SVA_A
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001067 |
|---|---|
| TE superfamily | SVA |
| TE class | Retroposon |
| Species | Hominoidea |
| Length | 1387 |
| Kimura value | 9.61 |
| Tau index | 0.7858 |
| Description | Composite retroelement: (SINE-R + VNTR + Alu), SVA_A 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 |
CTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCCTCTTTCCACGGTCTCCCTCTGTTGCCGAGGCTGGACTGCACTGCCGTGATCTCGGCTCGCTGCAACCTCCCTGCCTCGGGCTCCAGCGATCCTCCTGCCTCGGCCTCCCGAGTGCCTGGGATTGCAGGCGCGCGCCGCCACGCCTGACTGGTTTTTGTATTTTTGGTGGAGACGGGGTCTCGCCGTGTTGNCCGGGCTGGTCTCNAGCTCCTGGCCTCGAGCGATCCGCCCGCCTCGGCCTCCCGAGGTGCTGGGATTGCAGACGGAGTCTCGCTCACTCAATGCTCAATGTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCGCTACAACCTCCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGTGCTAGGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGGGANGTGAGGAGCGCCTCTGCCCGGCCGCCCCGTCTGGGAAGTGAGGAGCGCCTCTGCCCGGCCGCCGCCCCGTCTGGGAAGTGAGGAGCGCCTCTGCCCGGCCGCCCNTCGTCTGGGANGTGAGGAGCGCCTCCGCCCGGCCGCCCCGTCTGGGANGTGAGGAGCGCCTCCGCCCGGCCAGCCGCCCCGTCCGGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGAGGTGGGGGGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGTGAGGGGCGCCTCTGCCCGGCCGCCCCNNCTGGGAAGTGAGGAGCCCCTCTGCCCGGCCGCCGCCCCGTCCGGGAGGTGTACCCAGCGACCATCGAGAACGGGCCATGATGACGATGGCGGTTTTGTCGAAAAGAAAAGGGGGAAATGTGGGGAAAAGAAAGAGAGATCAGATTGTTACTGTGTCTGTGTAGAAAGAAGTAGACATAGGAGACTCCATTTTGTTCTGTACTAAGAAAAATTCTTCTGCCTTGGGATGCTGTTAATCTATAACCTTACCCCCAACCCCGTGCTCTCTGAAACATGTGCTGTGTCAACTCAGGGTTAAATGGATTAAGGGCGGTGCAAGATGTGCTTTGTTAAACAGATGCTTGAAGGCAGCATGCTCGTTAAGAGTCATCACCACTCCCTAATCTCAAGTACCCAGGGACACAAACACTGCGGAAGGCCGCAGGGACCTCTGCCTAGGAAAACCAGAGACCTTTGTTCACGTGTTTATCTGCTGACCTTCTCTCCACTATTATCCTATGACCCTGCCACATCCCCCTCTCCGAGAAACACCCAAGAATGATCAATAAATACTAAAAAAAAAAAAA
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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_A | BPC5 | 39 | 68 | - | -43.49 | AGGGAGACCGTGGAAAGAGGGGAGAGGGAG |
| SVA_A | BPC5 | 934 | 963 | + | -43.99 | GGGAAATGTGGGGAAAAGAAAGAGAGATCA |
| SVA_A | BPC5 | 41 | 70 | - | -45.49 | AGAGGGAGACCGTGGAAAGAGGGGAGAGGG |
| SVA_A | BPC5 | 35 | 64 | - | -47.39 | AGACCGTGGAAAGAGGGGAGAGGGAGAGGG |
| SVA_A | BPC5 | 29 | 58 | - | -48.51 | TGGAAAGAGGGGAGAGGGAGAGGGAGAGGG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
