SVA_D
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001070 |
|---|---|
| TE superfamily | SVA |
| TE class | Retroposon |
| Species | Hominidae |
| Length | 1386 |
| Kimura value | 5.34 |
| Tau index | 0.8567 |
| Description | Composite retroelement: (SINE-R + VNTR + Alu), SVA_D subfamily |
| Comment | SVA retroelements are hominid-specific chimeras, some of which are still active in the human population. These SINEs are a unique combination of features. The 5' end begins with hexamer repeats, followed by two Alus in reverse orientation. The center is comprised of a number of VNTR regions (Variable Number of Tandem Repeats) that may span a few hundred basepairs, up to 2000bp. The 3' end is formed by a portion of a HERVK LTR (the SINE-R feature). |
| Sequence |
CTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCCTCTTTCCACGGTCTCCCTCTGATGCCGAGCCGAAGCTGGACTGTACTGCTGCCATCTCGGCTCACTGCAACCTCCCTGCCTGATTCTCCTGCCTCAGCCTGCCGAGTGCCTGCGATTGCAGGCGCGCGCCGCCACGCCTGACTGGTTTTCGTATTTTTTTGGTGGAGACGGGGTTTCGCTGTGTTGGCCGGGCTGGTCTCCAGCTCCTAACCGCGAGTGATCCGCCAGCCTCGGCCTCCCGAGGTGCCGGGATTGCAGACGGAGTCTCGTTCACTCAGTGCTCAATGGTGCCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCGCTACAACCTCCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGTGCCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGGGATGTGAGGAGCCCCTCTGCCCGGCCGCCCAGTCTGGGAAGTGAGGAGCGCCTCTGCCCGGCCGCCATCCCGTCTAGGAAGTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGAGATGTGGGGAGCGCCTCTGCCCCGCCGCCCCGTCTGGGATGTGAGGAGCGCCTCTGCCCGGCCAGCCGCCCCGTCCGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCTACTGGGAAGTGAGGAGCCCCTCTGCCCGGCCACCACCCCGTCTGGGAGGTGTACCCAACAGCTCATTGAGAACGGGCCATGATGACAATGGCGGTTTTGTGGAATAGAAAGGGGGGAAAGGTGGGGAAAAGATTGAGAAATCGGATGGTTGCCGTGTCTGTGTAGAAAGAAGTAGACATGGGAGACTTTTCATTTTGTTCTGTACTAAGAAAAATTCTTCTGCCTTGGGATCCTGTTGATCTGTGACCTTACCCCCAACCCTGTGCTCTCTGAAACATGTGCTGTGTCCACTCAGGGTTAAATGGATTAAGGGCGGTGCAAGATGTGCTTTGTTAAACAGATGCTTGAAGGCAGCATGCTCGTTAAGAGTCATCACCACTCCCTAATCTCAAGTACCCAGGGACACAAACACTGCGGAAGGCCGCAGGGTCCTCTGCCTAGGAAAACCAGAGACCTTTGTTCACTTGTTTATCTGCTGACCTTCCCTCCACTATTGTCCTATGACCCTGCCAAATCCCCCTCTGCGAGAAACACCCAAGAATGATCAATAAAAAAAAAAAAAAAAAAAA
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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 |
|---|---|---|---|---|---|---|
| SVA_D | BPC1 | 14 | 37 | - | 30.33 | GGGAGAGGGAGAGGGAGAGGGAGA |
| SVA_D | BPC1 | 20 | 43 | - | 30.33 | GGGAGAGGGAGAGGGAGAGGGAGA |
| SVA_D | BPC1 | 2 | 25 | - | 30.33 | GGGAGAGGGAGAGGGAGAGGGAGA |
| SVA_D | BPC1 | 26 | 49 | - | 30.33 | GGGAGAGGGAGAGGGAGAGGGAGA |
| SVA_D | BPC1 | 8 | 31 | - | 30.33 | GGGAGAGGGAGAGGGAGAGGGAGA |
| SVA_D | ZNF460 | 278 | 293 | + | 26.54 | GCCTCGGCCTCCCGAG |
| SVA_D | BPC1 | 10 | 33 | - | 25.15 | GAGGGAGAGGGAGAGGGAGAGGGA |
| SVA_D | BPC1 | 16 | 39 | - | 25.15 | GAGGGAGAGGGAGAGGGAGAGGGA |
| SVA_D | BPC1 | 22 | 45 | - | 25.15 | GAGGGAGAGGGAGAGGGAGAGGGA |
| SVA_D | BPC1 | 4 | 27 | - | 25.15 | GAGGGAGAGGGAGAGGGAGAGGGA |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
