caa a22 4500 467893411 CHVBK 20180406152755.0 cr unu---uuuuu 170328e20060101xx s 000 0 eng 10.1007/s11103-005-2564-9 doi (NATIONALLICENCE)springer-10.1007/s11103-005-2564-9 Features of Arabidopsis Genes and Genome Discovered using Full-length cDNAs [Elektronische Daten] [Nickolai Alexandrov, Maxim Troukhan, Vyacheslav Brover, Tatiana Tatarinova, Richard Flavell, Kenneth Feldmann] 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. Springer, 2006 Alternative splicing nationallicence Arabidopsis genome nationallicence Full-length cDNA nationallicence Gene prediction nationallicence Genome statistics nationallicence Alexandrov Nickolai Ceres Inc., 1535 Rancho Conejo Blvd., 91320, Thousand Oaks, CA, USA aut Troukhan Maxim Ceres Inc., 1535 Rancho Conejo Blvd., 91320, Thousand Oaks, CA, USA aut Brover Vyacheslav Ceres Inc., 1535 Rancho Conejo Blvd., 91320, Thousand Oaks, CA, USA aut Tatarinova Tatiana Ceres Inc., 1535 Rancho Conejo Blvd., 91320, Thousand Oaks, CA, USA aut Flavell Richard Ceres Inc., 1535 Rancho Conejo Blvd., 91320, Thousand Oaks, CA, USA aut Feldmann Kenneth Ceres Inc., 1535 Rancho Conejo Blvd., 91320, Thousand Oaks, CA, USA aut Plant Molecular Biology Kluwer Academic Publishers 60/1(2006-01-01), 69-85 0167-4412 60:1<69 2006 60 11103 https://doi.org/10.1007/s11103-005-2564-9 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s11103-005-2564-9 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Alexandrov Nickolai Ceres Inc., 1535 Rancho Conejo Blvd., 91320, Thousand Oaks, CA, USA aut NATIONALLICENCE 700 1- Troukhan Maxim Ceres Inc., 1535 Rancho Conejo Blvd., 91320, Thousand Oaks, CA, USA aut NATIONALLICENCE 700 1- Brover Vyacheslav Ceres Inc., 1535 Rancho Conejo Blvd., 91320, Thousand Oaks, CA, USA aut NATIONALLICENCE 700 1- Tatarinova Tatiana Ceres Inc., 1535 Rancho Conejo Blvd., 91320, Thousand Oaks, CA, USA aut NATIONALLICENCE 700 1- Flavell Richard Ceres Inc., 1535 Rancho Conejo Blvd., 91320, Thousand Oaks, CA, USA aut NATIONALLICENCE 700 1- Feldmann Kenneth Ceres Inc., 1535 Rancho Conejo Blvd., 91320, Thousand Oaks, CA, USA aut NATIONALLICENCE 773 0- Plant Molecular Biology Kluwer Academic Publishers 60/1(2006-01-01), 69-85 0167-4412 60:1<69 2006 60 11103 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer