Table 7.
In Silico Promoter Analysis of the 5 Zyxin-Dependent Candidate Genes for Putative PyPu Binding Sites
| Gene | Matrix | Start | End | C.S | M.S | Sequence |
|---|---|---|---|---|---|---|
| CyclinE2 | V$HSF1.04 | −663 | −687 | 1 | 0.851 | caaagcttctctgggagcTTCTctg |
| ITGA8 | V$HSF1.04 | −3817 | −3841 | 1 | 0.791 | gttgaagcctcaggatccTTCTctc |
| V$HSF1.04 | −3522 | −3546 | 1 | 0.761 | accccttatgaaggaaacTTCTctc | |
| MMP13 | V$HSF1.04 | −3761 | −3785 | 0.85 | 0.838 | tttacatattcttaaaatTTCAatc |
| RGS5 | V$HSF1.04 | −3577 | −3601 | 0.973 | 0.805 | tagagataatctccaaagTTCCatg |
| V$HSF1.04 | −2489 | −2513 | 1 | 0.779 | tggggtccttcttgttggTTCTatg | |
| V$HSF1.04 | −1621 | −1645 | 1 | 0.775 | tgcaggctgtcctcaaacTTCTgtt | |
| V$HSF1.04 | −236 | −260 | 1 | 0.789 | gggcatgtttctggtggcTTCTgtc |
In silico promoter analysis of the 5 zyxin-dependent candidate genes for putative PyPu binding sites. Putative binding sites which remotely resemble the PyPu box are tabulated. The HSF has some similarity to the PyPu sequence but a prominent and reproducible stretch of pyrimidines was not detectable compared to that observed in ECs.4 A maximum C.S is obtained when there is a strong match between highly conserved bases of the matrix and the input sequence. A good match to the matrix or the M.S has a value >0.80. Promoter sequences ≈4000 bp upstream of the transcription start site were analyzed for this purpose. C.S indicates core similarity; ECs, endothelial cells; HSF, heat shock factor; ITGA8, integrin α8; M.S, matrix similarity; MMP13, matrix metalloproteinase 13; RGS5, regulator of G-protein signaling 5.