HY5‐215The Arabidopsis HY5 gene encodes a bZIP protein that regulates stimulus‐induced development of root and hypocotyl, Genes Dev. 1997 Nov 15; 11(22): 2983–2995.In the genome of hy5‐215, the splicing acceptor site of the first intron (=G) was replaced by A, suggesting that this mutation causes aberrant RNA processingIn hy5‐215, the nucleotide g‐1117 (white letter), which is the last nucleotide in the first intron, is replaced by an aHY5‐215的突变位点与野生型相比，并没有酶切位点的变化。
引物在有一个错配位点的情况下，可以产生一个新的酶切位点PsiI，从而将野生型、杂合、纯合进行区分。
Design proper primers and choose proper a enzyme by dCAPS Finder 2.0(/dcaps/dcaps.html)HY5proF GAGAGAATATGCGAGTGAATGAC Len 22 TM 54 HY5proR TCTAAAGTCTCTTTTATGTTTTA T A Len 25 TM 50.8PsiI:但是，实验室并没有PsiI ，所以只能再去寻找新的内切酶。
在设计的引物有2个错配位点时，可以产生新的酶切位点，AluI 将野生型切断。
HY5-215 F CGTATCTCCTCATCGCTTTCAATAG Len 25 TM 60.0 HY5-215 R GTCCCGCTCTTTTCCTCTTTATC Len 23 TM 60.8AluI:MYCTThe Arabidopsis bHLH Transcription Factors MYC3 and MYC4 Are Targets of JAZ Repressors and Act Additively with MYC2 in the Activation of Jasmonate Responses, Plant Cell. 2011 Feb; 23(2): 701–715.MYC2Mutagen : T‐DNA insertionInsertion FlankingSequence:TAAAACCGCCGGAGAATCAGATCACTCCGATCTAGAAGCT(Length:40)根据T‐DNA PrimerDesign（/tdnaprimers.2.html）设计引物PRODUCT_SIZE 1186Myc2LP TGGTTTTTCTTGGTTTCGATG Len 21 TM 59.96Myc2RP CTCTAATCATTGCGTCCCAAC Len 21 TM 59.58LBb1.3 ATTTTGCCGATTTCGGAAC BP+RP_PRODUCT_SIZE 558‐858MYC3Mutagen : T‐DNA insertionmyc3 F AAGGTGGGTTGTTGAAATCTAATG Len 24 TM 58.3myc3 R GTTTTCTCCGACTTTCGTCATCA Len 23 TM 61T-DNA ATATTGACCATCATACTCATTGC Len 23 TM 55.2MYC4Mutagen : T‐DNA insertionmyc4 F TCTCTCACAACTTGATCCAGCTAA Len 24 TM 60.0myc4 R TAACCGATTACCATCTCAACCAA Len 23 TM 59.2T-DNA ATATTGACCATCATACTCATTGC Len 23 TM 55.2Phyb‐9Mutations in the gene for the red/far‐red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development. Plant Cell v.5(2); 1993 Febhy3-EMS742 is a G-toA mutationphyb9 F CTGTTCAATCGCAGAAACTCGCGGT Len25phyb9 R CCGTCACATTTCACTAAGTCCAT Len 23 TM58.6MnlI:但是，实验室并没有MnlI，所以只能再去寻找新的内切酶。
在设计的引物有1个错配位点时，可以产生新的酶切位点，AluI将突变型切断。
phyb-9 F TCCAGCGAGGTGGTTACATTCAG Len 23 TM 63.9phyb-9 R AAGTGTGATGGCAAACAACCAAAGC Len 25 TM 64AluI:COP1‐4The weak copl-4 allele represents a C-to T mutation that changes theGln-283 CAA codon to a UAA stop codon.cop1‐4的突变位点与野生型相比，并没有酶切位点的变化。
引物在有一个错配位点的情况下，可以产生一个新的酶切位点MaeIII，可以将突变体的切断，从而将野生型、杂合、纯合进行区分。
cop1--4 F GGAAGCACTACAAAGGGTCGGTT TM 63.7cop1--4 R TGAGACAGTTGACTGATTCAAACGTT TM 61.9MaeIII:但是，实验室并没有MaeIII，所以只能再去寻找新的内切酶。
在设计的引物有2个错配位点时，可以产生新的酶切位点，MluI将突变型切断。
cop1‐4 F GGATGCGCTGAGTGGGTCAGACGCG Len 25 TM 72.0cop1‐4 R TCACCTTGATACAATGTTGGCTG Len 23 TM 60.3MluI:pifqMultiple phytochrome‐interacting bHLH transcription factors repress premature seedling photomorphogenesis in darkness. Curr. Biol. 2008a;18:1815–1823.pif1Phytochrome‐interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis, Science 305, 1937‐1941Mutagen T-DNA insertionpif1‐1 F ACTTCTTGGCTTCATTATCCTCT Len 23 TM 56.5pif1‐1 R CTCAATAGCTTCATCTAGCATCG Len 23 TM 56.9LBb1.3 ATTTTGCCGATTTCGGAAC Len 19 TM 55.2pif3The phytochrome‐interacting transcription factor, PIF3, acts early, selectively, and positively in light‐induced chloroplast development. Proc Natl Acad Sci U S A 101, 16091‐16098.pif3‐3 wt‐F AGAAGCAATTTGGTCACCATGCTCpif3‐3 wt‐R TGCATACAAATAGTCGATCGTATGpif3‐3 del‐F GGTGTGTATGTGAGAAGGTACATCCATCGpif3‐3 del‐R AAGCTTAGCTTTGGTGAGCCTGAAAAGCTCpif4The Arabidopsis phytochrome‐interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels. Plant Cell 20, 337‐352.Mutagen T-DNA insertionpif4‐2 WT F TTCATTCATTGGTGTGTTTTTGCpif4‐2 WT R TCCAAACGAGAACCGTCGGTpif4‐2 T‐DNA TAGCATCTGAATTTCATAACCAATCTCGATACACpif5The basic helix‐loop‐helix transcription factor PIF5 acts on ethylene biosynthesis and phytochrome signaling by distinct mechanisms. Plant Cell 19, 3915‐3929.根据T‐DNA PrimerDesign（/tdnaprimers.2.html）设计引物pif5-3 F CCTTGCTCGATTTTTGTTACG Len 21 TM 59.77pif5-3 R CGATTTGTTACCCATGGTTTG Len 21 TM 60.10LBb1.3 ATTTTGCCGATTTCGGAAC。