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Coding transcripts

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Transcriptomics analysis of Toxoplasma gondii-infected mouse macrophages reveals coding and noncoding signatures in the presence and absence of MyD88

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BMDM from MyD88 KO mice were infected with either the RH or PTG strain, and 6 h later RNA was isolated for sequencing. a Classification of differentially expressed MyD88 KO transcripts as either protein-coding, non-coding, pseudogene, or TEC (To be Experimentally Confirmed). c Venn diagrams of differentially expressed protein-coding transcripts. d Classification of differentially expressed MyD88 KO non-coding transcripts by type. 6 A minimal number of protein-coding genes were differentially expressed

Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis

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Then, we characterized the functional distribu- tion of protein-coding transcripts expressed in the L..

Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response

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Of the 95,523 assembled tran- scripts, CPC2 annotation identified 31,967 non-coding transcripts (CPC2 score <. Additional file 1: Fig. of the total . Most (61%, or 9341 of 15,312) TE- lncRNAs showed similarity to TEs over ≥90% of their length (Fig. Hereafter we refer to lncRNAs with se- quence similarity to TEs as “TE-lncRNAs”.. We further investigated the superfamily of TEs that were similar to the 15,312 TE-lncRNAs.

Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats

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A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly ( p ≤ 0.01) among the different lactation stages. Conclusions: Our results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation..

Comparative transcriptome analysis uncovers regulatory roles of long noncoding RNAs involved in resistance to powdery mildew in melon

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The length and exon number of melon lncRNAs were analyzed compared with protein-coding transcripts for their characterization. These results indicated that the majority of melon lncRNAs were relatively shorter in length and contained fewer exons compare to protein-coding transcripts.. Differential expression of lncRNAs in response to PM infection.

Transcriptome analysis of the almond moth, Cadra cautella, female abdominal tissues and identification of reproduction control genes

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Most highly abundant transcripts in the Cadra cautella female abdominal tissue. The transcripts that were most highly expressed in the C. Moreover, apolipophorin III and Vg genes were also among the highly expressed transcripts in the. The functions of each class are provide in the notation on the right. The abundance of the reproduction control genes and yolk polypeptide en- coding transcripts in the data reflects their key role in the development of future embryos inside the eggs..

High-resolution profile of transcriptomes reveals a role of alternative splicing for modulating response to nitrogen in maize

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Com- pared with these coding isoforms and the non-coding transcripts identified in the previous study [18], however, not only the relatively low number of novel non-coding transcripts were identified, but also only the minority of them were found similar to the known functional ones, suggesting that long-read sequencing has its limitation in finding non-coding RNAs (ncRNAs). Some 1000 genes were specifically undergone AS events in the treated sample (AS+N genes).

Third-generation sequencing found LncRNA associated with heat shock protein response to heat stress in Populus qiongdaoensis seedlings

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CPC used to assess the degree and quality of ORFs in transcripts, set the e value to “1e-10”, and use the NCBI eukaryote protein database search sequence to distinguish between coding and non-coding transcripts. The DESeq R software package (1.10.1) was used for the expression analysis. Using the miRBase20.0 as a reference, modified software mirdeep2_0_0_5, set the parameter to “quanti- fier.pl -p -m -r -y -g 0 -T 10”, and potential miRNAs were obtained using srna-tools-cli.

The whole-transcriptome landscape of muscle and adipose tissues reveals the ceRNA regulation network related to intramuscular fat deposition in yak

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The annotated and unannotated transcripts were obtained using Cufflinks after reconstruction of the transcripts from our RNA-seq data. Those transcripts that were predicted to have coding potential by two or all of the above three tools named as candi- date set of novel protein-coding transcripts, whereas those without coding potential were named as novel lncRNAs. 0.05 were then assigned as differentially expressed transcripts..

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells

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The selected non-coding transcripts/isoforms from the two software tools were used as input to draw the Venn diagram and those transcripts/isoforms which were in the intersection between the two software tools were selected for Cis and Trans target genes prediction.. LncRNA cis- and trans-target genes prediction analyses The basic principle of predicting if a lncRNA targets a gene is that, lncRNAs are regulators of protein-coding genes that lie near their genomic locations or coordi- nates.

JCDB: A comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants

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Utilizing sequence intrinsic composition to classify protein-coding and long non- coding transcripts. PNRD: a plant non-coding RNA database.

Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio)

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To account for the extensive fragmentation of the re-scaffolded genome draft we used the “PASA_comprehensive_db” pipeline to add to the PASA assemblies those de-novo or genome- guided assembled transcripts that align partially to the genome but extend onto sequencing gaps (>. The blastp hits of the resulting set of coding transcripts were sorted by alignment score, length and E-value and the top-hit blast results were used to annotate the tran- scripts using Annie [75].

Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

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Based on these features, a third filter was applied, and transcripts in the liver and transcripts in the adrenal glands were removed.. Finally, the coding-non-coding index (CNCI), the coding potential assessment tool (CPAT), and the predictor of lncRNAs and mRNAs based on the k-mer scheme (PLEK) were used to evaluate the protein-coding poten- tial, and 4498 and 7627 transcripts in the liver and adrenal gland tissues were retained (Fig.

A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum)

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The most abundant transcripts in tobacco were coding RNAs. This difference could partially be the result of the many different bioinformatics tools having been used in cir- cRNA identification in A.

Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

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Venn diagram of coding – noncoding NAT pairs of which enriched in GO terms related to drought stress in Nip, BJ89, and BJ278. Sequence alignments of 10 coding – noncoding NAT pairs related to GO enrichment terms for the drought stress response. Statis- tics of paired-end reads generated by ssRNA-seq analysis of 18 cDNA libraries of Nipponbare (Nip), BJ89, and BJ278 samples treated with or without drought stress.

Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq

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UTRs which overlap the protein-coding sequence of the neighbouring gene. In an extreme example, 2432 nt of the protein-coding region of Pf3D7_1244400 overlaps with the 3′ UTR of the adjacent gene ( Pf3D7_. In several instances we could detect transcription up- stream of the 5′ UTRs of mRNA transcripts on the strand opposite to that of the coding mRNA.

Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons

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A lower fraction had an in-frame uATG, 13.6 and 21.5% of the human and mouse protein-coding repertoires, respectively (Table 1).. Protein-coding OR genes with coding sequences split across two exons. We identified 47 mouse OR transcripts (from 41 genes) satisfying these criteria (Supplementary File 3), which we will refer to as split OR genes (Fig.

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

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Identification of long non-coding RNAs. In the first, transcripts shorter than 200 nt and those overlapped with protein-coding genes in the same sense of strand were discarded. Tissue-specific lncRNAs refer to lncRNAs that have ex- tremely high expression in the given tissue [18]. cucurbitae, DESeq was used to analyze the significance of the differential expression of lncRNAs in each two tis- sues [55].

Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

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We used StringTie 1.3.4d [54] for transcript assembly on each individual RNA-Seq library to identify transcripts missing from the Eutrema salsugineum reference annota- tion. Assembled transcripts that were not found in the Eutrema salsugineum reference annotation, or were not previously identified by Champigny et al. Gene-specific primers used were as reported by MacLeod et al.

Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells

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Similarly, 13 and 63% of the total 6042 TSSs identified in Borrelia burgdorferi during the infection of mammalian host have also been classified as antisense and internal TSSs, respectively [65]. conorii, the biogenesis and roles of antisense transcripts in the regulation of the coding transcriptome is not yet clear.