Addgene pCY 3040-04 Sequencing Result - Sequence Analyzer Skip to main content
Addgene

Sequence Analyzer: pCY 3040-04 Sequencing Result

Map View

800 600 400 200 End (850) PmlI (837) BstZ17I (830) AccI (829) AseI (784) BstAPI (721) XbaI (709) PspFI (692) BseYI (688) MfeI (653) Bsu36I (552) BstXI (503) MslI (495) BsgI (386) BfuAI - PaqCI - BspMI (360) BmrI (303) HindIII (280) BsaHI (251) ApaLI (82) SacI (26) AvaI - BsoBI (25) Eco53kI (24) EcoRI (16) ClaI - BspDI (11) Start (0) TRP1 pCY 3040-04 850 bp

Sequence View

BspDIClaIEcoRIEco53kIBsoBIAvaISacIStart (0) 5ʹ 3ʹ 60 t c t g a t a t c a t c g a t g a a t t c g a g c t c g g g t a t t t t c t c c t t a c g c a t c t g t g c g g t a t t a g a c t a t a g t a g c t a c t t a a g c t c g a g c c c a t a a a a g a g g a a t g c g t a g a c a c g c c a t a a

ApaLI 120 t c a c a c c g c a t a g a t c g g c a a g t g c a c a a a c a a t a c t t a a a t a a a t a c t a c t c a g t a a t a a g t g t g g c g t a t c t a g c c g t t c a c g t g t t t g t t a t g a a t t t a t t t a t g a t g a g t c a t t a t

180 225 220 215 210 *KKANKVFNAIKNSDKVGN TRP1 *KKANKVFNAIKNSDKVGN a c c t a t t t c t t a g c a t t t t t g a c g a a a t t t g c t a t t t t g t t a g a g t c t t t t a c a c c a t t t t g g a t a a a g a a t c g t a a a a a c t g c t t t a a a c g a t a a a a c a a t c t c a g a a a a t g t g g t a a a

240 205 200 195 190 TEVGGSVDVGIVGNLRLADG TRP1 TEVGGSVDVGIVGNLRLADG g t c t c c a c a c c t c c g c t t a c a t c a a c a c c a a t a a c g c c a t t t a a t c t a a g c g c a t c a c c a c a g a g g t g t g g a g g c g a a t g t a g t t g t g g t t a t t g c g g t a a a t t a g a t t c g c g t a g t g g t

HindIIIBsaHI 300 185 180 175 170 VNEPTLGGALMFHLSEPSEQ TRP1 VNEPTLGGALMFHLSEPSEQ a c a t t t t c t g g c g t c a g t c c a c c a g c t a a c a t a a a a t g t a a g c t t t c g g g g c t c t c t t g c t g t a a a a g a c c g c a g t c a g g t g g t c g a t t g t a t t t t a c a t t c g a a a g c c c c g a g a g a a c g

BmrI 360 165 160 155 150 RGVWDSISNWDLLEGTGGAE TRP1 RGVWDSISNWDLLEGTGGAE c t t c c a a c c c a g t c a g a a a t c g a g t t c c a a t c c a a a a g t t c a c c t g t c c c a c c t g c t t c t g a a g g t t g g g t c a g t c t t t a g c t c a a g g t t a g g t t t t c a a g t g g a c a g g g t g g a c g a a g a

BsgIBspMIPaqCIBfuAI 420 145 140 135 130 SDFLPIFSHPKQSAASLLIN TRP1 SDFLPIFSHPKQSAASLLIN g a a t c a a a c a a g g g a a t a a a c g a a t g a g g t t t c t g t g a a g c t g c a c t g a g t a g t a t g t t g c t t a g t t t g t t c c c t t a t t t g c t t a c t c c a a a g a c a c t t c g a c g t g a c t c a t c a t a c a a c

480 125 120 115 110 CDKPFVLRKIVPLGLFEQYE TRP1 CDKPFVLRKIVPLGLFEQYE c a g t c t t t t g g a a a t a c g a g t c t t t t a a t a a c t g g c a a a c c g a g g a a c t c t t g g t a t t c t g t c a g a a a a c c t t t a t g c t c a g a a a a t t a t t g a c c g t t t g g c t c c t t g a g a a c c a t a a g a

BstXIMslI 540 105 100 95 90 QWSEDGHLQVIDIGYDNVLA TRP1 QWSEDGHLQVIDIGYDNVLA t g c c a c g a c t c a t c t c c a t g c a g t t g g a c g a t a t c a a t g c c g t a a t c a t t g a c c a g a g c c a c g g t g c t g a g t a g a g g t a c g t c a a c c t g c t a t a g t t a c g g c a t t a g t a a c t g g t c t c g g

Bsu36I 600 85 80 75 70 LVDEKPQNRFVGVLYKPTGS TRP1 LVDEKPQNRFVGVLYKPTGS a a a a c a t c c t c c t t a g g t t g a t t a c g a a a c a c g c c a a c c a a g t a t t t c g g a g t g c c t g a a t t t t g t a g g a g g a a t c c a a c t a a t g c t t t g t g c g g t t g g t t c a t a a a g c c t c a c g g a c t t

MfeI 660 65 60 55 50 SNKYAKVLSSIKRAIVPDIT TRP1 SNKYAKVLSSIKRAIVPDIT c t a t t t t t a t a t g c t t t t a c a a g a c t t g a a a t t t t c c t t g c a a t a a c c g g g t c a a t t g t t g a t a a a a a t a t a c g a a a a t g t t c t g a a c t t t a a a a g g a a c g t t a t t g g c c c a g t t a a c a a

XbaIBseYIPspFI 720 45 40 35 30 RKRNPVCIIGLLDADSDLAC TRP1 RKRNPVCIIGLLDADSDLAC c t c t t t c t a t t g g g c a c a c a t a t a a t a c c c a g c a a g t c a g c a t c g g a a t c t a g a g c a c a t g a g a a a g a t a a c c c g t g t g t a t a t t a t g g g t c g t t c a g t c g t a g c c t t a g a t c t c g t g t a

BstAPI 780 25 20 15 10 EAAETSQLGCVKVLPGSSGT TRP1 EAAETSQLGCVKVLPGSSGT t c t g c g g c c t c t g t g c t c t g c a a g c c g c a a a c t t t c a c c a a t g g a c c a g a a c t a c c t g t g a g a c g c c g g a g a c a c g a g a c g t t c g g c g t t t g a a a g t g g t t a c c t g g t c t t g a t g g a c a c

PmlIAccIBstZ17IAseI 840 5 1 FNIVSM TRP1 FNIVSM a a a t t a a t a a c a g a c a t a c t c c a a g c t g c c t t t g t g t g c t t a a t c a c g t a t a c t c a c g t g t t t a a t t a t t g t c t g t a t g a g g t t c g a c g g a a a c a c a c g a a t t a g t g c a t a t g a g t g c a c

End (850) 3ʹ 5ʹ 850 c t c a a t a g t c g a g t t a t c a g

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.