Basic Information  Top

Basic information include Gene ID (locus ID for Arabidopsis and MSU locus ID for rice), Gene Name, Gene Alias (IRGSP locus ID for rice), Gene Type, and Description.

GO Information  Top

The GO (Gene Ontology) project uses three structured controlled vocabularies (ontologies) to describe gene products in terms of their associated biological processes (process), cellular components (component) and molecular functions (function).

UniGene Information  Top

UniGene of NCBI is "An Orgnized View of the Transcriptome". Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene). The expression pattern can be roughly infered from the abundance of EST sequences derived from different tissues.

Expression Profile  Top

The gene expression profile images (.png) are drawn by plot function in R. The y-axis is intensity. The x-axis is a series of samples (Arabidopsis, rice). Arabidopsis samples are devided into eight groups. While rice samples are devided into five groups. Neighbor types are seperated by a vertical line.

Gene Structure  Top

Gene intron-exon structures are indicated by blue rectangles (UTR), red rectangles (CDS exon), and lines (intron). Their exact positions are indicated by numbers.

Protein Domain Infomation  Top

SeedGeneDB protein domain information are derived from Pfam. A fast HAMMER scan was run using pfam_scan.pl with Pfam-A database (version 23.0).

Mutant Infomation  Top

The mutant information are derived and sorted from TAIR ABRC. Only mutant name, TAIR stock number, TAIR accession number, mutagen, stock description and phenotype are listed here. Please follow the TAIR ABRC link of each mutant for more details.

Publication  Top

Some of publications related to a seed-related gene are derived from NCBI gene2pubmed. And the others are manually collected. The titles, authors, magzines, volumns, pages, published time and abstracts of these publications are downloaded using Batch Entrez tool.

Sequence  Top

Four types of sequences of a gene are provided for downloading: CDS (coding sequence), Protein sequence, cDNA sequence (coding sequence + UTR) and genomic sequence (coding sequence + UTR + intron sequence). All sequences are in FASTA format.