Accompanying notes to PGene


The database works on the basis of submitting a search which results in a summary listing of entries. Record details are returned when the magnifying glass on the summary listing line is clicked. No report facilities are available at the present time. Individual pages can be printed off in the usual way.

Search Options

The searches have been organised on the basis of users requirements and organised in such a way as to be extracting manageable subsets of entries. This should help maintain good response times over the web.

Four search routines are currently available. The use of Locus for the default search may be reviewed on the basis of feedback from users. For those familiar with pea genetics this should present few problems. A better search for those less familiar would be either the class or sub-class searches. The Phenotype search option performs an ‘approximate string search’ of the phenotype description data eg. the search ‘orange’ would report back records for orange cotyleodns (Orc), orange leaves (Orl) and orange pods (Orp).

*A note on gene symbols*

Gene symbols are in the process of revision. The guidelines for the registration of gene symbols were laid down by Stig Blixt. 1977. The Gene Symbols of Pisum. Pisum Newsletter 9, supplement. Symbols in the database have been revised for consistency and integrity of the database on the basis of a consensus over the use of the hyphen (Murfet, I.C. 1997, Pisum Genetics, vol. 30: 47 and Ellis, T.N. and Ambrose M.J. Pea. Ed. Wood, R. In: Genetic Nomenclature Guide. West Sussex (UK), Elsevier, 1998, S.22-23). Historically hyphens were used between the base symbol and number. Current use of hyphens for morphological characters is restricted to allele designations. Hyphens in extant names have been dropped. For the two genes er-1 and er-2 are now designated er1 and er2.

The use of hyphens in isozyme locus names is used to designate cellular compartmentalisation where appropriate (e.g. -p indicates plastid).

1. Locus - The input of symbols should be on the basis of current symbols.

2. Linkage Group - Revised in accordance to the current consensus map. Pisum Genetics Volume 30, pages 1-4.
3. Class -Gene symbols are assigned to a mutation class on the basis of the initial description of a mutant. In a number of cases further effects of the gene are noted which may be quite different. Searching on class alone does not guarantee that all genes of interested will be selected. An example is the case for bronze leaves brz. The gene was first isolated in a screen for low nodulation with the pleiotrophic effect of bronze spots on leaves. The gene is classified under 6. Root system and would not be picked up on a search on 4. Foliage and emergences.

The list of classes is as follows;


1.      Physiological characters

2.      Seed characters

3.      Shoot system

4.      Foliage and emergences

5.      Chlorophyll mutations

6.      Root system

7.      Flower and generative apparatus

8.      Pods

9.      Complex mutants

10.  Chromosome mutation


 


4. Sub-class - All ten classes are sub-divided to allow for refining of searches. The pick list presents the class description as a header.

Search Coverage

Gene symbols are classified into a series of categories (Valid, Provisional, Invalid, Synonyms, Homonyms, Extinct and Base). The default for all searches is on Valid and Provisional symbols only. By clicking in the box marked Select all genes, the search is extended to include Synonyms, Invalid, Extinct and Base symbols.

*Please note* The Previous gene symbol for Synonyms is the one first published. The Current gene symbol for Synonyms is the Valid symbol. Look through list or do a new search for the Valid symbol record details.

Invalid gene symbols have no Current Valid symbol.

Descriptions

The main description field is being reformatted to remove details referring to interaction, pleiotrophy, complementary and hypostatic actions. Editing of these new fields is still in progress.

Bibliography

References are listed by author and year. The inclusion of references covers three main classes. The first mention of the mutation, the first defining of a gene symbol and the first genetic analysis. It has been an active policy to include further references that provide substantial additional details of a mutation and any gene interactions, the physiological and biochemical basis of the gene and any sequencing work.

Images

Images are stored in two sizes. The first as a thumb nail on the record detail. Clicking on the image will bring up a larger version where they are maintained. Good images that illustrate the characters well will be considered for inclusion.

Genetic Stocks

Information on all lines is presented whether or not the lines have been registered in the John Innes Pisum Collection. Any authors of mutants are urged to consider sending samples of lines appearing in the Gene List to the reference collection. While a number of mutants have been successfully traced in recent years, many have been lost. This is tragic loss and the deposition of a safety duplicate in the reference collection should be considered essential to ensuring that no further losses occur.

Progenitor - New field. The line from which a mutant has been derived. Resulted in the inclusion of progenitor lines as representative lines.

Mutagenic Agent - New field.

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Screen view at start of session

 

 

tl entered into ‘locus/Gene symbol’ box and click on search

 

 

 

 

Click on magnifying glass to expand full record

 

 

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Any enquiries or feedback relating to this application please contact: Mike Ambrose John Innes Centre, Norwich Research Park Colney Lane, Norwich, NR4 7UH. TEL: +01603 450630


Page maintained by Mike Ambrose Genetic Resources Unit Manager (mike.ambrose@BBSRC.AC.UK)