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The upstream regions of the 1,642 TSSs, which were identified at the 5′-UTR of annotated genes (see section "Detection of putative transcription start sites from RNA-seq data of enriched 5′ ends of primary transcripts") were searched for conserved motifs within 70 bases upstream of each TSS using Improbizer [ 23].
For the determination of the nucleotide distribution in TLSs of B. methanolicus MGA3, the initiation codons of 1,270 genes, for which a 5′-UTR was identified (section "Detection of putative transcription start sites from RNA-seq data of enriched 5′ ends of primary transcripts"), were analyzed.
Altogether, 525 TSSs belonging to novel transcripts (section "Detection of putative transcription start sites from RNA-seq data of enriched 5′ ends of primary transcripts") were detected by analysis of the primary transcriptome data set and classified into three categories according to their genomic context: intergenic (83), intragenic (227) or antisense (215).
5′ ends of primary transcripts were selectively determined (see Methods), identifying a total of 1,861 TSSs from the different antibiotics treatment conditions (Fig. 2A and Supplementary Dataset S2).
Instead, clear and sharp bands representing both primary transcripts were observed.
Interestingly, miR162a and miR869 primary transcripts were originally described as ncRNAs, demonstrating the efficacy of finding miRNA-like sequences by characterizing ncRNAs.
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In all Metazoa where transcription has been documented, the primary transcripts are polycistronic and must be processed to yield the necessary messenger (mRNA), tRNA, and rRNA transcripts.
Alternative splicing is a post-transcriptional mechanism in which the exon sequences of primary transcripts are differently included in mature RNAs.
Instead, their genome is organised into long polycistronic transcription units in which genes are co-transcribed [ 15], primary transcripts being resolved into mRNAs by concerted trans-splicing and polyadenylation reactions [ 16].
The possibilities of intron splicing from the primary transcripts are also discussed.
circRNAs, which originate through back-splicing events from primary transcripts, are resistant to exonucleases and typically not polyadenylated.
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