Gramene Release 14.0
Molly Fogleman
mam94 at cornell.edu
Wed Aug 11 16:10:12 EDT 2004
Dear Cereal Researchers,
The Gramene database (http://www.gramene.org) emails its registered users
an announcement each time a new release is made. The announcement
includes information on new or updated data and software.
Sincerely,
The Gramene Database
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Gramene website features:
*********************
-New organization of the Site Map, including addition of a ¡§How to Use
Gramene¡¨ link. This new page provides links to all existing tutorials
for each of the main search modules. We advise our users to browse
through the help pages, the existing browsable tutorials and the
downloadable tutorials and exercises that were developed in early 2004
before starting. These demonstrations can be located by visiting the
¡§How to Use Gramene¡¨ link.
-A link to download Gramene¡¦s newly developed brochure has also been
added to the Site Map under ¡§About Gramene.¡¨
Databases:
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QTL (updated)
************
We are pleased to announce an update of the Gramene QTL Database. Release
1.2 includes entries on 7,389 QTLs for rice, maize, barley, oat, and wild
rice, curated from public references. The current version provides core
information for QTLs, including published symbols, traits, linkage groups,
map positions, and associated reference(s). Users can search QTLs via
trait name, trait symbol, trait category, published QTL symbol, linkage
group, and species by using the Gramene QTL Search.
Genome Browser (updated)
**********************
The Genome Browser now contains the TIGR Assembly Release #2. Three new
tracks have been added: Swissprot_Trembl_Proteins,
Rice_Brachyantha_BACend, and Sugarcane_est.
BLAST
******
Two new BLAST databases have been added: Sugarcane_EST and
Rice_Brachyantha_BACend.
CMap (updated)
*************
Newly curated or updated QTL maps:
Accession id Mapset Name
rgp2000a JRGP Nipponbare/Kasalath RFLP 2000
liz1995a TAMU Lemont/Teqing RI RFLP QTL 1995
shl1998a IGCN ZhaiYeQing 8/JingXi 17 1998
raj2003a IRRI IR64/Azucena DH RFLP QTL 2003
zhj2002a CNRRI Zhenshan97 B/Milyang 46 RI QTL 2002
anv2003a UCD M-202/IR50 RI SSR QTL 2003
fuk2003a IRRI Milyang23/Akihikari RI RFLP QTL 2003
tsh1996a TKU Asominori/IR24 RI RFLP QTL 1996
mac2000a OSU Harrington/Morex DH RFLP QTL 2000
odl1995a Cornell Kanota/Ogle RI RFLP QTL 1995
lad1995a Cornell Igri/Triumph DH RFLP QTL 1995
pra1997a UKUW Bala/Azucena F2 QTL 1997
lih1997a CNHZAU 3037/2428//3037 BC1F1 RFLP QTL 1997
lih1997b CNHZAU 3037/2428 F2 RFLP QTL 1997
zhj1997a CNRRI Tesanai2/CB F2 RFLP QTL 1997
ros2003a IRRI IR62266-42-6-2/IR60080-46A BCL RFLP/SSR QTL 2003
tag2004a CNWHU B5/Minghui63 RIL RFLP QTL 2004
see2003a Cornell IR64/IRGC105491 (O. rufipogon) BC2F2 SSR/RFLP QTL
2003
jig2004a CNHZAU Zhenshan97/Wuyujing2 DH SSR QTL 2004
zhb2003a CNZU IR1552/Azucena RI QTL 2003
lih2004a CNSIPPE Nona Bokra/Koshihikari F2 RFLP QTL 2004
wag1994a IRRI Moroberekan/CO39 RI RFLP QTL 1994
ree1998a UCD Labelle/Black Gora F2 RFLP QTL 1998
yunxu1995a IGCAS ZYQ8/JX17 F2 QTL 1995
wup1995a IRRI Pal/IR42 F2 QTL 1995
linhx1996b CNRRI Wai/CB QTL 1996
xiaoj1996a Cornell 9024/LH422 RI QTL 1996
xuk1996a UCD IR40931/PI543851 F3 QTL
Updated Maps:
Rice-Gramene Tos17 Insertion Map 04 replaces
„X Rice-Gramene Tos17 Insertion Map
„X Rice-Tos17 Insertion Map
Rice-Gramene TIGR Assembly 2004 replaces
„X Rice-Gramene TIGR Assembly 2003
„X Rice-Gramene BAC 2003
Maize-Curated FPC Jan23 2004 replaces
„X Maize-Gramene Curated AGI FPC Jan
„X Maize-Gramene Curated AGI FPC JanII
„X Maize-Gramene Curated AGI FPC JanIII
„X Maize-Gramene Curated FPC03
Maize-AGI FPC JAN23 2004 replaces
„X Maize-AGI FPC Jan 2004
„X Maize-AGI FPC 2003
„X Maize-AGI FPC 2002
Protein (updated)
**************
The Gramene protein database includes 27,454 gene products drawn from
SwissProt (418) and SP-TREMBL (27,036). These proteins are annotated
using Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and
Predotar (plastid, mitochrondrial and secretory pathway targeting) and
Interpro categories. A total of 19,255 gene products are associated with
946 Gene Ontology terms.
Mutant (updated)
**************
The Gramene Mutant genes database contains 1320 genes from rice
characterized by phenotype. Among them, 424 genes have been fully
annotated with phenotypic descriptions, associations to trait, plant and
gene ontologies, map positions, alleles, phenotypic studies, germplasms,
sequences and gene products, and related public references. Other genes in
the database are currently under curation. However, we are providing core
information such as gene name and symbol, phenotypic image(s), map
position, and a cross-reference to Oryzabase. Users can search for the
gene symbol or gene name by using the Gramene Mutant Search.
In this release, we curated and updated nucleotide and protein sequence
information for most of the phenotype-related mutant genes in rice. Also,
we are currently providing GenBank accessions to present nucleotide
sequence information.
Ontology (updated)
****************
Trait Ontology: Updated. Total number of terms = 614.
Includes associations to rice mutants
Gene Ontology: Updated with GO database, go_200406 release
Total number of terms = 17371
A total of 19,255 rice gene products are
associated with 946 Gene Ontology terms.
Plant ontology: Updated. Total number of terms = 750
Contains Cereal Plant Anatomy and growth stage
ontologies
Includes associations to rice mutants
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Molly Fogleman
Gramene Outreach Coordinator
G-15 Bradfield Hall
Cornell University
Ithaca, NY 14853
(607) 255-3103
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