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In some cases, translation initiates at an alternative initiation codon, such as ACG, CUG, or GUG [7], [8].
For example, some mRNAs may escape NMD if translation initiates at an alternative initiation codon and the ORF terminates less than 35-nucleotides upstream of an EJC in the 3' UTR, or downstream of this EJC.
In contrast, introduction of an alternative initiation of replication region from the β-globin gene locus, instead of EBV OriP and the EBV nuclear antigen-1 gene, restored replicative capacity and enhanced episome retention mediated by the S/MAR.
The brain-expressed splice variant is generated from an alternative initiation site within exon 2 of the dominant placentally-expressed form of the gene.
Similarly, selection of an alternative initiation codon can account for the observation that the 5' ends of some endonuclease ORFs include intron core sequences.
This would be a strong candidate for phase variation if an alternative initiation codon 5' of the repeat was chosen rather than that annotated.
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In case of the human sequence, a GUG alternative initiation codon is found at position −35.
Insertions close to the 5' end may also be possible if a suitable alternative initiation codon is available.
No introns were identified, and the genetic code appears to be the standard one with the exception of a supposed alternative initiation codon in atp1.
While the scanning model of translation initiation applies to many transcripts under basal conditions, a variety of alternative initiation mechanisms exist that bypass these requirements.
We have analyzed the Drosophila PHD locus, fatiga, which encodes 3 isoforms, FgaA, FgaB and FgaC that are originated through a combination of alternative initiation of transcription and alternative splicing.
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