95 | CCTAACCCCGCCCCCACCCC |
| HAL1b | Klf15 | 114 | 135 | + | 20.14 | TCCTAACCCCGCCCCCACCCCC |
| HAL1b | Ar | 1302 | 1317 | - | 19.72 | TGGAACACGGTGTGCC |
| HAL1b | ZNF281 | 120 | 129 | - | 18.37 | GGGGGCGGGG |
| HAL1b | KLF12 | 120 | 128 | - | 18.01 | GGGGCGGGG |
| HAL1b | NR3C2 | 1302 | 1316 | - | 17.98 | GGAACACGGTGTGCC |
| HAL1b | KLF10 | 120 | 128 | - | 17.88 | GGGGCGGGG |
| HAL1b | SP1 | 120 | 128 | - | 17.80 | GGGGCGGGG |
| HAL1b | Klf15 | 120 | 141 | + | 17.75 | CCCCGCCCCCACCCCCCAGAAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
