We are analyzing https://link.springer.com/article/10.1007/s11103-005-2564-9.

Title:
Features of Arabidopsis Genes and Genome Discovered using Full-length cDNAs | Plant Molecular Biology
Description:
Arabidopsis is currently the reference genome for higher plants. A new, more detailed statistical analysis of Arabidopsis gene structure is presented including intron and exon lengths, intergenic distances, features of promoters, and variant 5′-ends of mRNAs transcribed from the same transcription unit. We also provide a statistical characterization of Arabidopsis transcripts in terms of their size, UTR lengths, 3′-end cleavage sites, splicing variants, and coding potential. These analyses were facilitated by scrutiny of our collection of sequenced full-length cDNAs and much larger collection of 5′-ESTs, together with another set of full-length cDNAs from Salk/Stanford/Plant Gene Expression Center/RIKEN. Examples of alternative splicing are observed for transcripts from 7% of the genes and many of these genes display multiple spliced isoforms. Most splicing variants lie in non-coding regions of the transcripts. Non-canonical splice sites constitute less than 1% of all splice sites. Genes with fewer than four introns display reduced average mRNA levels. Putative alternative transcription start sites were observed in 30% of highly expressed genes and in more than 50% of the genes with low expression. Transcription start sites correlate remarkably well with a CG skew peak in the DNA sequences. The intergenic distances vary considerably, those where genes are transcribed towards one another being significantly shorter. New transcripts, missing in the current TIGR genome annotation and ESTs that are non-coding, including those antisense to known genes, are derived and cataloged in the Supplementary Material. They identify 148 new loci in the Arabidopsis genome. The conclusions drawn provide a better understanding of the Arabidopsis genome and how the gene transcripts are processed. The results also allow better predictions to be made for, as yet, poorly defined genes and provide a reference for comparisons with other plant genomes whose complete sequences are currently being determined. Some comparisons with rice are included in this paper.
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Keywords {🔍}

article, google, scholar, pubmed, cas, genome, arabidopsis, science, plant, res, genes, fulllength, splicing, sequences, sequence, analysis, gene, dna, nucleic, acids, alternative, annotation, access, rna, biol, cdna, cdnas, transcription, thaliana, bioinformatics, privacy, cookies, content, transcripts, sites, mrna, mol, nature, information, publish, research, search, biology, alexandrov, intron, collection, expression, noncoding, rice, open,

Topics {✒️}

full-length cdna sequences alternative pre-mrna splicing month download article/chapter full-length cdnas published sequenced full-length cdnas splicing plant physiol rnase iii-mediated degradation strand-specific compositional asymmetries full-length cdnas full article pdf arabidopsis thaliana based gene expression independent gene expression map arabidopsis gene structure alternative splicing arabidopsis genome annotation strand compositional asymmetry privacy choices/manage cookies splicing variants lie related subjects arabidopsis information resource arabidopsis genome initiative maize plant mol cg skew peak optimal spliced alignment arabidopsis biology unique intron sequences mrna synthesis microbiol conditions privacy policy highly expressed genes genome-wide analysis 3′-end cleavage sites eukaryotic cdnas correlates check access instant access escherichia coli proc intron-mediated enhancement dc%2bd3cxkvfars7k%3d 10 dc%2bd38xjvv2lsl0%3d 10 dc%2bd3sxksvojt7c%3d 10 dc%2bd38xmt1whu7g%3d 10 dc%2bd38xivvsqtrw%3d 10 dc%2bd3sxns1cntbs%3d 10 dc%2bd2cxotlwmur0%3d 10 dc%2bd3mxhsfcjtlc%3d 10 dc%2bd3cxksfeis70%3d 10 dc%2bd2cxpt1gntlg%3d 10 dc%2bd3cxjsveru7y%3d 10 dc%2bd3cxns1shsr8%3d 10 dc%2bd3sxhvfsnurk%3d 10

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         description: Arabidopsis is currently the reference genome for higher plants. A new, more detailed statistical analysis of Arabidopsis gene structure is presented including intron and exon lengths, intergenic distances, features of promoters, and variant 5′-ends of mRNAs transcribed from the same transcription unit. We also provide a statistical characterization of Arabidopsis transcripts in terms of their size, UTR lengths, 3′-end cleavage sites, splicing variants, and coding potential. These analyses were facilitated by scrutiny of our collection of sequenced full-length cDNAs and much larger collection of 5′-ESTs, together with another set of full-length cDNAs from Salk/Stanford/Plant Gene Expression Center/RIKEN. Examples of alternative splicing are observed for transcripts from 7% of the genes and many of these genes display multiple spliced isoforms. Most splicing variants lie in non-coding regions of the transcripts. Non-canonical splice sites constitute less than 1% of all splice sites. Genes with fewer than four introns display reduced average mRNA levels. Putative alternative transcription start sites were observed in 30% of highly expressed genes and in more than 50% of the genes with low expression. Transcription start sites correlate remarkably well with a CG skew peak in the DNA sequences. The intergenic distances vary considerably, those where genes are transcribed towards one another being significantly shorter. New transcripts, missing in the current TIGR genome annotation and ESTs that are non-coding, including those antisense to known genes, are derived and cataloged in the Supplementary Material. They identify 148 new loci in the Arabidopsis genome. The conclusions drawn provide a better understanding of the Arabidopsis genome and how the gene transcripts are processed. The results also allow better predictions to be made for, as yet, poorly defined genes and provide a reference for comparisons with other plant genomes whose complete sequences are currently being determined. Some comparisons with rice are included in this paper.
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