1. Protocol for T-DNA primer design

Note: N - Difference of the actual insertion site and the flanked sequence position, usually 0 - 300 bases LP - Left genomic primer RP - Right genomic primer LB - Left border primer of the T-DNA insertion. It should be located about 110 bases from left border. Please contact the T-DNA line provider for it.

2. Rice T-DNA verification primer design The program will pick up LP and RP for you. Its product size is around 900 bps. If you want to confirm whether the design is right, simply cut and paste the LP and RP sequences together (you can cut/paste whole returned primer info line) to the blast textarea of RiceGE page, hit "Return" if only one line of text and submit it. Note: If you could not get primers or high quality of primers for a line, it is possible that 1. the list you input is "NOT RIGHT". 2. the genomic region you get is "NOT GOOD ENOUGH" for picking up primers. However, you can change your settings, especially MAX_N, or use the Rice iSect tool to get the genomic sequences around the line and then to design primers. If you want to design primers within your sequences, please click here.  Primer Tool :

Primer size - Opt: Min: Max: Primer TM - Opt: Min: Max: GC Content - Min: Max: Clamp: Max N: Ext5: Ext3: Primer Zone: BPos: Format: Rice TDNA Lines ( Please paste a list of names below <= 96 Only ), like ZJ000001 T07348T SAO3E04 RMD_05Z11HM81 RDs1782_5 M0030894 ZHU1025_B8-3-2-601-3_Ds3 PFG_4A-00482