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European Union Reference Laboratory for Genetically Modified Food and Feed (EURL GMFF)

Match details

Record ID: AF489904.1
Database: nt Go to original record
Description: Cloning vector pHellsgate 8, complete sequence.
Taxon: Cloning vector pHellsgate 8
Original size: 17485 bp

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Method: QL-CON-00-014 Go to GMOMETHODS record
View in JRC GMO-Matrix
Description:Qualitative PCR method for detection of the junction between the nos promoter and the neomycin phosphotransferase II gene
Target:P-nos-nptII

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Predicted amplification details:
Mismatches Gaps From To Strand Amplicon size
0 0 392 561 + 170 bp
Amplicon: 170 bp 
1     ttcccctcgg tatccaatta gagtctcata ttcactctca atccaaataa
51    tctgcaatgg caattacctt atccgcaact tctttaccta tttccgcccg
101   gatccgggca ggttctccgg ccgcttgggt ggagaggcta ttcggctatg
151   actgggcaca acagacaatc

View other 96 matches with an identical amplicon

Primers and probe alignment:
Primer/Probe % Identity Length Mismatches Gaps From To Score
primerA 100.0 23 bp 0 0 1 23 2.10e-10
primerB 100.0 22 bp 0 0 170 149 7.11e-10
probe 100.0 25 bp 0 0 147 123 1.82e-11

Related publications:

Petrillo, M., et al. “JRC GMO-Amplicons: A Collection of Nucleic Acid Sequences Related to Genetically Modified Organisms.” Database (Oxford), vol. 2015 bav101, 30 Sep. 2015, doi:10.1093/database/bav101. 

Angers-Loustau, A., et al. “Using the EURL GMFF Online Bioinformatics Resources: A how-to Guide for Practical JRC GMO-Matrix and JRC GMO-Amplicons Case Uses.” European Commission, Ispra, JRC101853, 2016.