Addgene pCMMP-NGFR:LMP1-IRES-mRFP Sequencing Result - Sequence Analyzer Skip to main content
Addgene

Sequence Analyzer: pCMMP-NGFR:LMP1-IRES-mRFP Sequencing Result

Map View

800 600 400 200 End (823) BsrFI - SgrAI (805) BssHII (783) AleI (766) TaqII (736) DsRed1-C (731 .. 754) BsgI (718) PvuII MspA1I (702) DrdI (664) BsrBI (582) PspFI (567) PflMI - BseYI (563) BbsI (559) MmeI (554) mCherry-F (537 .. 556) PstI - SbfI (479) SfcI (475) BsaAI (354) AhdI (318) mCherry-R (269 .. 287) BssSI BssSαI (211) BanII (199) FspI - FspAI (187) AatII (158) ZraI (156) BmgBI (95) PciI - AflIII (42) BsiHKAI (33) ApaLI (29) MflI * - BstYI (9) Start (0) mRFP1 mRFP1 pCMMP-NGFR:LMP1-IRES-mRFP 823 bp

Sequence View

AflIIIPciIApaLIBsiHKAIBstYIMflI*Start (0) 5ʹ 3ʹ 60 *MHKTST a t t g t a t g g g a t c t g a t c t g g g g c c t c g g t g c a c a t g c t t t a c a t g t g t t t a g t c g a g g t t a a c a t a c c c t a g a c t a g a c c c c g g a g c c a c g t g t a c g a a a t g t a c a c a a a t c a g c t c c a

BmgBI 120 LFVDLGGSGRPRPKGKFFVI t a a a a a a a c g t c t a g g c c c c c c g a a c c a c g g g g a c g t g g t t t t c c t t t g a a a a a c a c g a t a t t t t t t t g c a g a t c c g g g g g g c t t g g t g c c c c t g c a c c a a a a g g a a a c t t t t t g t g c t a

ZraIAatII 180 1 5 10 MASSEDVIKEFMRF mRFP1 1 5 10 MASSEDVIKEFMRF mRFP1 MATTMASSEDVIKEFMRF IIHGCGHGGGLVDDLLEHAE g a t a a t a t g g c c a c a a c c a t g g c c t c c t c c g a g g a c g t c a t c a a g g a g t t c a t g c g c t t c c t a t t a t a c c g g t g t t g g t a c c g g a g g a g g c t c c t g c a g t a g t t c c t c a a g t a c g c g a a g

BssSαIBssSIBanIIFspAIFspI 240 15 20 25 30 KVRMEGSVNGHEFEIEGEGE mRFP1 15 20 25 30 KVRMEGSVNGHEFEIEGEGE mRFP1 KVRMEGSVNGHEFEIEGEGE LHAHLAGHVAVLELDLALAL a a g g t g c g c a t g g a g g g c t c c g 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 t t c c a c g c g t a c c t c c c g a g g 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

300 35 40 45 50 GRPYEGTQTAKLKVTKGGPL mRFP1 35 40 45 50 GRPYEGTQTAKLKVTKGGPL mRFP1 G G T T C G A C T T C C A C T G G T T mCherry-R GRPYEGTQTAKLKVTKGGPL AAGVLAGLGGLQLHGLAAGQ g g c c g c c c c t a c g a g g g c a c c c 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 c g g c c c c c t g c c g g c g g g g a t g c t c c c g t g g g 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 g c c g g g g g a c

BsaAIAhdI 360 55 60 65 70 PFAWDILSPQFQYGSKAYVK mRFP1 55 60 65 70 PFAWDILSPQFQYGSKAYVK mRFP1 PFAWDILSPQFQYGSKAYVK GEGPVDQGRLELVAGLGVHL c c c t t c g c c t g g g a c a t c c t g t c c c c t c a g t t c c a 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 g g g a a g c g g a c c c t g t a g g a c a g g g g a g t c a a g g t 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

420 75 80 85 90 HPADIPDYLKLSFPEGFKWE mRFP1 75 80 85 90 HPADIPDYLKLSFPEGFKWE mRFP1 HPADIPDYLKLSFPEGFKWE VGGVDGVVQLQGEGLAELPL c a c c c c g c c g a c a t c c c c g a c t 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 g t g g g g c g g c t g t a g g g g c t g a 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

SbfIPstISfcI 480 95 100 105 110 RVMNFEDGGVVTVTQDSSLQ mRFP1 95 100 105 110 RVMNFEDGGVVTVTQDSSLQ mRFP1 RVMNFEDGGVVTVTQDSSLQ AHHVELVAAHHGHGLVGGQL c g c g t g a t g a a c t t c g a g g a c g 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 c g c a c t a c t t g a a g c t c c t g c 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

540 115 120 125 130 DGEFIYKVKLRGTNFPSDGP mRFP1 115 120 125 130 DGEFIYKVKLRGTNFPSDGP mRFP1 C C C C mCherry-F DGEFIYKVKLRGTNFPSDGP VALEDVLHLQAAGVEGGVAG g a c g g c g a g t t c a t c t a c a a g g 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 c t g c c g c t c a a g t a g a t g t t c c 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

BsrBIMmeIBbsIBseYIPflMIPspFI 600 135 140 145 150 VMQKKTMGWEASTERMYPED mRFP1 135 140 145 150 VMQKKTMGWEASTERMYPED mRFP1 G T A A T G C A G A A G A A G A mCherry-F VMQKKTMGWEASTERMYPED YHLLLGHAPLGGGLPHVGLV g t a a t g c a g a a g a a g a c c a t g g g c t g g g a g g c c t c c a c c g a g c g g a t g t a c c c c g a g g a c c a t t a c g t c t t c t t c t g g t a c c c g a c c c t c c g g a g g t g g c t c g c c t a c a t g g g g c t c c t g

660 155 160 165 170 GALKGEIKMRLKLKDGGHYD mRFP1 155 160 165 170 GALKGEIKMRLKLKDGGHYD mRFP1 GALKGEIKMRLKLKDGGHYD AGQLALDLHPQLQLVAAVVV g g c g c c c t g a a g g g c g a g a t c a a g a t 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 c c g c g g g a c t t c c c g c t c t a g t t c t a 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

BsgIMspA1IPvuIIDrdI 720 175 180 185 190 AEVKTTYMAKKPVQLPGAYK mRFP1 175 180 185 190 AEVKTTYMAKKPVQLPGAYK mRFP1 AEVKTTYMAKKPVQLPGAYK GLDLGGVHGLLGHLQGAGVL g c c g a g g t c a a g a c c a c c t a c a t 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 g c g g c t c c a g t t c t g g t g g a t g t a 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 c

AleITaqII 780 195 200 205 210 TDIKLDITSHNEDYTIVEQY mRFP1 195 200 205 210 TDIKLDITSHNEDYTIVEQY mRFP1 A G C T G G A C A T C A C C T C C C A C A A C G DsRed1-C TDIKLDITSHNEDYTIVEQY GVDLQVDGGVVLVVGDHFLV a c c g a c a t c a a g c t g g a c a t c a 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 t g g c t g t a g t t c g a c c t g t a g 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

End (823) SgrAIBsrFIBssHII 3ʹ 5ʹ 823 215 220 225 ERAEGRHSTGA* mRFP1 215 220 225 ERAEGRHSTGA* mRFP1 ERAEGRHSTGA* LAGLAAVGGAGLSN g a g c g c g c c g a g g g c c g c c a c t c c a c c g g c g c c t a a t g a a t t a c t c g c g c g g c t c c c g g c g g t g a g g t g g c c g c g g a t t a c t t a a t

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.