Why Is There A Stop Codon Before Cds For Nm_000277.1

Question

[ppkjref]

since there is an in frame stop codon before the cds wouldn't translation stop before phenylalanine hydroxylase is synthesized? http://www.ncbi.nlm.nih.gov/nuccore/NM_000277.1

[David Quigley]

Are you sure you're reading the strand in the correct direction? The refseq version of PAH starts with a methionine, the standard start codon, and ends with an ochre UAA.

[ppkjref]

yes correct direction 5' to 3'. The refseq indicates the cds begins on first exon with methionine however it also indicates a misc_feature (a stop codon) before the start codon.

[Neilfws]

It's upstream of PAH. Why do you think would that affect translation of PAH?

[ppkjref]

i don't. i just thought it was strange for there to be a stop codon outside and before the coding region.

[Larry_Parnell]

uORFs cause translating ribosomes to pause and even fall off before translation of the main (ie, long) ORF. Some ribosomes escape the stop codon of the uORF and translate the long ORF, but not all. One thought is this is a mechanism of control of translation.

Answer 1

[JC]

I'm not sure if this is the case, but it's known that some transcripts have a short ORF in the 5' UTR, commonly called uORFs.

[ppkjref]

wouldn't there need to be a start codon for the uORF then as well?

[Larry_Parnell]

No, uORFs tend to use alternate start codons.

Answer 2

[Manu Prestat]

Just a guess, I'm not an expert so I'm not sure: it could be an alternative splicing case.