Open Reading Frame

In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the potential to code for a protein or peptide. An ORF is a continuous stretch of codons that do not contain a stop codon (But it is at the end) (usually UAA, UAG or UGA). So an ORF is a sequence beginning with a start codon and ending in a stop codon. An AUG codon within the ORF (not necessarily the first) may indicate where translation starts. The transcription termination site is located after the ORF, beyond the translation stop codon, because if transcription were to cease before the stop codon, an incomplete protein would be made during translation. In eukaryotic genes with multiple exons, ORFs may span exons. These would be spliced into an ORF in the mRNA.  But remember the ORF may not itself code for the protein, but it may be a part of a gene that does, the ORF itself may have promoters

Sample sequence showing three different possible reading frames. Start codons are highlighted in purple, and stop codons are highlighted in red.

Because codons occur in nucleotide triplets, from any point within the genome there are six possible reading frames (three in each direction). Open reading frames (ORFs) are those sequences of DNA or RNA that code for translation at ribosomes into polypeptides or proteins. Within the genome, (ORFs) lie between codons for initiation (start-code sequence) and termination (stop-code sequence).

A DNA open reading frame starts with ATG—coding for Met—in most species, and ends with a stop codon (TAA, TAG, or TGA).

In prokaryotes, ORFs are usually the longest sequence without a stop codon (without introns).

In eukaryotes, long ORFs can continue over non-translatable intron gaps, so spliced mRNA must be employed to determine ORFs. Short ORFs can occur outside genes – within the intron, segments of DNA outside genes that were formerly considered ‘junk’ DNA.

CDS - coding dna sequence - > only sequence that is translated into protein-- the ORF may not be as it may contain Introns.

ORF - open reading frame -> entire gene sequence 5'-utr + transcript (all exons + introns) + 3'-utr

The region of the nucleotide sequences from the start codon (ATG) to the stop codon is called the Open Reading frame.

Gene finding in organism specially prokaryotes starts form searching for an open reading frames (ORF). An ORF is a sequence of DNA that starts with start codon “ATG” (not always) and ends with any of the three termination codons (TAA, TAG, TGA). Depending on the starting point, there are six possible ways (three on forward strand and three on complementary strand) of translating any nucleotide sequence into amino acid sequence according to the genetic code .These are called reading frames.

While eukaryotic gene finding is altogether a different task as the eukaryotic genes are not continuous and interrupted by intervening noncoding sequences called ‘introns’. Moreover organization of genetic information in eukaryotes and prokaryotes is different.

CDS:

The Coding Sequence (CDS) is the actual region of DNA that is translated to form proteins. While the ORF may contain introns as well, the CDS refers to those nucleotides(concatenated exons) that can be divided into codons which are actually translated into amino acids by the ribosomal translation machinery.

Mainly: CDS means only that the sequence is known to be transcribed and, therefore, it is coding for something -- neither gene nor protein has to be known. Any full mRNA sequence (obtained from cDNA sequencing) will have a full coding sequence. ORF is usually predicted based on DNA sequence and not proven to be transcribed.

Open Reading Frame

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