Journal:

Article Title: Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping 1

doi: 10.1104/pp.102.018101

Figure Lengend Snippet: Visual assessment of EST clustering and gene characteristics for a region of the Arabidopsis genome. In the display, which is available for all genomic regions at http://www.plantgdb.org/AtGDB/, pcSPAs originating from EST spliced alignments are shown in red and non-pcSPAs in pink. For multi-exon alignments, the arrow indicates the direction of transcription, inferred from the implied splice site patterns (Usuka et al., 2000). Multi-exon 5′ ESTs are marked by green color at their 5′ terminus, and multi-exon 3′ ESTs are marked by blue color at their 3′ terminus. Single-exon ESTs have corresponding 5′/3′ labels at the center of their representations. Pairs of 5′ and 3′ ESTs from the same clone are grouped by green boxes. PcSPAs originating from cDNA spliced alignments are shown in light blue, and non-pcSPAs are shown in gray. Dark-blue gene structures represent the current GenBank gene annotations for this region. The 5′ and 3′ boundaries of the corresponding coding regions are indicated by green and red triangles, respectively. Note that the current annotation misses the gene represented by clone pair ESTs gi:19867004 and gi:19822861 and gi:19878951 and gi:19799838. The purple structures represent the spliced alignments of TIGR Arabidopsis Gene Index tentative contigs. The figure also shows an alternatively spliced internal mini-exon. This exon of 16 nucleotides occurs in the 5′-UTR of At4g38510, an H+-transporting ATPase (EC 3.6.1.35). The transcript isoform including this intron is supported by ESTs gi:9785303 and gi:8722457. In the same region, EST gi:9787070 supports a different internal exon of 73 nucleotides, and EST gi:19867985 (equal to RAFL-15010615) indicates an alternative transcription start. Note that all sequence records at AtGDB are identified by their unique GenBank gi identifiers. The Riken Arabidopsis full-length (RAFL) cDNAs (Seki et al., 2002) thus indicated as RAFL-15451093, RAFL-18377451, RAFL-20268790, RAFL-21689814, RAFL-15010783, RAFL-14517367, RAFL-16323357, RAFL-15010615, and RAFL-19699257 correspond to clones RAFL05-11-M12, U16016, RAFL06-81-F18, U11966, RAFL03-01-G10, RAFL04-09-A19, U12748, RAFL07-17-H08, and U12937, respectively.

Article Snippet: The 5′ site motif ATCC in positions +3 to +6 is highly conserved in U12 introns ( Wu and Krainer, 1996 ; Sharp and Burge, 1997 ; Burge et al., 1998 ), where the numbering +1 to +6 denotes the first six nucleotides of the intron starting at the 5′ splice site.

Techniques: Sequencing, Clone Assay

Journal:

Article Title: Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping 1

doi: 10.1104/pp.102.018101

Figure Lengend Snippet: Non-canonical introns (NN represents any dinucleotide) The intron types were assigned by the terminal intron dinucleotides based on high-quality spliced alignments.

Article Snippet: The 5′ site motif ATCC in positions +3 to +6 is highly conserved in U12 introns ( Wu and Krainer, 1996 ; Sharp and Burge, 1997 ; Burge et al., 1998 ), where the numbering +1 to +6 denotes the first six nucleotides of the intron starting at the 5′ splice site.

Techniques:

Journal:

Article Title: Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping 1

doi: 10.1104/pp.102.018101

Figure Lengend Snippet: Spliced alignment of Arabidopsis EST gi:5839990 with: A, the Arabidopsis At3g53520 gene encoding a dTDP-Glc 4-6-dehydratase-like protein; and B, a rice (Oryza sativa) genomic sequence (accession no. AP003271). The two alignments reveal conserved gene structure between Arabidopsis and rice, including a conserved AT-AC intron. C, Pair-wise alignment of the orthologous AT-AC intron sequences. The conserved donor site (ATATCCTY) and branch site motifs (TCCTTRAY) are highlighted in red color.

Article Snippet: The 5′ site motif ATCC in positions +3 to +6 is highly conserved in U12 introns ( Wu and Krainer, 1996 ; Sharp and Burge, 1997 ; Burge et al., 1998 ), where the numbering +1 to +6 denotes the first six nucleotides of the intron starting at the 5′ splice site.

Techniques: Sequencing

Journal:

Article Title: Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping 1

doi: 10.1104/pp.102.018101

Figure Lengend Snippet: Evolutionary conservation of a miniexon. A, Spliced alignment of the translated ORF (bottom lines) originating from the EST cluster shown in Figure 7 with a rice genomic clone (GenBank accession no. AP003727); the alignment was made with the GeneSeqer program (Usuka and Brendel, 2000). B, Alignment of the Arabidopsis mini-exon and its flanking introns with a homologous region of the rice genome. The mini-exon is highlighted in red characters, the intron donor sites in green, and the intron acceptor sites in blue.

Article Snippet: The 5′ site motif ATCC in positions +3 to +6 is highly conserved in U12 introns ( Wu and Krainer, 1996 ; Sharp and Burge, 1997 ; Burge et al., 1998 ), where the numbering +1 to +6 denotes the first six nucleotides of the intron starting at the 5′ splice site.

Techniques: