Browse Element(s) Details


Os.3409.1.S1_at

Description gb:AB007501.1
DB_XREF= gi:2463564
TID=Os.3409.1
CNT=11
FEA=FLmRNA
TIER=FL
STK=3
UG=Os.3409 (NCBI UniGene Cluster)
DEF=Oryza sativa (japonica cultivar-group) mRNA for squalene synthase, complete cds.
PROD=squalene synthase
FL= gb:AB007501.1
REP_ORG=O. sativa
Associated TIGR Gene Locus
TIGR LocusMatching ProbesDescription
LOC_Os03g5904011/11Squalene synthetase, putative, expressed
Gene Context (flanking 25kb)
TIGR LocusMatching ProbesetMatching ProbesChrStrandCoordinatesDescription
LOC_Os03g58970Os.46759.1.S1_at11/113+33518427..33524163expressed protein
LOC_Os03g58970Os.19308.1.S1_x_at11/113+33518427..33524163expressed protein
LOC_Os03g58980Os.2219.1.S1_at11/113+33525399..33526254Germin-like protein subfamily T member 1 precursor, putative, expressed
LOC_Os03g58990OsAffx.13545.1.S1_at11/113+33527651..33528340Cupin family protein
LOC_Os03g59010OsAffx.13545.1.S1_at2/113+33530129..33530806Germin-like protein subfamily T member 1 precursor, putative
LOC_Os03g59010Os.2219.1.S1_at1/113+33530129..33530806Germin-like protein subfamily T member 1 precursor, putative
LOC_Os03g59020Os.20293.1.S1_at10/113+33531696..33537008T-complex protein 1, theta subunit, putative, expressed
LOC_Os03g59030OsAffx.25762.1.S1_x_at11/113+33537989..33539777Glycosyltransferase family 28 N-terminal domain containing protein, expressed
LOC_Os03g59040Os.3409.1.S1_at11/113+33544237..33551375Squalene synthetase, putative, expressed
LOC_Os03g59050Os.12218.1.S1_at11/113+33551445..33556713ATP-dependent RNA helicase An3, putative, expressed
LOC_Os03g59060Os.9183.1.S1_at11/113+33560904..33565466Serine/threonine protein phosphatase PP2A catalytic subunit, putative, expressed
LOC_Os03g59070Os.22413.1.S1_at10/113+33566308..33569219phosphatidic acid phosphatase family protein, putative, expressed
LOC_Os03g59080Os.22872.1.S1_at11/113+33570865..33575781acyl-activating enzyme 18, putative, expressed

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Gene Ontology Classification
GO idTypeName
GO:0016126biological_processsterol biosynthesis
GO:0005789cellular_componentendoplasmic reticulum membrane
GO:0004310molecular_functionfarnesyl-diphosphate farnesyltransferase activity
Probe Info
Probe NameHit(s)LocationSequenceTIGR Locus
Os.3409.1.S1_at--1118--3691Chr03:33550132..33550156 (25 bp)
CTATGAGTTCTCTTCGCTGATAGAA
LOC_Os03g59040
Os.3409.1.S1_at--211--1891Chr03:33550544..33550568 (25 bp)
AATGCTTCCCTAACGCGGAAACGTG
LOC_Os03g59040
Os.3409.1.S1_at--1021--5431Chr03:33550584..33550608 (25 bp)
GAACCTGCAAGTCATCTTGCTCACT
LOC_Os03g59040
Os.3409.1.S1_at--590--5331Chr03:33550714..33550738 (25 bp)
GAAGTCAAAGTACAACTCCATGCTG
LOC_Os03g59040
Os.3409.1.S1_at--847--7531Chr03:33550844..33550868 (25 bp)
GTGGCTATTGTTTTGGGCATGATAT
LOC_Os03g59040
Os.3409.1.S1_at--323--8591Chr03:33550891..33550915 (25 bp)
TGGTCCATTGCCCTCAACTAGACAA
LOC_Os03g59040
Os.3409.1.S1_at--833--2511Chr03:33550906..33550929 (24 bp)
AACTAGACAATCTATGCGCATCAGA
LOC_Os03g59040
Os.3409.1.S1_at--147--3571Chr03:33551031..33551052 (22 bp)
CATCAGATTTCTTATCAGCGCCAAC
LOC_Os03g59040
Os.3409.1.S1_at--147--1671Chr03:33551044..33551068 (25 bp)
AGCGCCAACTCCAAAGCACATGCAG
LOC_Os03g59040
Os.3409.1.S1_at--955--10151Chr03:33551073..33551097 (25 bp)
TATAAGTACTGACTGACTGCAAGAA
LOC_Os03g59040
Os.3409.1.S1_at--935--2811Chr03:33551115..33551139 (25 bp)
AAGTTGGATCTCTTCACCTATCTGT
LOC_Os03g59040
Target Sequence 
CTATGAGTTCTCTTCGCTGATAGAATCGAAGATTGATAATAATGATCCAAATGCTTCCCTAACGCGGAAACGTGTTGATG
CGATAAAGAGAACCTGCAAGTCATCTTGCTCACTAAAGAGAAGGGGATACGATTTGGAGAAGTCAAAGTACAACTCCATG
CTGATAATGGTTGTACTTCTGTTGGTGGCTATTGTTTTGGGCATGATATATGCCAAGTGATTCGTCCTAGGTGGTCCATT
GCCCTCAACTAGACAATCTATGCGCATCAGATTTCTTATCAGCGCCAACTCCAAAGCACATGCAGCAATTATAAGTACTG
ACTGACTGCAAGAATAGACTGTACTTCTATGAAGTTGGATCTCTTCACCTATCTGT

BLASTn GenBank NR

Expression Profiles Gene Chronologer
Gene Chronologer (Grouped)
Heterosis View
Gene Correlator (coexpression analysis)
SALK RiceGE
Rice MPSS  MPSS logo
RiceArray Coexpression Database
Miscellaneous SNP data between Minghui 63 and Zhenshan 97 from OryzaSNP project:
extend bp around Os.3409.1.S1_at     

Putative homologies in rice

Putative homologies in arabidopsis