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 or amino acid 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 or protein-translated 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.
tblastn: Designed for comparing protein sequences against a translated nucleotide sequence database.
Helpful for finding plasmids with codon-optimized sequences.
tblastn-fast: A faster version of tblastn that may return results more quickly, but is less sensitive
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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AAV expression of a fusion protein with scFV, catalytic domain of Dnmt3a and C terminal domain of Dnmt3l from Synapisin promoter for targeted DNA methylation editing
AAV expression of a fusion protein with scFV, catalytic domain of Dnmt3a and C terminal domain of Dnmt3l from doxycycine-inducible promoter for targeted DNA methylation editing
S. pyogenes dCas9 fused with the inactivated (E756A) catalytic domain of human DNMT3A (amino acids P602-V912) and T2A-EGFP (DNMT3A S. pyogenes, Synthetic, Human)
Use
CRISPR
Tags
3xFLAG, SV40 NLS, and T2A-EGFP
Expression
Mammalian
Mutation
D10A and H840A in S.pyogenes Cas9; E756A inactiva…
Expresses the scFv-GCN4-DNMT3a-DNMT3l fusion protein (more details are shown in the vectro map) for targeted DNA methylation. Should be used in a combination with the dCas9-SunTag systems.
S. pyogenes dCas9 fused with the inactivated (E756A) catalytic domain of human DNMT3A (amino acids P602-V912) and T2A-PuroR (DNMT3A S. pyogenes, Synthetic, Human)
Use
CRISPR
Tags
3xFLAG, SV40 NLS, and T2A-PuroR
Expression
Mammalian
Mutation
D10A and H840A in S.pyogenes Cas9; E756A inactiva…
Expression of dCas9-DNMT3A fusion with T2A-PuroR and specific sgRNA for targeted DNA methylation of BACH2 promoter in human cells; for use as a control
Expresses a higher specificity variant of scFv-GCN4-DNMT3a-DNMT3l, contains R887E mutation in DNMT3a. To be used with the dCas9-SunTag system for targeted DNA methylation.
S. pyogenes dCas9 fused with the inactivated (E756A) catalytic domain of human DNMT3A (amino acids P602-V912) and T2A-PuroR (v2) (DNMT3A S. pyogenes, Synthetic, Human)
Use
CRISPR
Tags
3xFLAG, SV40 NLS, and T2A-PuroR
Expression
Mammalian
Mutation
D10A and H840A in S.pyogenes Cas9; E756A inactiva…
Expression of mutant dCas9-DNMT3A fusion (inactive catalytic domain of DNMT3A) with T2A-PuroR and specific sgRNA for the human BACH2 promoter; for use as a control