It allows browsesearch the rice, maize and Arabidopsis genomes and mapped features such as marker ge

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The Gramene Database A Comparative Genomics
Resource for Grasses Pankaj Jaiswal (A), Doreen
Ware (B) (D),  Junjian Ni(A), Immanuel Yap (A),
Liya Ren (B), Ken Youens-Clark (B),
William Spooner (B), Kiran Ratnapu (B), 
Chengzhi Liang (B), Molly Fogleman (A), Claire
E. Hebbard (A), Terry M Casstevens (C), 
Edward S Buckler (C) (D), Lincoln Stein (B),
Susan R McCouch (A) (A) Department of
Department of Plant Breeding, 240 Emerson Hall,
Cornell University, Ithaca, NY, 14853, USA, (B)
Cold Spring Harbor Laboratory, 1 Bungtown Rd,
Cold Spring Harbor, NY 11724, USA, (C)
Institute for Genomic Diversity, Cornell
University, Ithaca, NY 14853, (D) USDA-ARS,
Cornell University, Ithaca NY 14853 USA
gramene_at_gramene.org
Web site www.gramene.org
Outreach and Education
Feedback button allows users to give feedback,
comments, suggestions and ask questions to the
Gramene developers.
Site map presents a guide to the entire database.
Navigation bar on the top of the page allows a
quick link to the respective database searches.
Gramene Tip provides useful information on how to
use Gramene
Species pages provide useful information for
everyone
Quick search or on top of every web page, with
options to limit your search.
Whats new provides news and announcements
GENOME BROWSER
MAPS
SYNTENY
It allows browse/search the rice, maize and
Arabidopsis genomes and mapped features such as
marker /gene/clone/CDS/cDNA/ESTs from major
cereal crops mapped on the rice genome and
examine their neighborhood. Users can find the
gene model of candidate gene(s), their molecular
function and putative orthologs from Arabidopsis.
CMap allows the viewing of various types of maps
from different species and constructs comparisons
between them. Users can view mapped genes,
markers, QTL and clones and can derive the
synteny.
Colinearity between rice and maize genomes shows
putative regions of synteny
Orthologs from rice and Arabidopsis genomes
QTL
Synteny
Maps
Markers
Genomes
GENES
Genes
Literature
Proteins
Ontology Function / Expression / Trait
QTL
ONTOLOGY
The QTL database allows for viewing which trait
is associated with a QTL of interest and finding
where it is located on a map, while constructing
comparisons with other maps.
Ontology (controlled vocabulary), allows you to
find the favorite, genes, proteins and QTL
associated to molecular function, role in a
biological pathway/process, location in a
cellular structure and phenotype traits.
The derivation section allows you to find the
associations to a more generic parent term or
precisely to a children term.
Gramene helps you find candidate genes,
orthologs, gene functions, syntenic regions,
phenotype, and much more !
The Gene database provides information on name of
the gene, its symbol, and related phenotypes
(traits), images, expression in plant structures
and growth stages, associated nucleotide and
protein sequences, mapped locus on the genome,
curated literature citations and cross references
to other databases such as Oryzabase.
Associated genes, proteins and QTL to the
described trait (TO) or Molecular function (GO)
terms.
PROTEINS
FUTURE DIRECTIONS

• Diversity Module to include germplasm, pedigree,
  phenotype and allelic diversity.
• Genes and QTL from other grass species.
• Pathway database.
• Add advanced search interfaces.
• Off-site curation tools, to help the users submit
  their data.
• Species specific pages.
• Organization of user workshops.

The Protein database can be used to research the
molecular function, biological process and
cellular location of a particular rice protein,
find its sequence information, orthologs from
other species, find which proteins are members of
the same protein family (Pfam) and share PROSITE
domains. You can determine the name of the gene,
its symbol, and related phenotype by visiting
the link to Gramene's gene database.