Catalogue of reference sequences for transgenic elements



Here you can find a list of reference sequences for the most common transgenic elements used in Genetically Modified (GM) plants.
It includes all elements described in the Centre for Biosafety and Sustainability (BATS) report as occurring in more than one approved GM crop and the most frequent in the GMOseek matrix.




The database was organized according to the most frequent type of element: promoters, protein-coding regions, terminators and junctions (of the previous categories).
The description of the genetic element and species of origin were obtained from the sources described above, published works and the Biosafety Clearing-House (BCH) website.

click on the element to see the complete list of reference sequences


The selection of a reference sequence for each genetic element was carried out using different strategies, depending on the nature of the element. In most cases, the NCBI Entrez Nucleotide database was searched using the name of the target region and the species (e.g., nos terminator AND Agrobacterium tumefaciens) or using accession numbers retrieved from published works.
Priority was given to sequences representing the complete element, identified with clear annotations and associated with published works. The reference sequences for some junctions were obtained by concatenating different sequences.
PROMOTORS
JUNCTIONS
PROTEIN-CODING SEQUENCES
JUNCTIONS
TERMINATORS

Genetic Element Reference Sequence
Category Abbreviation Genomic region Donor organism Accession number Source Reference Download JRC GMO-Amplicons BLAST GMOseek MATRIX EVENTS
Category Abbreviation Genomic region Donor organism Accession number Source Reference Download JRC GMO-Amplicons BLAST GMOseek MATRIX EVENTS
Promoters P35S (P-35s) Cauliflower Mosaic Virus (CaMV) 35S promoter Cauliflower mosaic virus NC_001497.1 Cauliflower mosaic virus 1 Save file
Show		 BLAST result
 Events
Promoters FMV35S (P-FMV) Figwort mosaic virus 35S promoter Figwort mosaic virus NC_003554.1 Figwort mosaic virus 2 Save file
Show		 BLAST result
 Events
Promoters TSF1 Elongation factor EF-1alpha promoter Arabidopsis thaliana NC_003070.9 complement Arabidopsis thaliana 3 Save file
Show		 BLAST result
 Events
Promoters FMV35S/TSF1 (pFMV/TSF1) Figwort mosaic virus 35S promoter (FMV35S) + Elongation factor EF-1alpha promoter (TSF1) -Figwort mosaic virus
- Arabidopsis thaliana
 		JN400388.1 complement Synthetic construct 4 Save file
Show		 BLAST result
 Events
Promoters pSsuAra (P-Ssu) ats1A gene for ribulose 1.5-biphoshate carboxylase small subunit promotor Arabidopsis thaliana X13611.1 Arabidopsis thaliana 5 Save file
Show		 BLAST result
 Events
Promoters pTA29 Tobacco anther-specific gene TA-29 promotor Nicotiana tabacum X52283.1 Nicotiana tabacum 6 Save file
Show		 BLAST result
 Events
Promoters pmas Mannopine Synthase gene promoter Arabidopsis thaliana X68599.1 Arabidopsis thaliana 7 Save file
Show		 BLAST result
 Events
Promoters pNOS Nopaline Synthase gene promoter Agrobacterium tumefaciens V00087 Agrobacterium tumefaciens 8 Save file
Show		 BLAST result
 Events
Promoters pActin1 (pRice Actin; P-ract) Rice actin 1 gene promoter Oryza sativa S44221.1 Oryza sativa 9 Save file
Show		 BLAST result
 Events
Promoters pUbiZM1 Ubiquitin gene promoter Zea mays S94464 Zea mays 10 Save file
Show		 BLAST result
 Events
Promoters pMTL (P-MT) Metallothionein-like gene promoter Zea mays S57628.1 Zea mays 11 Save file
Show		 BLAST result
 Events
Promoters P-E35s CaMV Enhanced 35S promoter Cauliflower mosaic virus AY739898.1 Synthetic construct 12 Save file
Show		 BLAST result
 Events
Terminators T-nos Nopaline Synthase Gene Terminator Agrobacterium tumefaciens EU880444.1 Oryza sativa Indica Group 13 14 Save file
Show		 BLAST result
 Events
Terminators t35S (T-35S) Cauliflower Mosaic Virus (CaMV) 35S terminator Cauliflower mosaic virus NC_001497.1 Cauliflower mosaic virus 1 Save file
Show		 BLAST result
 Events
Terminators t7S α' subunit of β-conglycinin gene terminator Glycine max AB610665.1 Glycine max 15 Save file
Show		 BLAST result
 Events
Terminators tE9 rbcS-E9 gene terminator Pisum sativum X00806.1 Pisum sativum 16 Save file
Show		 BLAST result
 Events
Terminators tORF25 ORF25 PolyA Terminator sequence Agrobacterium tumefaciens X00493.1 Agrobacterium tumefaciens 17 Save file
Show		 BLAST result
 Events
Terminators tTr7 (tg7) Transcript 7 gene 3' untranslated region Agrobacterium tumefaciens V00090 Agrobacterium tumefaciens 18 Save file
Show		 BLAST result
 Events
Terminators tocs Octopine Synthase Gene Terminator Agrobacterium tumefaciens CP011249 complement Agrobacterium tumefaciens 19 Save file
Show		 BLAST result
 Events
Terminators tpinII Proteinase inhibitor II gene terminator Solanum tuberosum X04118.1 Solanum tuberosum 20 Save file
Show		 BLAST result
 Events
Terminators ttml Tumour Morphology Large gene terminator Agrobacterium tumefaciens AF242881.1 complement Agrobacterium tumefaciens 17 Save file
Show		 BLAST result
 Events
Terminators tmas Mannopine synthase gene terminator Agrobacterium tumefaciens CP011249.1 Agrobacterium tumefaciens 19 Save file
Show		 BLAST result
 Events
Protein Coding Sequences bar Glufosinate ammonium tolerance gene (codes for phosphinothricin acetyltransferase - PAT) Streptomyces hygroscopicus X05822.1 Streptomyces hygroscopicus 21 Save file
Show		 BLAST result
 Events
Protein Coding Sequences Cry1Ab Cry1Ab delta-endotoxin gene Bacillus thuringiensis AX392802.1 Synthetic construct 22 Save file
Show		 BLAST result
 Events
Protein Coding Sequences AHAS (A.t) Acetohydroxy acid synthase gene (also known as acetolactate synthase) Arabidopsis thaliana X51514.1 Arabidopsis thaliana 23 Save file
Show		 BLAST result
 Events
Protein Coding Sequences bla Beta-lactamase gene Escherichia coli NC_011751.1 Escherichia coli 24 Save file
Show		 BLAST result
 Events
Protein Coding Sequences cry1F cry1F delta-endotoxin gene Bacillus thuringiensis EU679501.1 Bacillus thuringiensis GenBank direct submission Save file
Show		 BLAST result
 Events
Protein Coding Sequences cry3A cry3A delta-endotoxin gene Bacillus thuringiensis EU332160.1 Bacillus thuringiensis GenBank direct submission Save file
Show		 BLAST result
 Events
Protein Coding Sequences cp4epsps 5-enolpyruvulshikimate-3-phosphate synthase gene (epsps) Agrobacterium tumefaciens strain CP4 AB209952.1 Synthetic construct (Glycine max) GenBank direct submission Save file
Show		 BLAST result
 Events
Protein Coding Sequences nptII Neomycin Phosphotransferase II Escherichia coli V00618.1 Escherichia coli 25 Save file
Show		 BLAST result
 Events
Protein Coding Sequences manA Phosphomannose Isomerase gene Escherichia coli M15380.1 Escherichia coli 26 Save file
Show		 BLAST result
 Events
Protein Coding Sequences pat-STRVR Phosphinothricin N-acetyltransferase gene Streptomyces viridochromogenes M22827.1 Streptomyces viridochromogenes 27 Save file
Show		 BLAST result
 Events
Protein Coding Sequences cry1Ac Cry1Ac delta-endotoxin gene Bacillus thuringiensis U89872.1 Bacillus thuringiensis 28 Save file
Show		 BLAST result
 Events
Protein Coding Sequences vip3A(a) Insecticidal protein (vip3A(a)) gene Bacillus thuringiensis L48811.1 Bacillus thuringiensis 29 Save file
Show		 BLAST result
 Events
Protein Coding Sequences cpTi Cowpea trypsin inhibitor gene Vigna unguiculata AJ271752.1 Vigna unguiculata GenBank direct submission Save file
Show		 BLAST result
 Events
Protein Coding Sequences bxn Bromoxynil-specific nitrilase Klebsiella pneumoniae J03196.1 Klebsiella pneumoniae 30 Save file
Show		 BLAST result
 Events
Protein Coding Sequences gox Glyphosate oxidoreductase gene Ochrobactrum anthropi GU214711.1 Ochrobactrum sp. GenBank direct submission Save file
Show		 BLAST result
 Events
Protein Coding Sequences gat4621 Glyphosate-N-Acteyltransferase gene Bacillus licheniformis CP012110.1 Bacillus licheniformis 31 Save file
Show		 BLAST result
 Events
Protein Coding Sequences cry2Ab2 (cry2Ab) Cry2Ab2 delta-endotoxin gene Bacillus thuringiensis JN415485.1 Bacillus thuringiensis 32 Save file
Show		 BLAST result
 Events
Protein Coding Sequences cry3Bb1 (CryIIIB2) Cry3Bb1 delta-endotoxin gene Bacillus thuringiensis M89794.1 Bacillus thuringiensis 33 Save file
Show		 BLAST result
 Events
Protein Coding Sequences cry1A.105 Cry1A.105 delta-endotoxin gene Bacillus thuringiensis FB707511.1 Synthetic construct Patent WO2007027777 Save file
Show		 BLAST result
 Events
Protein Coding Sequences CMV CP Cucumber mosaic virus viral coat gene Cucumber mosaic virus NC_001440.1 Cucumber mosaic virus 34 Save file
Show		 BLAST result
 Events
Protein Coding Sequences barstar barstar ribonuclease inhibitor Bacillus amyloliquefaciens X15545.1 Bacillus amyloliquefaciens 35 Save file
Show		 BLAST result
 Events
Protein Coding Sequences barnase Barnase ribonuclease inhibitor Bacillus amyloliquefaciens X12871.1 Bacillus amyloliquefaciens 35 Save file
Show		 BLAST result
 Events
Protein Coding Sequences GUS Beta-Glucuronidase coding sequence Escherichia coli M14641.1 Escherichia coli 36 Save file
Show		 BLAST result
 Events
Protein Coding Sequences PG Polygalacturonase gene Solanum lycopersicum M37304.1 Solanum lycopersicum 37 Save file
Show		 BLAST result
 Events
Protein Coding Sequences PLRVrep Potato leafroll virus (PLRV) replicase gene Potato leafroll virus NC_001747.1 Potato leafroll virus 38 Save file
Show		 BLAST result
 Events
Junctions ctp2-cp4epsps Chloroplast transit peptide (ctp2) + 5-enolpyruvulshikimate-3-phosphate synthase gene (epsps) -Arabidopsis thaliana (ctp2)
- Agrobacterium tumefaciens strain CP4 (epsps)
 		-FN550387.1
- JN400385.1
- AB209952.1
 		Concatenated sequence 4 13 Save file
Show		 BLAST result
 Events
Junctions P35S-pat1 CaMV P-35S promoter + synthetic Phosphinothricin N-acetyltransferase gene (pat) -Cauliflower Mosaic Virus
- Streptomyces viridochromogenes
 		DL476427.1 Synthetic construct 13 39 Save file
Show		 BLAST result
 Events
Junctions P35S-pat2 CaMV P-35S promoter + synthetic Phosphinothricin N-acetyltransferase gene (pat) -Cauliflower Mosaic Virus
- Streptomyces viridochromogenes
 		AY629236.1 Synthetic construct 40 Save file
Show		 BLAST result
 Events
Junctions P35S-nptII CaMV P-35S promoter + Neomycin Phosphotransferase II -Cauliflower Mosaic Virus
- Escherichia coli
 		-NC_001497.1 (6101-7445)
- V00618.1 (151-945)
 		Concatenated sequence (Cauliflower Mosaic Virus + Escherichia coli) 1 25 Save file
Show		 BLAST result
 Events
Junctions P35S-bar CaMV P-35S promoter + Glufosinate ammonium tolerance gene -Cauliflower Mosaic Virus
- Streptomyces hygroscopicus
-NC_001497.1 (6101-7445)
- X05822.1
 		Concatenated sequence (Cauliflower Mosaic Virus + Streptomyces hygroscopicus) 1 21 Save file
Show		 BLAST result
 Events



Download the complete database of reference sequences

Citation

A proposal for standardization of transgenic reference sequences used in food forensics
Filipa Moreira, Joao Carneiro and Filipe Pereira
Forensic Science International: Genetics, Volume 29, July 2017, Pages e26-e28, https://doi.org/10.1016/j.fsigen.2017.04.022.