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Gene Query Documentation

Any combination of fields may be entered to specify the desired query conditions.

Field Name Field Description
Data Source: Select one of four options for the origin of the data; the options are "mitochondrial", "chloroplast", "bacterial" or "all". Default value is "all".
Show Oversampled Data: In cases where GenBank contains more than five copies of the same gene from the same organism, we in GOBASE select the five most divergent copies as type examples. Selecting "Yes" here will display all the copies of these genes; selecting "No" shows type examples only. Default value is "No".
Gene Name: Enter the gene name here. Accepts * as an initial or terminal wildcard. A link is provided to a list of all gene and product names currently contained in GOBASE.
Product Type: Select one of five options for the type of gene product sought; the options are ribosomal RNA, transfer RNA, other RNA, protein or all. Default value is all.
Product Name: Select the name of the desired gene product from a scrolling list.
General Function: Select the name of the desired gene function from a scrolling list.
Ontology: Select a Gene Ontology ID or term related to the genes of interest. Only one of these fields can be filled at any given time.
Taxon Name: Enter the taxon name here. Accepts * as an initial or terminal wildcard.
Taxon Division: Mark any of the boxes to receive results from that subset of taxon divisions; options are Fungi, Metazoa, Plants. Protista, α-proteobacteria, γ-proteobacteria and Cyanobacteria. Default behaviour with no boxes marked is to return data from all taxonomic divisions.
ORF: Select by whether genes are marked as ORFs [ unidentified proteins ]. Default value "not set".
Gene Included in Intron: Select by whether genes are included in introns of another gene. Default value "not set".
Contains Intron: Select by whether genes contain introns. Default value "not set".
Pseudogene: Select pseudogenes. Default value "not set".
Partial Gene: Select partial genes. Default value "not set".
Plasmid Encoded: Select by whether genes are carried on a plasmid. Default value "not set".
Trans-spliced Gene: Select trans-spliced genes. Default value "not set".
Gene Location on Sequence
From: Specify position on sequence after which gene must start.
To: Specify position on sequence before which gene must end.
Segment Number: For genes split up across more than one GenBank entry, specify which segment.
Strand: specify strand on which the gene occurs.
Upstream Genes
Gene Name: Enter name of gene upstream of which to search.
Segment Number: For genes split up across more than one GenBank entry, specify which segment.
Strand: specify strand on which the gene occurs.
Downstream Genes
Gene Name: Enter name of gene downstream of which to search.
Segment Number: For genes split up across more than one GenBank entry, specify which segment.
Strand: Specify strand on which the gene occurs.
Database-related Specifications
NCBI Entrez GI: Specify an NCBI "gi" identifier.
GenBank Accession: Specify a GenBank accession number.
GOBASE Feature ID: Specify a GOBASE feature ID for the desired gene.
GOBASE Sequence ID: Specify a GOBASE sequence ID for the sequence containing the desired genes.
Sort Results by: Specify the order in which the results will be sorted; options are by gene name or species name.


© 2010 Department of Biochemistry, Universite de Montreal
gobase@bch.umontreal.ca