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[User's Guide] [AS Lists] [Text Info] [All Seq Info] [Hyperlinks] [Related db]
The above figure is a sample of all the hyperlinks provided in the header of "AS Lists" and "All Seq Info", except that in the "AS Lists" page the "Summary" hyperlink is replaced by "Details". The "Details", "Summary" and "Text" links are explained in "All Seq Info", "AS Lists" and "Text Info" respectively.
The "dbSNP" button will use the accession number of reference sequence to query single nucleotide polymorphism database at NCBI, so the users can examine the role of single nucleotide polymorphism on alternative splicing. The "SAGE" button will use the UniGene cluster number to query serial analysis of gene expression (SAGE) database at NCBI, so the qualitative level of gene expression can be estimated. If the reference sequence is a disease gene, relevant information in Online Mandelian Inheritance in Man (OMIM) can be retrieved by pressing the "OMIM" button. These related web sites would help the users to compare AS information of reference sequence to other types of information easily.
The "Ensembl" and "GeneCards" buttons will use the accession number to query Ensembl and GeneCards databases, respectively. The former will be useful to look for genome organization information of the reference sequence. The latter will connect to the GeneCards database that integrates human genes, their products and their involvement in diseases.
If you are investigating a mouse gene, then the hyperlink to GeneCards database will automatically hide because there is no mouse gene information in GeneCards database.
The iProClass button will retrieve the protein sequence encoded by this reference sequence and paste it into a new window, so you can then submit it to iProClass to look for proteins in the same superfamily. The "InterPro" button will assist users to search InterPro to look for motif and domain information on this gene product. The "CDD" and "DART" buttons will help users to submit protein sequence to NCBI's Conserved Domain Database (CDD) and Domain Architecture Retrieval Tool (DART), resepctively. The former tool has similar function to InterPro and the latter tool will list all the proteins that have similar domain architecture to the given protein sequence. By comparing the search results of these three motif or domain analysis tools with alternative splicing information, the effect of alternative splicing on protein motifs / domains will be revealed.
We used the homologs information in NCBI LocusLink to link the mouse homologs to human genes and vise versa. As the fast accumulation of mouse data (both the genomic sequences and EST sequences), it is becoming more and more exciting in comparing the differences between human and mouse studies.
The variations in the putative AS patterns between organisms is interesting. The complexity in physiology may be explained in part by those pattern variations. Besides, the sources of mouse and human EST are quite different. In human, about 45% of EST (UniGene Human Build #138, 2001/08) are derived from cancerous tissues. By contrast, about 90% of mouse EST (UniGene Mouse Build#93, 2001/08) are from normal tissues. Moreover, there are many mouse EST libraries are of embryos. As the ethical issues are concerned, we cannot directly use human embryos to perform experiments. On the contrary, many mouse EST libraries are derived from embryos. Consequently, putative AS sites derived from mouse EST sequences may be considered an invaluable information resource.
In some cases, there is no homologous gene to this gene you are investigating. The hyperlink "Homologs" will automatically hide to avoid confusing.
NCBI LocusLink provides us the homologous gene by performing the comparison in a stringent way. In most cases, NCBI LocusLink provides us one mouse gene best homologous to one human gene. However, it is common that more than one mouse gene are very similar to a human gene. The situation is also true to the case of looking up human genes similar to a mouse gene. Besides, sometimes the NCBI LocusLink fails to provide us the homolog information between human and mouse genes. We used the information from NCBI HomoloGene database to compensate the limitation of NCBI LocusLink. The HomoloGene database provides us the homologs between several organisms by sequence similarities. By the using similar gene lists in NCBI HomoloGene, we provides the hyperlink to the AS information of the similar genes in other organisms. In the following figure, there are three similar genes to the human FOS gene. One is from the annotation of MGI and the final two are also quite similar to the Fos gene (91.49% and 91.42% identities). Users can follow the hyperlinks to view the AS information of these similar mouse genes in PALS db.
