SVA_B
Basic information Differential Expression Stage analysis Survival analysis Correlation analysis| DF ID | DF0001068 |
|---|---|
| TE superfamily | SVA |
| TE class | Retroposon |
| Species | Hominidae |
| Length | 1383 |
| Kimura value | 5.80 |
| Tau index | 0.6953 |
| Description | Composite retroelement: (SINE-R + VNTR + Alu), SVA_B 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 |
CTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTNTCCCCTCTTTCCACGGTCTCCCTCTGATGCCGAGCCGAGGCTGGACTGTACTGCCGCCATCTCGGCTCACTGCAACCTCCCTGCCTGATTCTCCTGCCTCAGCCTGCCGAGTGCCTGGGATTGCAGGCGCGCGCCGCCACGCCTGACTGGTTTTCGTATTTTTTGGTGGAGACGGGGTTTCGCCGTGTTGGCCGGGCTGGTCTCCAGCTCCTGACCGCGAGTGATCTGCCNGCCTCGGCCTCCCGAGGTGCCGGGATTGCAGACGGAGTCTCGCTCACTCAGTGCTCAATGTTGCCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCGCTACAACCTCCACCTCCCAGCCGCCTGCCTTGGCCTCCCAAAGTGCCGAGATTGCAGCCTCTGCCCGGCCGCCACCCCGTCTGGGAAGTGAGGAGCGTCTCTGCCTGGCCGCCCATCGTCTGGGATGTGAGGAGCCCCTCTGCCCGGCCGCCCAGTCTGGGAAGTGAGGAGCGCCTCTTCCCGGCCGCCATCCCGTCTGGGAAGTGAGGAGCGTCTCTGCCCGGCCGCCCATCGTCTGGGATGTGGGGAGCGCCTCTGCCCCGCCGCCCCGTCTGGGANGTGAGGAGCGCCTCTGCCCGGCCAGCCGCCCCGTCTGGGAGGTGAGGAGGTCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGAGGTGGGGGGNNCAGCCCCCCGCCCGGCCAGCCGCCCCGTCCGGGAGGTGGGGGGCGCCTCTGCCCGGCCGCCCCGTCTGGGAAGTGAGGAGCCCCTCTGCCCGGCCGCCACCCCGTCTGGGAGGTGTACCCAACAGCTCATTGAGAACGGGCCATGATGACGATGGCGGTTTTGTCGAATAGAAAAGGGGGAAATGTGGGGAAAAGAAAGAGAGATCAGATTGTTACTGTGTCTGTGTAGAAAGAAGTAGACATAGGAGACTCCATTTTGTTCTGTACTAAGAAAAATTCTTCTGCCTTGGGATGCTGTTAATCTATAACCTTACCCCCAACCCCGTGCTCTCTGAAACATGTGCTGTGTCCACTCAGGGTTAAATGGATTAAGGGCGGTGCAAGATGTGCTTTGTTAAACAGATGCTTGAAGGCAGCATGCTCGTTAAGAGTCATCACCACTCCCTAATCTCAAGTACCCAGGGACACAAACACTGCGGAAGGCCGCAGGGTCCTCTGCCTAGGAAAACCAGAGACCCTTGTTCACATGTTTATCTGCTGACCTTCCCTCCACTATTGTCCTATGACCCTGCCAAATCCCCCTCTCCGAGAAACACCCAAGAATGATCAATAAATACTAAAAAAAAAAAAA
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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_B | PAX8 | 180 | 195 | + | 18.29 | CGCCACGCCTGACTGG |
| SVA_B | SREBP | 356 | 365 | - | 18.13 | ATCACGCCAC |
| SVA_B | ZNF213 | 339 | 350 | + | 18.09 | GCCCAGGCTGGA |
| SVA_B | ZNF135 | 381 | 394 | + | 17.98 | CCTCCACCTCCCAG |
| SVA_B | BPC6 | 11 | 31 | + | 17.91 | CCCTCTCCCTCTCCCTCTCCC |
| SVA_B | BPC6 | 17 | 37 | + | 17.91 | CCCTCTCCCTCTCCCTCTCCC |
| SVA_B | BPC6 | 23 | 43 | + | 17.91 | CCCTCTCCCTCTCCCTCTCCC |
| SVA_B | BPC6 | 5 | 25 | + | 17.91 | CCCTCTCCCTCTCCCTCTCCC |
| SVA_B | EREB29 | 634 | 643 | + | 17.61 | CCCGCCGCCC |
| SVA_B | BPC5 | 15 | 44 | - | 17.32 | AGGGAGAGGGAGAGGGAGAGGGAGAGGGAG |
TFBS enrichment in GRCh38
Use Fisher's exact test to perform enrichment analysis of transcription factor binding sites in the TE family of GRCh38.
