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Gramene v.19
Welcome to the Gene
and Allele Database Tutorial
This tutorial will describe how to navigate the
section of Gramene that provides
descriptions of alleles associated with
morphological, developmental, and
agronomically important phenotypes and
variants of physiological characters,
biochemical functions and isozymes.
Many genes in Gramene also have map
positions and sequencing data.
e
a
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c
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Gene
Gramene ID
Alphabetical Browse
M
a
p
Gene Symbol
Term Search
Chromosome
Synonym
Phenotypic
Description
Literature
General
Information
Gene Name
References
Phenotypic
Image
Allele Summary
Allele and
Germplasm
Olryzabase
Phenotypic
Description
Study Name
Study Info
Study Type
Study location
Study year
Allelic Interaction
Germplasm Summary
Wildtype
Location
Allele Description
Germplasm
Accession
Mutagen
Mutants studied
Study references
Allele symbol
Study Season
NCBI
Map and Sequence
GenBank Accession
Protein
Database
Mutagenesis Method
Gene Product
Map Set Name
Associated Features
Map Position
Linkage Group
Start position
Trait
Anatomy location
Evidence code
Developmental stage
Ontology
Stop position
Tutorial Help
The hand icon indicates a link that
allows you to go to the same page
in your web browser.
If you are viewing this tutorial with Adobe
Acrobat Reader, click the "bookmarks"
on the left hand side of the Reader for
easier navigation.
Action Options are noted in this type of
font.
Notes or comments use this style font.
Gramene Home Page
Click here to open
gene search
Gene & Allele Database Home Page
Click here to open
search page
Step one: Search Genes
4 methods
1. Type either a gene symbol, a gene
name, a Gramene Association or a
keyword. Entering “%” will result in
displaying the entire gene list.
1a. Click “Search” to view the gene detail page
OR
2a. Click “alphabetical order” to
view the entire gene list.
2b. Or select the letter of the desired
subset (such as “D” for dwarf.)
3. Click to browse genes by searching
for a trait in the Ontology Database
4. Click to browse genes by searching
literature citations in the Literature Database
Step Two: Results for Gene Search by Term / Key word
There are 82 entries for “dwarf”,
with 25 entries per page
2. Click on a gene name to view the
detail page for that particular gene.
1. Click to view next page of
results as needed.
Step Two: Results of Gene Search for Alphabetical Search “D”
1. Click on a column title to
sort results by that column.
2. Click on a gene name to view the detail
page for that particular gene.
3. You may wish to select a letter
to view another subset list (such as
“S” for semi-dwarf.)
Step three: Gene Detail Page
General Info for Gene
Select desired detailed info
from menu and click.
Click a thumbnail to
enlarge image.
Step three: Gene Detail Page
Allele and Germplasm
Click to view summary of allele.
Click to view
summary of the
germplasm
Step three: Gene Detail Page
Allele and Germplasm
View of Allele Summary Page
Select for more detailed
information on the
referenced study.
Select to return to gene
detail page.
Step three: Gene Detail Page
Allele and Germplasm
View of Allele Study Page
Select to view related references.
Select for detailed information on
other genes in the study.
Step three: Gene Detail Page
Allele and Germplasm
View of Germplasm Summary Page
Select to return to gene
detail page.
Step three: Gene Detail Page
Map and Sequence Info
Click to view the nucleotide sequence link for
each from the National Center for
Biotechnology Information.
Select to view more information from
Gramene’s Protein database (See
Protein tutorial).
Select to view the gene displayed in CMap (See
CMap tutorial).
Step three: Gene Detail Page
Associated Features
Click to sort by Trait
ontology
Click to sort by
Developmental Stage
Click to go to the Trait Ontology
Database within Gramene (See
Ontology tutorial).
Click to go to the Plant Ontology
Database within Gramene. (See
Ontology tutorial).
Step three: Gene Detail Page
References
Click to view Oryzabase’s
information on the selected gene.
Click to go to the related reference in
Gramene Literature database (See
Literature tutorial).
How to Submit Newly Identified Genes
Contact Gramene
Use the feedback button, located at the top of every page, to
provide feedback or to ask questions about Gramene.
or
Email Gramene at [email protected]