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

 

Copyright © 2006-2007. All rights reserved. |Bio-Computing Lab, Institute of Bioinformatics, Zhejiang University, Hangzhou, P.R.China

Please mail your comments and suggestions to: wuwr@zju.edu.cn