Addgene pAAV-hSyn-HA-hM4D(Gi)-IRES-mCitrine Sequencing Result - Sequence Analyzer Skip to main content
Addgene

Sequence Analyzer: pAAV-hSyn-HA-hM4D(Gi)-IRES-mCitrine Sequencing Result

Map View

800 600 400 200 End (906) PflMI (900) BsiHKAI (873) ApaLI (869) PciI - AflIII (856) BmgBI (807) StyI - NcoI (768) BseRI (742) BanI (731) EGFP-N (705 .. 726) BtgZI (645) BsrFI (616) BssSI - BssSαI (586) PfoI * (485) EXFP-R (446 .. 465) Bpu10I (164) EGFP-C (97 .. 118) BsrGI (57) ApoI - EcoRI (43) EcoRV (39) HindIII (31) ClaI - BspDI (26) Start (0) Citrine Kozak sequence pAAV-hSyn-HA-hM4D(Gi)-IRES-mCitrine 906 bp

Sequence View

BsrGIBspDIClaIHindIIIEcoRVEcoRIApoIStart (0) 5ʹ 3ʹ 60 * KY Citrine NFVIQRLIIDKLDIEFLSLV *RYAQYRIGIVQV *KY a a t t t t g t a a t c c a g a g g t t g a t t a t c g a t a a g c t t g a t a t c g a a t t c c t a t c a c t t g t a t t a a a a c a t t a g g t c t c c a a c t a a t a g c t a t t c g a a c t a t a g c t t a a g g a t a g t g a a c a t

120 235 230 225 220 LEDMGLTIGAATVFELLVMH Citrine G T G C T T G A G G T C G T C C T G G T A C EGFP-C QLVHAESDPGGGHELQQDHV ARGHRSHDRRRDRVGAPGHS LEDMGLTIGAATVFELLVMH c a g c t c g t c c a t g c c g a g a g t g a t c c c g g c g g c g g t c a c g a a c t c c a g c a g g a c c a t g t g g t c g a g c a g g t a c g g c t c t c a c t a g g g c c g c c g c c a g t g c t t g a g g t c g t c c t g g t a c a c

Bpu10I 180 215 210 205 200 DRKENPDKSLKSQYSLYHND Citrine IALLVGVFAQFGLVAQVVVV RAERQPRQETQVPLEPLPQR DRKENPDKSLKSQYSLYHND a t c g c g c t t c t c g t t g g g g t c t t t g c t c a g t t t g g a c t g g t a g c t c a g g t a g t g g t t g t c t a g c g c g a a g a g c a a c c c c a g a a a c g a g t c a a a c c t g a c c a t c g a g t c c a t c a c c a a c a g

240 195 190 185 180 PLLVPGDGIPTNQQYHDALQ Citrine GQQHGAVADGGVLLVVVGEL AAARPRRRHPHEAPLPRRAA PLLVPGDGIPTNQQYHDALQ g g g c a g c a g c a c g g g g c c g t c g c c g a t g g g g g t g t t c t g c t g g t a g t g g t c g g c g a g c t g c c c g t c g t c g t g c c c c g g c a g c g g c t a c c c c c a c a a g a c g a c c a t c a c c a g c c g c t c g a c

300 175 170 165 160 VSGDEINHRIKFNVKIGNKQ Citrine HAAVLDVVADLEVHLDAVLL RQRGRHQPPDQLEGQHREEA VSGDEINHRIKFNVKIGNKQ c a c g c t g c c g t c c t c g a t g t t g t g g c g g a t c t t g a a g t t c a c c t t g a t g c c g t t c t t c t g g t g c g a c g g c a g g a g c t a c a a c a c c g c c t a g a a c t t c a a g t g g a a c t a c g g c a a g a a g a c

360 155 150 145 140 KDAMIYVNHSNYNYELKHGL Citrine LVGHDIDVVAVVVVLQLVPQ QRGHYLRQPQQLQVGAQAGP KDAMIYVNHSNYNYELKHGL c t t g t c g g c c a t g a t a t a g a c g t t g t g g c t g t t g t a g t t g t a c t c c a g c t t g t g c c c c a g g a a c a g c c g g t a c t a t a t c t g c a a c a c c g a c a a c a t c a a c a t g a g g t c g a a c a c g g g g t c

420 135 130 125 120 INGDEKFDIGKLEIRNVLTD Citrine DVAVLLEVDALQLDAVHQGV HQRGGQLRHGEARHPEGPHR INGDEKFDIGKLEIRNVLTD g a t g t t g c c g t c c t c c t t g a a g t c g a t g c c c t t c a g c t c g a t g c g g t t c a c c a g g g t g t c c t a c a a c g g c a g g a g g a a c t t c a g c t a c g g g a a g t c g a g c t a c g c c a a g t g g t c c c a c a g

480 115 110 105 100 GEFKVEARTKYNGDDKFFIT Citrine G T C T T G T A G T T G C C G T C G T C EXFP-R ALELHLGAGLVVAVVLEEDG GRVEGRRPDQLQRRGQLLHH GEFKVEARTKYNGDDKFFIT g c c c t c g a a c t t c a c c t c g g c g c g g g t c t t g t a g t t g c c g t c g t c c t t g a a g a a g a t g g t c g g g a g c t t g a a g t g g a g c c g c g c c c a g a a c a t c a a c g g c a g c a g g a a c t t c t t c t a c c a

PfoI* 540 95 90 85 80 REQVYGEPMASKFFDHQKMH Citrine ALLDVAFGHGGLEEVVLLHV AGPRLRRAHRVQLLRAAEHP REQVYGEPMASKFFDHQKMH g c g c t c c t g g a c g t a g c c t t c g g g c a t g g c g g a c t t g a a g a a g t c g t g c t g c t t c a t g t g c g c g a g g a c c t g c a t c g g a a g c c c g t a c c g c c t g a a c t t c t t c a g c a c g a c g a a g t a c a c

BssSαIBssSI 600 75 70 65 60 DPYRAFCMLGYGFTTVLTPW Citrine VGVAGEAHQAVAEGGHEGGP RPLPRLVDPRLRLHDRPHAL DPYRAFCMLGYGFTTVLTPW g t c g g g g t a g c g g g c g a a g c a c a t c a g g c c g t a g c c g a a g g t g g t c a c g a g g g t g g g c c a c a g c c c c a t c g c c c g c t t c g t g t a g t c c g g c a t c g g c t t c c a c c a g t g c t c c c a c c c g g t

BtgZIBsrFI 660 55 50 45 40 PVPLKGTTCIFKLTLKGYTA Citrine GHGQLAGGADELQGQLAVGG ARAAQRHHLHVEPDAQRLHC PVPLKGTTCIFKLTLKGYTA g g g c a c g g g c a g c t t g c c g g t g g t g c a g a t g a a c t t c a g g g t c a g c t t g c c g t a g g t g g c c c c g t g c c c g t c g a a c g g c c a c c a c g t c t a c t t g a a g t c c c a g t c g a a c g g c a t c c a c c g

720 35 30 25 20 DGEGEGSVSFKHGNVDGDLE Citrine C G T C G C C G T C C A G C T C EGFP-N IALALAGHAELVAVYVAVQL RGRGRRVRQVQPRKRRRGAR DGEGEGSVSFKHGNVDGDLE a t c g c c c t c g c c c t c g c c g g a c a c g c t g a a c t t g t g g c c g t t t a c g t c g c c g t c c a g c t c t a g c g g g a g c g g g a g c g g c c t g t g c g a c t t g a a c a c c g g c a a a t g c a g c g g c a g g t c g a g

NcoIStyIBseRIBanI 780 15 10 5 VLIPVVGTFLEEGKS 1a V 1 M Citrine Kozak sequence G A C C A G EGFP-N DQDGHHPGEQLLALAHHGGL GPHAGGRHVAGRGQEGHHSI VLIPVVGTFLEEGKSVM g a c c a g g a t g g g c a c c a c c c c g g t g a a c a g c t c c t c g c c c t t g c t c a c c a t g g t g g c t t a c t g g t c c t a c c c g t g g t g g g g c c a c t t g t c g a g g a g c g g g a a c g a g t g g t a c c a c c g a a t

BmgBI 840 SSCFSKENHVPVVRGA* MTNKLPFGRGRPEPPRSTKK t c a t c g t g t t t t t c a a a g g a a a a c c a c g t c c c c g t g g t t c g g g g g g c c t a g a c g t t t t t t a g t a g c a c a a a a a g t t t c c t t t t g g t g c a g g g g c a c c a a g c c c c c c g g a t c t g c a a a a a a

PflMIApaLIBsiHKAIAflIIIPciI 900 VEVLCMYLM t a a c c t c g a c t a a a c a c a t g t a a a g c a t g t g c a c c g a g g c c c c a g a t c a g a t c c c a t a c a a t t g g a g c t g a t t t g t g t a c a t t t c g t a c a c g t g g c t c c g g g g t c t a g t c t a g g g t a t g t

End (906) 3ʹ 5ʹ 906 a t g g g g t a c c c 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.