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Transcription Starts and Transcription Ends denote the start and end of transcripts (containing coding genes or ncRNA genes), whereas Translation Starts and Translation Ends (denoted as TS i and TE i, respectively, where i is the frame of the corresponding codon in the sequence) enable to, respectively, start or end a CDS inside a transcript and possibly inside another CDS in a different frame.
Several protocols have been developed to capture the 5′ end of transcripts via Cap Analysis of Gene Expression (CAGE) or linker-ligation strategies such as Paired-End Analysis of Transcription Start Sites (PEAT), but often require large amounts of tissue.
In addition, the use of oligo dT primers, instead of random hexamers, can be biased towards the 3′ end of transcripts.
Additionally, usage of poly dT priming introduces a bias towards overrepresentation of the 3' end of transcripts, particularly in the case of large transcripts.
Biased amplification of the 3′ end of transcripts does not have a major impact on the overall transcript profile due to the 3′ bias of probe sets incorporated in the array design.
Primers specific for the 3′ end of transcripts were designed by use of PRIMER EXPRESS 3.0 (Applied Biosystems).
Similar(10)
5'SOLiD tags identify the 5'-end of transcripts.
Lower percentages (~48%) were obtained when considering the 3'-end of transcripts.
All tags were reverse-complemented because the tags were sequenced from 3′-end of transcripts.
Extension of the 5′-end of transcripts compromises coding sequence translation as expected.
The presence/absence of the 5′-end of transcripts was determined after aligning them with their best eukaryotic and/or prokaryotic homologs.
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