The Introduction of the PASDB (Plant Alternative Splicing Database)
To browse the data the in the PASDB
  - To browse with the Species List
- To browse with the Gene List
- To browse with the Products List
- To browse with the Catalogs List [Biological Process] [Molecular Function] [Taxonomy]
To Search the data the in the PASDB [Search Gene List] [Search Product List]

 
     
 

1.Introduction

Primary description of our plant alternative splicing database website.

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2. Browse

(1)    Species List

List the species name and corresponding gene number we have found currently which have alternative splicing isforms.

Figure 1. Species list of plant alternative splicing database. species name and corresponding gene number is noted. Detailed gene information list is available by linkage on gene name.

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(2)    Gene List

We are listing the gene detailed information of which we have found currently have alternative splicing isforms.


Figure 2
. Gene list of plant alternative splicing database. Gene name, species, gene length, exon number, intron number, as number ,as type and related publication on NCBI are noted.
Classification of Alternative Splicing Types
We classify alternative splicing forms into seven types: (I) retained intron; (II) alternative donor site; (III) alternative acceptor site; (IV) exon skip; (V) mutually exclusive exons; (VI) alternative initiation site; and (VII) alternative termination site.
The former five AS types are shown in the figure below. If two gene products are different at the start position on genome, they will be considered as type VI, and if they are different at the termination site, they will be type VII.
All the AS types of a gene are listed in the database joint with '+'. If there are not enough evidences to confirm the AS type, we will list the potential AS types like 'IV/V' or just fill with 'unclear'.

Five models of alternative splicing types.

         We provide you with detail list of alternative splicing product with list and graph. Here is an example of spliced product of gene named "succinate dehydrogenase iron-protein subunit".

Figure 3. Spliced product of gene named "succinate dehydrogenase iron-protein subunit". Blue line indicates exon while red dot line indicates intron. Gene and spliced product structure is shown with alignment graphic view. Mouse over intron or exon will show you the start and end base pair.

Allow filter out genes with species name.

Figure 4.  Filter out genes with species name.

         Allow set gene number displayed one page.

Figure 5. Set record number displayed on page.

         Allow order genes list order by special fields incrementally or descendingly.

Figure 6. Example of gene list order by gene name incrementally.

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(3)    Product List

We are listing the spliced product detailed information.

Figure 7. Alternative splicing product list. Product name, gene name, species are noted on the list. Related publication reference is provided the same. Corresponding sequence with fasta file can be obtained.

Allow filter out product list with species name.

Figure 8. Filter out alternative splicing products with species name.

       Allow order spliced product list order by special fields incrementally or descendingly.

Figure 9.  Example of spliced product list order by product name descendingly.

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(4)    Catalogues

We match the plant genes, which have been proved to be alternative spliced, with GO database provided by Gene Ontology Consortium (http://www.geneontology.org/).

Figure 10.  Matched plant alternative spliced genes with Biological Process, one branch of GO database.

Figure 11.  Matched plant alternative spliced genes with Molecular Function, one branch of GO database.

Figure 12.  Grouped plant alternative spliced genes by taxonomy. The number follows species name indicates the total number of plant alternative splicing genes found in this species. Detailed genes information is available by clicking species name.

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3.         Search

We provide you with powerful search engine.

You may search gene in our plant alternative splicing database by given key words: gene name or alias, gene accession number on NCBI, organism, exon or intron number, spliced product number, tissue, author and publication date. After submission, you will get a detailed gene information list if hits.

Figure 13.  Search genes in our plant alternative spliced database.

Search result with matched organism in gene list:

Figure 14.  Search result with organism as "Oryza".

Another search strategy is applied for spliced product. With suitable product name, protein accession number on NCBI, mRNA accession number on NCBI, accession number on Swissprot, splice type, splicing factor and gene name, it can hit what you want.

Figure 15.  Search spliced product in our plant alternative splicing database.

Search result with matched product name in spliced product list:

Figure 16.  Search result with product name as "switch".

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Created by Hangzhou Genomics Institute,2002
Maintained by Chinese National Human Genome Center at Shanghai
Webmaster: pasdb@chgc.sh.cn