Open reading frame

Open reading frame

In molecular genetics, an open reading frame (ORF) is a DNA sequence that does not contain a stop codon in a given reading frame[1]. Normally, inserts which interrupt the reading frame of a subsequent region after the start codon, cause frameshift mutation of the sequence and dislocate the sequences for stop codons.

Contents

Significance

Normally, inserts which interrupt the reading frame of a subsequent region after the start codon, cause frameshift mutation of the sequence and dislocate the sequences for stop codons. One common use of open reading frames are as one piece of evidence to assist in gene prediction. Long ORFs are often used, along with other evidence, to initially identify candidate protein coding regions in a DNA sequence[1]. The presence of an ORF does not necessarily mean that the region is ever translated. For example in a randomly generated DNA sequence with an equal percentage of each nucleotide, a stop-codon would be expected once every 21 codons[1]. A simple gene prediction algorithm for prokaryotes might look for a start codon followed by an open reading frame that is long enough to encode a typical protein, where the codon usage of that region matches the frequency characteristic for the given organism's coding regions[1]. By itself even a long open reading frame is not conclusive evidence for the presence of a gene[1].

Example

If a portion of a genome has been sequenced (e.g. 5'-ATCTAAAATGGGTGCC-3'), ORFs can be located by examining each of the three possible reading frames on each strand. In this sequence two out of three possible reading frames are entirely open, meaning that they do not contain a stop codon:

  1. ...A TCT AAA ATG GGT GCC...
  2. ...AT CTA AAA TGG GTG CC...
  3. ...ATC TAA AAT GGG TGC C...

Possible stop codons in DNA are "TGA", "TAA" and "TAG". Thus, the last reading frame in this example contains a stop codon (TAA), unlike the first two.

See also

Notes

  1. ^ a b c d e Deonier 2005, p. 25

References

  • Deonier, Richard; Simon Tavaré, Michael Waterman (2005). Computational Genome Analysis: an introduction. Springer-Verlag. ISBN 0387987851. 

External links

  • Translation and Open Reading Frames
  • NCBI ORF finder - A web based interactive tool for predicting and analysing ORFs from nucleotide sequences.
  • ORF finder - A web based interactive tool for predicting and analysing ORFs from nucleotide sequences - hosted at bioinformatics.org
  • hORFeome V5.1 - A web based interactive tool for CCSB Human ORFeome Collection
  • ORF Marker - A free, fast and multi-platform desktop GUI tool for predicting and analyzing ORFs
  • StarORF - A multi-platform, java based, GUI tool for predicting and analyzing ORFs and obtaining reverse complement sequence

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Look at other dictionaries:

  • open reading frame — open reading frame. См. открытая рамка считывания. (Источник: «Англо русский толковый словарь генетических терминов». Арефьев В.А., Лисовенко Л.А., Москва: Изд во ВНИРО, 1995 г.) …   Молекулярная биология и генетика. Толковый словарь.

  • Open reading frame — (genetics) An open reading frame in DNA has no termination codon, no signal to stop reading the nucleotide sequence, and so may be translated into protein. * * * open read·ing frame rēd iŋ n a reading frame that does not contain a nucleotide… …   Medical dictionary

  • Open Reading Frame — Als offener Leserahmen (OLR) oder offenes Leseraster (als Übersetzung von engl. open reading frame, ORF) wird in der Genetik derjenige Bereich der DNA bzw. mRNA bezeichnet, dessen Leserahmen zwischen einem Start Codon und einem Stopp Codon liegt …   Deutsch Wikipedia

  • Open reading frame — Als offener Leserahmen (OLR) oder offenes Leseraster (als Übersetzung von engl. open reading frame, ORF) wird in der Genetik derjenige Bereich der DNA bzw. mRNA bezeichnet, dessen Leserahmen zwischen einem Start Codon und einem Stopp Codon liegt …   Deutsch Wikipedia

  • open reading frame — (ORF) A reading frame sequence not interrupted by a stop codon; it is usually determined by nucleic acid sequencing studies …   Dictionary of microbiology

  • open reading frame — A possible reading frame of DNA which is capable of being translated into protein, ie. is not punctuated by stop codons. (This capacity does not indicate per se that the ORF is translated.) …   Dictionary of molecular biology

  • open reading frame — noun : a reading frame that does not contain a nucleotide triplet which stops translation before formation of a complete polypeptide …   Useful english dictionary

  • open reading frame — noun A sequence of DNA triplets, between the initiator and terminator codons, that can be transcribed into mRNA and later translated into protein …   Wiktionary

  • open reading frame — Abbreviation: ORF A sequence of nucleotides in a DNA molecule that has the potential to encode a peptide or protein: comprisesa start triplet (ATG), followed by a series of triplets (each of which encodes an amino acid), and ending with a stop… …   Glossary of Biotechnology

  • Reading frame — One of the three possible ways to read a nucleotide sequence in DNA (depending upon whether reading starts with the first, second or third base in a triplet). * * * The grouping of nucleotides by threes into codons. See frame shift mutation.… …   Medical dictionary

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