HAL1ME
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0000157 |
|---|---|
| TE superfamily | L1 |
| TE class | LINE |
| Species | Eutheria |
| Length | 2465 |
| Kimura value | 32.00 |
| Tau index | 0.8302 |
| Description | L1 retrotransposon, HAL1ME subfamily |
| Comment | Full ORF1 between ~724-1707. |
| Sequence |
GGCTTCCGGTTCAAGATGGCGGACTGAGCACACGCGTCTACCTCCCCTCCCTCCCAAAATCCCATTGAAATGACAGAAAAGATATTTTTAAAAGAATGAAACCATAACAGCGCTGGAAAACAAGAAAGGGTGCCATCAGCGGACCAGAAATTTTGAGGAATTCCTGGAAGATAGAAAGCAGATGGGATCGGATTGACGGAGAAANCAGAGCAGAGGAAACCGCAGCCCAAAACACCGGAGGTAAGAGCGGTTCTTCCCAAGGGAGCCCCGGAGAAGCTCCAAGCTCGGAGTCAACAAATACAAAGAGCAGGAGTGGGCCGTGGGGCAATCATCAGGGTAATTAATTAAAGAACTGCATTCGGAACAGCTGGGCCAGTGGGTCCTCCCTCCCCCTCTCCCGCGTANACANAGAGCAGCTGGCAGCAGCGGCTTTTGCCCCCAGGCTAAAGCCCGAGAACTGCTCTCTAAAGAAAGTGGGCGATCTGCCTGGGGAGGGCTCCTAGTGTGGGTGTTGGGGCCTGAGAGAGAAGCAGAGCAGAGCTTGAGGTAACTCCGGACCTCCACAACAGACACGGAGGGGAAAAAGGAAAGGGAAGAGGCAGCTCCGCCCAGGAGTGAAATACACTAAAGCGCTCCACCCCCAGAGTAAAGCCCTCCTTACTTTGGCAATTGTGGGGGTCCCCAGCCTGCCTGCCTGCTCCCTGCCCACGCACCCTAAAGGGAAGCCTGCCTGTCGACACGCCCCGCCCACTTACACAGGAGCCCGCAGTCAGCCCTCCCATTCAAGGGAGAGGCCTGTTGGGGAAACAGACCTACACAACTGCAGAGGAAACCCACGCCAGCTACCTATACTAATCAACCTAGTCCTTCATTCATAAATATGAACGGACAACCAAGGATCACCAGACATTTGAGGAAAACCAACAGCATGAAAGAGAAGGACCAAGATGAACAAACAGAACAACTGACCCCGGAGGAAACAGAGATAATTCAGGGAACAGAAGAGAACTTTAAAAAAATTCTAATTAGTATCCTCAGAGAGATTCGAGAAGATATTGCATCCATAAAACAAGAACAGGNTGCTATGAAAAAGAAGCAATCAGAGAACAAGAAAGAGTTCTTGGAAATTAAAAATATGATTGCCAAAATNAAAAATTCAATAGAAGGGTTGGAAGATAAAGTCGAGGAAATCTCCCAGAACGTAGAGCAAAAAGACAAAGAGATGGAAAATATGAGAGAAAAGTTAAGAGACATGGAGGATAGATCCAGGAGGTCCAACATCCATCTAATAGGAGTTCCAGAAGGAGAGAACAGAGANAATGGAGGGGAGGAAATAATCAAAGAAATAATAGAAGAAAATTTCCCNGAGCTGAAGAAAGACACGAGTCTTCAGATTGAAAGGGCCCACCGAGTGCCGAGCAGGATGAATGAAAAAAGACCCACACCTAGACACATCNTNGTGAAATTTCAGAACNCCAAGGATAAAGAGAAAATCCTAAAAGCTTCCAGAGAGAAAAAACAGGTTACCTACAAAGGAACGAGAATCAGACTGGCATCAGACTTCTCATCAGCAACACTGGATGCTAGAAGACAATGGAGCAATGTCTTCAAAGTTCTGAGGGAAAATNATTTTGAACCTAGAATTCTATACCCAGCCAAACTATCAATCAAGTGTGAGGGCAAAATAAAGACATTTTCAGACATGCAAGGACTCAGAAAGTTTACCNCCCACGTACCCTNTNTGAAAAAATTACTCGAGGATGTACTCCAGCAAAACGAAAAAGGAATCCAAGAAAGAGGANGACATGGGATACAAGAAACAGTGGCAGCTGAGTATGACCCAGAAGAAGTGAAGGAAGCTAAAAAGAAATTAAAAGAGAATCCATTTGACCTTGACGCTTGGAANATTCTCCTTCGAGCGGCANAGGTTTAGTGACATAGGATTACATTTCCTTCTCTATGGGTCCAATCACACTACTTGGTTCTGCAGTGAATAATATTTACATAATCATAATANTGTAAATGCTGTTTATTGGTTTTCAATTTTTAGAATCAACCTATAGACAAAGCACGGAAGACTTAATTATAGTTACAGAACAGAATGTAAATGTTATAAACCTTGACAATGTAAAAATAATANAATAACNAAAATTGGGAGGTAGAAGGGGGAAGAGAGGTGGAAGGAAGTGTAAGNGCGCTAANTTCCTCATCTTNCATAGCGGGGAGTCAANAGATACTGTCTAAAGTTGATAAATCAAGAAATAGAGGTNTAAGTATATTATTTAAAGTTATAAAGGTAACCANTAGAAGAACTAAAAATAANTAACAGTNAAAAGTGGTTGCCTCTGGGGAGTGGGATNGAGATGGAAGAGGGNAGGGANAGGGACTACTTTTCATTTTATACCCTTCTGTACTGTTTGAATTTTTTNNACCATGTGCATGTATTACTTTTATAAAAATAAAAA
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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 |
|---|---|---|---|---|---|---|
| HAL1ME | CG3065 | 741 | 751 | + | 17.44 | GCCCCGCCCAC |
| HAL1ME | CDF5 | 1861 | 1881 | - | 17.30 | TTCTCTTTTAATTTCTTTTTA |
| HAL1ME | DOF3.6 | 1861 | 1881 | - | 17.21 | TTCTCTTTTAATTTCTTTTTA |
| HAL1ME | Ebf2 | 256 | 264 | + | 16.79 | CCCAAGGGA |
| HAL1ME | ZNF530 | 587 | 600 | + | 16.61 | GAAAGGGAAGAGGC |
| HAL1ME | EBF3 | 256 | 264 | + | 16.59 | CCCAAGGGA |
| HAL1ME | IDD7 | 1207 | 1220 | + | 16.56 | GCAAAAAGACAAAG |
| HAL1ME | KLF16 | 741 | 751 | + | 16.53 | GCCCCGCCCAC |
| HAL1ME | RVE4 | 80 | 88 | + | 16.53 | AGATATTTT |
| HAL1ME | FOXB1 | 1997 | 2007 | - | 16.46 | TATGTAAATAT |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
