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Using the Gene Search

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The TAIR Gene Search window provides three ways of searching for a gene: simple search by name only, feature search using more limits, and search by position. These are offered in three distinct sections of the window.

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This simple search is case insensitive and allows wildcard searching (see "Using Wildcards").

Search by Name, Description,

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UniProt ID

Use this drop down menu to search either by gene name, description or GenBank Accession., phenotype or UniProt ID or TAIR locus ID and TAIR accession. You can choose exact, contains or start with search for names, descriptions and phenotypes. Identifier searches are

exact matches.

Name types

In TAIR, there are four types of names associated with a Gene. Searching by name will search all gene names and gene aliases. For more information about the name types see below:

• Symbol

  This is the mnemonic naming used for gene names by researchers. Examples include AG (Agamous), and QRT1 (Quartet1). A symbol for a gene is designated when a gene has been published or if the name and symbol have been registered at Oklahoma State, currently maintained by David Meinke's group or in GenBank.(http://mutant.lse.okstate.edu/genepage/genepage.html).

• ORF name

  An open reading frame (ORF) name from the Arabidopsis Genome Initiative (AGI) groups' annotations. Usually, the convention for naming an ORF in Arabidopsis has been using the clone name followed by a number suffix (e.g., F23H14.13). For chromosome arms that have been completely sequenced, a standard ORF name designation is used:

  • AT (Arabidopsis thaliana)
  • 2 (chromosome number)
  • G (for Gene)
  • 01130 (Number)

    Examples: At2g01130, AT4g00010

• Full name

  The full descriptive name of a gene.Examples: Agamous, Aspartate aminotransferase deficient 3

• Gene product name

  Name of a gene product.Examples: ASPARTATE AMINOTRANSFERASE, CYTOPLASMIC ISOZYME 1, CHALCONE SYNTHASE.For the genes that do not have a full name or symbol (largely the predicted genes (ORFs) from AGI sequencing and annotation), the following product names have been used:

  • Hypothetical protein

    Gene models without any database matches.

  • Unknown protein

    Gene models with only EST matches.

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Search by Gene List and Bulk Downloads

Users can now search in bulk and upload a list of AGI Locus identifiers.  This feature can also be used as a starting point for bulk downloading of data (see YouTube Tutorial ).

1. Paste or upload a list of AGI  identifiers (one ID per row)
2. Apply any additional search parameters to the gene list or click submit
3.  On the results screen at the top will be a number of options for retrieving data for all or a subset of the results
   1. Get GO annotations- retrieve Gene Ontology annotations 
   2. Get PO annotations-retrieve Plant Ontology annotations
   3. Get Sequences-retrieve FASTA formatted sequences 
   4. Get Gene Descriptions- retrieves gene summaries and aliases
   5. Get Locus  History- retrieves history of loci such as create date, merges , deletes etc.
   6. Get Microarray Elements- retrieves corresponding microarray element IDs 

Search by Keyword

This option allows you to search for genes by keywords.Genes are annotated with keywords describing molecular function,subcellular localization and biological process with controlled vocabularies from the Gene Ontology Consortium. Genes are also annotated with controlled vocabulary terms for plant structures and developmental stages for describing phenotypes and where and when the genes are expressed. Plant structure and development terms are from the Plant Ontology Consortium. Each annotation is associated to an evidence code and one or more reference (the source of the evidence for the annotation).

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