user-defined upper limit for the number of target sequences returned
Alignment
region of similarity between target and query sequences
E-value
a BLAST statistic representing the significance of an alignment, values close to zero
indicate high sequence similarity with low probability of the similarity occurring by chance
Identities
the number of exact nucleotide matches over the alignment, expressed as a fraction
and a percentage
Query Coverage
the length of the query sequence that matches the target sequence in the
alignment
Bit Score
a BLAST statistic measuring the quality of an alignment, higher values indicate a
more significant match
Span
the length of the alignment, including gaps
About Search by Sequence
Search by Sequence performs a nucleotide-nucleotide BLAST search against Addgene’s plasmid sequence database.
BLAST returns plasmids with similarity to the query sequence.
Results are sorted by E-value, a statistic from BLAST that describes the significance of a match.
Lower values are considered better matches.
FASTA headers and numbers at the beginning of each line will be removed.
The query should only contain DNA characters.
Tips for Success
Enter a distinct sequence that is an important, differentiating feature. For example, the coding region of
a gene, instead of the plasmid origin of replication.
Inspect the percent identity, query coverage, and alignment details to determine if a result match is satisfactory.
Visit the corresponding plasmid webpage to view additional details about a matching plasmid.
If no results are returned:
Try a different isoform or region of the desired sequence.
Choose a different BLAST database. Try the general “All Addgene Plasmids” (default selection),
instead of a specific database, such as “Plant Expression Plasmids”
Try selecting a different BLAST algorithm:
megablast: Designed for comparing sequences within the same, or closely related, species.
Default selection.
blastn: Designed for comparing sequences from different species. May return additional results,
if exact species match is not required.
blastn-short: Optimized for searching with shorter sequences (<= 30 nucleotides)
but can still be effective with slightly larger sequences.
There may not be a match in our database.
You can adjust the Max Results setting on the results page from 25 to 500. If many sequences share the same top E-value,
only a truncated set of equally high-scoring matches will be shown. Set the Max Results to 500 to see more matches.
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ZF1 domain from pie-1
N-terminal half of yfp with introns
intron containing floxed unc-119 gene in reverse orientation
C-terminal half of yfp with introns
Mammalian expression of a sgRNA targeting the intron 1of rat Actb (Zhong et al, eLife 2021) under the U6 promotor and hSpCas9 under the CAG promotor. This construct is based on pX330.
Mammalian expression of a sgRNA targeting the intron 1 of Tuba1b (Zhong et al, eLife 2021) under the U6 promotor and hSpCas9 under the CAG promotor. This construct is based on pX330.
AAV TALE synthesis backbone with NI half repeat; fused to nuclear localization sequence linker and SID4X transcriptional repressor effector domain. Synapsin promoter for neuronal expression.
AAV TALE synthesis backbone with HD half repeat; fused to nuclear localization sequence linker and VP64 transcriptional activator effector domain. Synapsin promoter for neuronal expression.
Mammalian expression of a sgRNA targeting the intron 21 (last intron) of rSyn1 (Zhong et al, eLife 2021) under the U6 promotor and hSpCas9 under the CAG promotor. This construct is based on pX330.
Genetically encoded FRET-based sensor for monitoring ERK activity near a protein of interest. Must pair with GFP11-tagged POI to reconstitute donor fluorescence.
AAV TALE synthesis backbone with NN half repeat; fused to nuclear localization sequence linker and VP64 transcriptional activator effector domain. Synapsin promoter for neuronal expression.
LITE1.0 CRY2PHR fused to VP64 transcriptional activator domain. Binds to CIB1 upon blue light stimulation. Synapsin promoter for neuronal expression. See LITE2.0 for optimized LITE activators.
AAV TALE synthesis backbone with NG half repeat; fused to nuclear localization sequence linker and SID4X transcriptional repressor effector domain. Synapsin promoter for neuronal expression.
AAV TALE synthesis backbone with NI half repeat; fused to nuclear localization sequence linker and VP64 transcriptional activator effector domain. Synapsin promoter for neuronal expression.
AAV TALE synthesis backbone with NN half repeat; fused to nuclear localization sequence linker and SID4X transcriptional repressor effector domain. Synapsin promoter for neuronal expression.
AAV TALE synthesis backbone with NG half repeat; fused to nuclear localization sequence linker and VP64 transcriptional activator effector domain. Synapsin promoter for neuronal expression.