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Welcome to the database of potential intron polymorphism (PIP) markers
With the
recent progress made in large-scale plant functional genome sequencing
projects, a great amount of EST data is becoming available. With the
help of complete genomic sequence information of model plants (rice and
Arabidopsis), it is possible to predict the
exon-intron structures in homologous ESTs of other plants. This would allow
developing PIP markers in these plants by designing primers in exons
flanking the target introns.
This
database provides detailed information of PIP
markers
developed in plant species with more than 10,000 PUTs (PlantGDB-assembled
Unique Transcripts) available in the public database
http://www.plantgdb.org/.
There are presently a total of 57,658 PIP markers for 59 plant species
in this database (Table 1).With evaluations performed in silico, we have found that the
intron position prediction is highly reliable and the polymorphism level
of PIP markers is highly enough for practical need.
Last modified on Apr.18, 2007
Quick Start
Methodology:
Introduce the methodology and flow chart for developing PIP markers.
Search:
Search for PIP markers of your interest.
Compare:
Find out PIP markers corresponding to the same genes of the model
plant in two species.
Develop:
Develop PIP markers based on EST sequences submitted by users.
Download:
Download data of PIP makers.
Links:
Some useful links.
Table 1
Statistics of PIP markers
|
Latin Name |
English Name |
No. of PIP
markers |
|
Monocot |
|
|
|
Allium cepa |
onion |
204 |
|
Festuca arundinacea |
tall fescue |
2535 |
|
Hordeum vulgare |
barley |
3510 |
|
Panicum virgatum |
switchgrass |
636 |
|
Saccharum officinarum |
sugarcane |
2632 |
|
Secale cereale |
rye |
158 |
|
Sorghum bicolor |
sorghum |
4314 |
|
Sorghum propinquum |
sorghum |
864 |
|
Triticum aestivum |
bread wheat |
3241 |
|
Triticum monococcum |
one-grained wheat |
335 |
|
Zea mays |
corn |
3439 |
|
Zingiber officinale |
garden ginger |
405 |
|
Dicot |
|
|
|
Antirrhinum
majus |
snapdragon |
473 |
|
Aquilegia
formosaxAquilegia
pubescens |
|
821 |
|
Beta vulgaris
|
beet |
293 |
|
Brassica napus
|
rape |
2909 |
|
Brassica rapa
|
field mustard |
2355 |
|
Capsicum annuum
|
chilli pepper |
383 |
|
Citrus
clementina |
|
702 |
|
Citrus sinensis
|
sweet orange |
1172 |
|
Coffea
canephora |
robusta coffee |
382 |
|
Euphorbia esula
|
leafy spurge |
988 |
|
Glycine max
|
soybean |
1346 |
|
Glycine soja
|
wild soybean |
328 |
|
Gossypium
arboreum |
tree cotton |
581 |
|
Gossypium
hirsutum |
upland cotton |
2022 |
|
Gossypium
raimondii |
cotton |
1703 |
|
Helianthus
annuus |
common
sunflower |
633 |
|
Helianthus
argophyllus |
silverleaf sunflower |
81 |
|
Helianthus
paradoxus |
paradox
sunflower |
82 |
|
Helianthus
petiolaris |
prairie
sunflower |
456 |
|
Ipomoea nil
|
japanese
morning glory |
574 |
|
Lactuca
perennis |
|
373 |
|
Lactuca saligna |
willowleaf
lettuce |
437 |
|
Lactuca sativa
|
garden lettuce |
832 |
|
Lactuca
serriola |
prickly lettuce |
604 |
|
Lactuca virosa |
bitter lettuce |
420 |
|
Lotus
corniculatus |
bird's-foot
trefoil |
507 |
|
Lotus japonicus |
|
570 |
|
Lycopersicon
esculentum |
tomato |
1003 |
|
Malus x
domestica |
apple |
1551 |
|
Medicago
truncatula |
barrel medic |
1120 |
|
Mesembryanthemum crystallinum |
common iceplant |
296 |
|
Nicotiana
tabacum |
common tobacco |
843 |
|
Nuphar advena |
yellow water
lily |
117 |
|
Phaseolus
coccineus |
scarlet runner |
184 |
|
Phaseolus
vulgaris |
kidney bean |
481 |
|
Poncirus
trifoliata |
hardy orange |
685 |
|
Populus tremula
|
european aspen |
424 |
|
Populus tremula
x Populus tremuloides |
aspen |
692 |
|
Populus tremuloides |
quaking aspen |
322 |
|
Populus
trichocarpa |
western balsam
poplar |
959 |
|
Populus
trichocarpa x Populus deltoides |
hybrid poplar |
753 |
|
Prunus persica
|
peach |
831 |
|
Solanum
tuberosum |
potato |
963 |
|
Taraxacum
officinale |
common
dandelion |
444 |
|
Trifolium
pratense |
red clover |
325 |
|
Vitis vinifera
|
wine grape |
1262 |
|
Zinnia elegans |
zinnia |
103 |
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