The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing

Abstract

A total of 74 small nuclear RNA (snRNA) genes and 395 genes encoding splicing-related proteins were identified in the Arabidopsis genome by sequence comparison and motif searches, including the previously elusive U4atac snRNA gene. Most of the genes have not been studied experimentally. Classification of these genes and detailed information on gene structure, alternative splicing, gene duplications and phylogenetic relationships are made accessible as a comprehensive database of Arabidopsis Splicing Related Genes (ASRG) on our website.

Figure 1

Sequence alignments of U4atac and U6atac snRNAs. The tentative Arabidopsis U4atac snRNA was aligned against the human U4atac snRNA (U62822) using CLUSTAL W [22]. Possible sequence domains are indicated by different background colors, with cyan indicating transcription signals (USE, upstream sequence element; TATA, TATA box), green indicating the region involved in the stem-loop-stem structure, and pink indicating the domain that binds Sm proteins. The corresponding interaction region in U6atac snRNA is also marked in green. Red background indicates G-T base-pairs in the stem-loop structure. Grey letters indicate the genome sequence upstream and downstream of the putative U4atac gene. Asterisks (upper panel) and black shading (lower panel) show conserved positions in the alignment.

Figure 2

Chromosomal locations of Arabidopsis snRNAs. Chromosomes 1 to 5 are represented to scale by the long thick lines in dark green. The small bars above the chromosomes indicate the presence of an snRNA gene in that region. Different colors represent different snRNA types: red, U1 snRNA; magenta, U2 snRNA; blue, U4 snRNA; green, U5 snRNA; yellow, U6 snRNA; black, minor snRNA. The seven U1-U4 snRNA gene clusters (red-blue) and the single U2-U5 snRNA gene cluster (magenta-green) are indicated by red circles.

Figure 3

Phylogenetic tree of the SC35 protein family. The phylogenetic tree was constructed on the basis of protein sequence alignments of the SC35 homologs in human, Drosophila, Arabidopsis and rice. The GenBank accession numbers for the sequences are as follows: hsSC35, Q01130; hsSRrp40, AAL57514; hsSRrp35: AAL57515; dmSC35, AAF53192; atSC35, NP_851261; atSR33/SCL33, NP_564685; atSCL30a, NP_187966; atSCL30, NP_567021; atSCL28, NP_197382; osSC35a, BAC79909; osSC35b, BAD09319; osSR33-1, AAP46199; osSCL30a/SR33-2, BAC799901; osSCL30-2, BAD19168. The sequences were aligned using CLUSTALW [22] with default parameters, and the phylogenetic tree was produced according to the neighbor-joining method using PAM substitution model distances as implemented in the PHYLIP package [103].