Addgene pGGD003 - Sequence Analyzer Skip to main content
Addgene

Sequence Analyzer: pGGD003

Map View

800 600 400 200 End (812) TatI - BsrGI (802) NmeAIII (790) XcmI (788) BsrFI - SgrAI (783) AleI - MslI (744) HincII (701) DrdI (642) BbvCI (640) AlwNI (608) BsrBI (560) PspFI (545) BseYI (541) BbsI (537) mCherry-F (515 .. 534) SbfI (457) BsaAI (332) AhdI (296) mCherry-R (247 .. 265) BssSI - BssSαI (189) BsiHKAI (166) ApaLI (162) MscI (132) BtgI - NcoI (100) PvuI - AsiSI (88) BspEI - BsaWI (27) NotI - EagI (7) Start (0) mCherry pGGD003 812 bp

Sequence View

BsaWIBspEIEagINotIStart (0) 5ʹ 3ʹ 60 AAAASGSGSGSGSGSGSGS *PT g t g c a g c g g c c g c t t c a g g g a g t g g t t c c g g a a g c g g c t c t g g a t c g g g c t c a g g g a g t g c a c g t c g c c g g c g a a g t c c c t c a c c a a g g c c t t c g c c g a g a c c t a g c c c g a g t c c c t c a c

NcoIBtgIAsiSIPvuI 120 1 5 MVSKGE mCherry GSGSGSGSAIAAAAMVSKGE TGAAARSRRDCSCGHHALAL g t t c c g g c a g c g g c t c t g g a t c g g c g a t c g c a g c t g c a g c c a t g g t g a g c a a g g g c g a g g c a a g g c c g t c g c c g a g a c c t a g c c g c t a g c g t c g a c g t c g g t a c c a c t c g t t c c c g c t c c

ApaLIBsiHKAIMscI 180 10 15 20 25 EDNMAIIKEFMRFKVHMEGS mCherry EDNMAIIKEFMRFKVHMEGS LIVHGDDLLEHAELHVHLAG a g g a t a a c a t g g c c a t c a t c a a g g a g t t c a t g c g c t t c a a g g t g c a c a t g g a g g g c t c c g t c c t a t t g t a c c g g t a g t a g t t c c t c a a g t a c g c g a a g t t c c a c g t g t a c c t c c c g a g g c

BssSαIBssSI 240 30 35 40 45 VNGHEFEIEGEGEGRPYEGT mCherry VNGHEFEIEGEGEGRPYEGT HVAVLELDLALALAAGVLAG t g a a c g g c c a c g a g t t c g a g a t c g a g g g c g a g g g c g a g g g c c g c c c c t a c g a g g g c a c c c a c t t g c c g g t g c t c a a g c t c t a g c t c c c g c t c c c g c t c c c g g c g g g g a t g c t c c c g t g g g

AhdI 300 50 55 60 65 QTAKLKVTKGGPLPFAWDIL mCherry G G T T C G A C T T C C A C T G G T T mCherry-R QTAKLKVTKGGPLPFAWDIL LGGLQLHGLTAGQGEGPVDQ a g a c c g c c a a g c t g a a g g t g a c c a a g g g t g g c c c c c t g c c c t t c g c c t g g g a c a t c c t g t t c t g g c g g t t c g a c t t c c a c t g g t t c c c a c c g g g g g a c g g g a a g c g g a c c c t g t a g g a c a

BsaAI 360 70 75 80 85 SPQFMYGSKAYVKHPADIPD mCherry SPQFMYGSKAYVKHPADIPD GRLEHVAGLGVHLVGGVDGV c c c c t c a g t t c a t g t a c g g c t c c a a g g c c t a c g t g a a g c a c c c c g c c g a c a t c c c c g a c t g g g g a g t c a a g t a c a t g c c g a g g t t c c g g a t g c a c t t c g t g g g g c g g c t g t a g g g g c t g a

420 90 95 100 105 YLKLSFPEGFKWERVMNFED mCherry YLKLSFPEGFKWERVMNFED VQLQGEGLAELPLAHHVELV a c t t g a a g c t g t c c t t c c c c g a g g g c t t c a a g t g g g a g c g c g t g a t g a a c t t c g a g g a c g t g a a c t t c g a c a g g a a g g g g c t c c c g a a g t t c a c c c t c g c g c a c t a c t t g a a g c t c c t g c

SbfI 480 110 115 120 125 GGVVTVTQDSSLQDGEFIYK mCherry GGVVTVTQDSSLQDGEFIYK AAHHGHGLVGGQLVALEDVL g c g g c g t g g t g a c c g t g a c c c a g g a c t c c t c c c t g c a g g a c g g c g a g t t c a t c t a c a a g g c g c c g c a c c a c t g g c a c t g g g t c c t g a g g a g g g a c g t c c t g c c g c t c a a g t a g a t g t t c c

BbsI 540 130 135 140 145 VKLRGTNFPSDGPVMQKKTM mCherry C C C C G T A A T G C A G A A G A A G A mCherry-F VKLRGTNFPSDGPVMQKKTM HLQAAGVEGGVAGYHLLLRH t g a a g c t g c g c g g c a c c a a c t t c c c c t c c g a c g g c c c c g t a a t g c a g a a g a a g a c g a t g g a c t t c g a c g c g c c g t g g t t g a a g g g g a g g c t g c c g g g g c a t t a c g t c t t c t t c t g c t a c c

BsrBIBseYIPspFI 600 150 155 160 165 GWEASSERMYPEDGALKGEI mCherry GWEASSERMYPEDGALKGEI APLGGGLPHVGLVAGQLALD g c t g g g a g g c c t c c t c c g a g c g g a t g t a c c c c g a g g a c g g c g c c c t g a a g g g c g a g a t c a c g a c c c t c c g g a g g a g g c t c g c c t a c a t g g g g c t c c t g c c g c g g g a c t t c c c g c t c t a g t

BbvCIDrdIAlwNI 660 170 175 180 185 KQRLKLKDGGHYDAEVKTTY mCherry KQRLKLKDGGHYDAEVKTTY LLPQLQLVAAVVVSLDLGGV a g c a g a g g c t g a a g c t g a a g g a c g g c g g c c a c t a c g a c g c t g a g g t c a a g a c c a c c t a c a t c g t c t c c g a c t t c g a c t t c c t g c c g c c g g t g a t g c t g c g a c t c c a g t t c t g g t g g a t g t

HincII 720 190 195 200 205 KAKKPVQLPGAYNVNIKLDI mCherry KAKKPVQLPGAYNVNIKLDI LGLLGHLQGAGVVDVDLQVD a g g c c a a g a a g c c c g t g c a g c t g c c c g g c g c c t a c a a c g t c a a c a t c a a g t t g g a c a t c a t c c g g t t c t t c g g g c a c g t c g a c g g g c c g c g g a t g t t g c a g t t g t a g t t c a a c c t g t a g t

MslIAleI 780 210 215 220 225 TSHNEDYTIVEQYERAEGRH mCherry TSHNEDYTIVEQYERAEGRH GGVVLVVGDHFLVFAGLAAV c c t c c c a c a a c g a g g a c t a c a c c a t c g t g g a a c a g t a c g a a c g c g c c g a g g g c c g c c a c t g g a g g g t g t t g c t c c t g a t g t g g t a g c a c c t t g t c a t g c t t g c g c g g c t c c c g g c g g t g a

End (812) BsrGITatISgrAIBsrFIXcmINmeAIII 3ʹ 5ʹ 812 230 235 STGGMDELYK* mCherry STGGMDELYK* GGAAHVLQVLL c c a c c g g c g g c a t g g a c g a g c t g t a c a a g t a g g g t g g c c g c c g t a c c t g c t c g a c a t g t t c a t c

Restriction Enzymes

Instructions: By default, all cutters are shown. Filter on number of cut sites or search by enzyme name.

Filter

Features

Primers

BLAST

BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. Click on the buttons below to submit a BLAST search to NCBI. The results will appear in a new window. See your recent BLAST results on NCBI's website.

  • Nucleotide-Nucleotide BLAST (BLASTN)

  • Translated Nucleotide-Protein BLAST (BLASTX)

  • Sequence alignment using BLAST (BLAST2)

Sequence Analyzer Guide

Map

Displays a graphical map based on nucleotide sequence data labeled with restriction enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. Hovering over data labels will display additional information (e.g. cut site)

To select a portion of sequence, click one location on the plasmid and then a second location to display the sequence between the two locations.

Sequence

Displays both strands of base paired nucleotide sequences with annotated enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. Hovering over data labels will display additional information (e.g. cut site).

To select a portion of sequence, click one location on the sequence and then a second location to display the sequence between the two locations.

Enzymes

List of restriction enzymes that can cut a given nucleotide sequence. Table lists enzyme name and the sequence location of the cut.

Features

List of common features detected in a given nucleotide sequence. Table lists feature name, location, size, color used to indicate its position on the map, and direction (if relevant).

Primers

List of commonly used primers detected in a given nucleotide sequence. Table lists primer name, sequence, length, binding site location, and direction.

BLAST

Use Basic Local Alignment Search Tool (BLAST) via the NCBI website to determine similarity between a given sequence and nucleotide (BLASTN) or protein (BLASTX) sequence databases. Additionally, align a custom nucleotide sequence against a given sequence using BLAST2.

File Downloads

GenBank

File contains the nucleotide sequence and annotated features in GenBank flat file format. Open the file with a text editor or plasmid mapping software to view the sequence.

SnapGene

File contains the nucleotide sequence and enhanced annotations from SnapGene Server. Open the file with SnapGene software or the free Viewer to view the plasmid map, sequence, and perform additional sequence analysis.