(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Eukaryota: NE > Viridiplantae: NE > Streptophyta: NE > Streptophytina: NE > Embryophyta: NE > Tracheophyta: NE > Euphyllophyta: NE > Spermatophyta: NE > Magnoliophyta: NE > Mesangiospermae: NE > Liliopsida: NE > Petrosaviidae: NE > commelinids: NE > Poales: NE > Poaceae: NE > PACMAD clade: NE > Panicoideae: NE > Andropogonodae: NE > Andropogoneae: NE > Tripsacinae: NE > Zea: NE > Zea mays: NE
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA KPFTAHYFPQLLDHFAFTPNASTVFRHKYLLNDTFWRRPGAGAGDDGPGP LFVYTGNEGDIEWFATNTGFMFDIAPTFGALLVFIEHRFYGESKPFGNDS YRSAETLGYLTSTQALADFAVVIRGLKRDLGAEAAPVVVFGGSYGGMLAS WFRLKYPHVAIGALASSAPILQFDHITPWSSFYDAVSQDFKSESSNCFGV IRAAWDVLDERGATDKGLLDLSKLFRACKTVKYAYSIRNWLWTAFTYTAM VDYPTPANFLENLPAYPVKEMCKTIDAFPAGADVLEKAFAAASLYYNYTG DQACNKIEDGDDPHGLDGWQWQACTEMIMPMTISNESMFPPSAFSYDDRS DECFQSWGVRPRPHWITTEYGGYKIDKVLKRFGSNIIFSNGMRDPWSRGG VLKNISSSIIALVTEKGAHHLDLRSSTKGDPDWLIEQRRQEVEIIQGWID QYHQDMAETSS
We present a large portion of the transcriptome of Zea mays, including ESTs representing 484,032 cDNA clones from 53 libraries and 36,565 fully sequenced cDNA clones, out of which 31,552 clones are non-redundant. These and other previously sequenced transcripts have been aligned with available genome sequences and have provided new insights into the characteristics of gene structures and promoters within this major crop species. We found that although the average number of introns per gene is about the same in corn and Arabidopsis, corn genes have more alternatively spliced isoforms. Examination of the nucleotide composition of coding regions reveals that corn genes, as well as genes of other Poaceae (Grass family), can be divided into two classes according to the GC content at the third position in the amino acid encoding codons. Many of the transcripts that have lower GC content at the third position have dicot homologs but the high GC content transcripts tend to be more specific to the grasses. The high GC content class is also enriched with intronless genes. Together this suggests that an identifiable class of genes in plants is associated with the Poaceae divergence. Furthermore, because many of these genes appear to be derived from ancestral genes that do not contain introns, this evolutionary divergence may be the result of horizontal gene transfer from species not only with different codon usage but possibly that did not have introns, perhaps outside of the plant kingdom. By comparing the cDNAs described herein with the non-redundant set of corn mRNAs in GenBank, we estimate that there are about 50,000 different protein coding genes in Zea. All of the sequence data from this study have been submitted to DDBJ/GenBank/EMBL under accession numbers EU940701-EU977132 (FLI cDNA) and FK944382-FL482108 (EST).
Full-length cDNA (FLcDNA) sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5' and 3' UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs), only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org).
Zea mays (Maize) ZmB6T1C9 ZmAPT2 Zm.98376 Acyl-protein thioesterase 2