PlantG4DB: A Database of G-Quadruplex Sequences in Plants
Data
PlantG4DB provides information about the genomic location and annotation of five different types of GQSes in 25 sequenced plant (14 dicots, 8 monocots and 3 others) genomes. The overall summary of different GQSes in different plant species is as below.
| Plant species | G2L1 | G2L1-2 | G2L1-4 | G3L1-3 | G3L1-7 |
|---|---|---|---|---|---|
| Arabidopsis thaliana | 7518 | 11661 | 42220 | 260 | 1219 |
| Arabidopsis lyrata | 9342 | 16440 | 71327 | 600 | 2071 |
| Brassica rapa | 15310 | 25512 | 95785 | 658 | 2785 |
| Brachypodium distachyon | 89189 | 165547 | 475214 | 8437 | 26044 |
| Cicer arietinum | 11487 | 25564 | 105861 | 996 | 4556 |
| Cyanidioschyzon merolae | 1805 | 1212 | 12451 | 9 | 70 |
| Glycine max | 64877 | 112705 | 390940 | 10761 | 20189 |
| Leersia perrieri | 90292 | 154870 | 404024 | 4891 | 16614 | Lotus japonicus | 31138 | 50368 | 140903 | 3524 | 8906 |
| Musa acuminata | 57500 | 104229 | 300956 | 6987 | 15106 |
| Medicago truncatula | 20755 | 40814 | 135897 | 3990 | 8106 |
| Oryza barthii | 118569 | 197009 | 477036 | 8011 | 22552 |
| Oryza glumaepatula | 136635 | 219038 | 511367 | 9301 | 24958 |
| Oryza sativa | 185375 | 309779 | 730718 | 13437 | 40759 |
| Phaseolus vulgaris | 31856 | 66476 | 240084 | 1985 | 7892 |
| Physcomitrella patens | 31223 | 54234 | 166629 | 5997 | 12138 |
| Poplus trichocarpa | 27334 | 52095 | 167013 | 4001 | 9025 |
| Prunus persica | 19942 | 42336 | 137616 | 3456 | 8967 |
| Sorghum bicolor | 134993 | 275171 | 862476 | 11709 | 42066 |
| Setaria italica | 149073 | 280208 | 743556 | 12698 | 40937 |
| Selaginella moellendorffii | 35998 | 61982 | 224849 | 3381 | 10019 |
| Solanum lycopersicum | 40453 | 103344 | 126279 | 9308 | 19791 |
| Solanum tuberosum | 42083 | 74087 | 253220 | 11251 | 25640 |
| Theobroma cacao | 15012 | 29224 | 106092 | 2726 | 5603 |
| Vitis vinifera | 32735 | 67757 | 243632 | 8722 | 17444 |
The database can be browsed and searched for all or individual type of GQS(es) present in each plant species and various information about the individual GQS can be viewed. The annotation of each GQS with respect to its location on the genomic features has been integrated. A search option to identify the GQSes in a given set of genes in individual plant species has been provided. In addition, users can search for GQSes present in the orthologs genes between any two plant species or conserved in monocots/docots. The Genome Browser can help visualizing the exact location of different types of GQSes on the genomes of different plants.
We have integrated a GQS prediction tool in the database to identify GQS(es) in a given query sequence using different parameters.
We are in the process of integrating more data on GQSes for additional plants with sequenced genome.
