pUC19 cloning vector
Find candidate ORFs in a common cloning vector.
ORF Finder
FigranPaste DNA or FASTA to list every open reading frame, read its protein and draw an ORF map.
- Six frames, any genetic code
- Multi-FASTA in one run
- Free SVG and 300 DPI PNG
Sequence
Search
≥ 24 aa for complete ORFsCalculating…
Enter a valid sequence to see its ORFs.
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ORF Finder examples
Explore plasmids, genomes and transcripts with different search settings.
pEGFP-N1: EGFP and NeoR/KanR
Locate the reporter and resistance ORFs.
E. coli lac operon with GTG and CTG starts
Explore alternative starts using bacterial code 11.
Human mitochondrial genome (genetic code 2)
Compare mitochondrial coding with the standard code.
E. coli ribosomal protein gene cluster
Find ORFs in a 23.4 kb bacterial operon region.
Longest ORF in three human mRNAs
Find coding sequences in three transcripts at once.
How to find ORFs in a DNA sequence
Find, inspect and export open reading frames in four steps.
1Enter your sequence
Paste DNA or FASTA, or open a sequence file.
2Choose search settings
Set the minimum length, start codons and genetic code.
3Inspect an ORF
Select an ORF in the map or table and copy its protein.
4Download results
Download the map or export your sequences and table.
How to read an ORF map
The six lanes show candidate ORFs on both strands.
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- 1Reading-frame lanes
- 2Arrow direction shows the strand
- 3Labels identify ORFs and lengths
- 4Coordinates use the input sequence
- 5Ticks mark start and stop codons
Open reading frames: start, stop and frame
An open reading frame runs from a start codon to an in-frame stop codon. The reading frame determines how bases are grouped into codons. Nested ORFs share a stop codon with an earlier start in the same frame.
+ frame = ((start − 1) mod 3) + 1
− frame = ((L − end) mod 3) + 1
aa = nt / 3 − 1
References: NCBI ORFfinder
Start codons and genetic codes
Alternative starts depend on the genetic code. The bacterial code, for example, permits GTG and CTG as initiators.
lac operon start positions
| Gene | ATG only | ATG + alternative | Any sense codon |
|---|---|---|---|
| lacI | 202 ATG | 70 GTG | 46 CGC |
| lacY | 4410 ATG | 4380 CTG | 4365 CCG |
| lacA | 5733 ATG | 5667 ATC | 5664 GCA |
Genetic code
| Genetic code | Start codon | Protein |
|---|---|---|
| 1. Standard | TTG, CTG, ATG | — |
| 2. Vertebrate Mitochondrial | ATT, ATC, ATA, ATG, GTG | TGA: * → W, ATA: I → M, AGA: R → *, AGG: R → * |
| 4. Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma | TTA, TTG, CTG, ATT, ATC, ATA, ATG, GTG | TGA: * → W |
| 5. Invertebrate Mitochondrial | TTG, ATT, ATC, ATA, ATG, GTG | TGA: * → W, ATA: I → M, AGA: R → S, AGG: R → S |
| 11. Bacterial, Archaeal and Plant Plastid | TTG, CTG, ATT, ATC, ATA, ATG, GTG | — |
| 12. Alternative Yeast Nuclear | CTG, ATG | CTG: L → S |
References: NCBI The Genetic Codes
ORF Finder FAQ
How do I find ORFs in a DNA sequence?
Paste or open a sequence, then set the minimum length, start codons and genetic code. The tool searches six reading frames in your browser and lists positions, lengths and proteins.
Why does an ORF start upstream of the annotated gene?
An earlier in-frame start can make an ORF longer than the annotated gene. For example, allowing alternative starts finds lacY from CTG at position 4,380. The actual start depends on biological and experimental evidence.
Why is one gene split into two ORFs, or missing?
Frameshifts, introns, incomplete stop codons or a different genetic code can split or hide an ORF. E. coli prfB uses a programmed +1 frameshift, and some human mitochondrial stop codons are completed by polyadenylation. Use mRNA or cDNA for spliced genes.
What minimum ORF length should I use?
Choose a threshold for your question: 75 nt is a common starting point, while 300 nt focuses on longer candidates. Short ORFs need independent evidence.
Which genetic code should I choose?
Choose the code appropriate to the organism and compartment: standard code 1 for most nuclear genes, 2 for vertebrate mitochondria, and 11 for bacteria, archaea and plastids.
How are ORF positions written for the reverse strand?
Positions use ascending coordinates on the original sequence and a separate strand column. For an ORF crossing the origin, the Location field lists both segments; Start and End are its ordered endpoints. NCBI ORFfinder writes reverse-strand positions in the opposite order.
How do results compare with NCBI ORFfinder and SMS?
With matching settings, the same start-to-stop ORFs are found. NCBI also offers SmartBLAST; this tool supports multiple sequences and map export in the browser.
Can I show ORFs on a circular plasmid map?
Yes. Export GenBank with ORF features and open it in the Plasmid Map Maker.
Can I translate a whole sequence without finding ORFs?
Yes. Use the Reverse Complement Calculator to translate DNA to protein across all six frames.