Browse Element(s) Details


Os.54855.1.S1_at

Description gb:AK106914.1
DB_XREF= gi:32992123
TID=Os.54855.1
CNT=1
FEA=FLmRNA
TIER=FL
STK=1
UG=Os.54855 (NCBI UniGene Cluster)
UG_TITLE=(japonica cultivar-group) cDNA clone:002-119-A10, full insert sequence
DEF=Oryza sativa (japonica cultivar-group) cDNA clone:002-119-A10, full insert sequence.
FL= gb:AK106914.1
REP_ORG=O. sativa
Associated TIGR Gene Locus
TIGR LocusMatching ProbesDescription
LOC_Os08g0748011/11DNA-directed RNA polymerase, beta subunit family protein, expressed
LOC_Os09g269701/11retrotransposon protein, putative, Ty1-copia subclass, expressed
Gene Context (flanking 25kb)
TIGR LocusMatching ProbesetMatching ProbesChrStrandCoordinatesDescription
LOC_Os08g07420NANA8+4157400..4163555retrotransposon protein, putative, unclassified
LOC_Os08g07430Os.53189.1.S1_at11/118+4165918..4169212expressed protein
LOC_Os08g07440Os.25571.1.S1_at11/118+4169528..4172195Protein BABY BOOM 2, putative, expressed
LOC_Os08g07440Os.10323.1.S1_at11/118+4169528..4172195Protein BABY BOOM 2, putative, expressed
LOC_Os08g07450OsAffx.29079.1.S1_at11/118+4173245..4174195Glutaredoxin family protein
LOC_Os08g07460NANA8+4177780..4180707transposon protein, putative, unclassified
LOC_Os08g07470NANA8+4183160..4183896hypothetical protein
LOC_Os08g07480Os.54855.1.S1_at11/118+4185262..4194621DNA-directed RNA polymerase, beta subunit family protein, expressed
LOC_Os08g07480OsAffx.29080.1.S1_x_at10/118+4185262..4194621DNA-directed RNA polymerase, beta subunit family protein, expressed
LOC_Os08g07490OsAffx.16877.1.S1_at8/118+4200074..4201570expressed protein
LOC_Os08g07500Os.49673.1.S1_at11/118+4205114..4206570uncharacterized plant-specific domain TIGR01570 family protein, expressed
LOC_Os08g07510NANA8+4210715..4211149hypothetical protein
LOC_Os08g07520OsAffx.16878.1.S1_at11/118+4213705..4214067hypothetical protein

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Gene Ontology Classification
GO idTypeName
GO:0006306biological_processDNA methylation
GO:0006350biological_processtranscription
GO:0030422biological_processRNA interference, production of siRNA
GO:0031047biological_processRNA-mediated gene silencing
GO:0035194biological_processRNA-mediated posttranscriptional gene silencing
GO:0005634cellular_componentnucleus
GO:0005720cellular_componentnuclear heterochromatin
GO:0016591cellular_componentDNA-directed RNA polymerase II, holoenzyme
GO:0030880cellular_componentRNA polymerase complex
GO:0003677molecular_functionDNA binding
GO:0003899molecular_functionDNA-directed RNA polymerase activity
Probe Info
Probe NameHit(s)LocationSequenceTIGR Locus
Os.54855.1.S1_at--800--1771Chr08:4185524..4185548 (25 bp)
ACCGAGCTCATCTAGAGTAGACTCT
LOC_Os08g07480
Os.54855.1.S1_at--599--1151Chr08:4185509..4185533 (25 bp)
AGTAGACTCTCAGCTTTGGACGGGA
LOC_Os08g07480
Os.54855.1.S1_at--257--3771Chr08:4185503..4185527 (25 bp)
CTCTCAGCTTTGGACGGGAAACATC
LOC_Os08g07480
Os.54855.1.S1_at--1029--7611Chr08:4185488..4185512 (25 bp)
GGGAAACATCATGATTTATTCTTTT
LOC_Os08g07480
Os.54855.1.S1_at--915--951Chr08:4185425..4185449 (25 bp)
AGGACATTTTAGTCTGGTGAGGAGA
LOC_Os08g07480
Os.54855.1.S1_at--1000--6011Chr08:4185404..4185428 (25 bp)
GAGAGTTGACAATTTACTCCATTCA
LOC_Os08g07480
Os.54855.1.S1_at--668--351Chr08:4185370..4185394 (25 bp)
ATAAGACGCTTTGGATTTGTCGTAA
LOC_Os08g07480
Os.54855.1.S1_at--73--7951Chr08:4185358..4185382 (25 bp)
GGATTTGTCGTAATAAGTCTCTTGA
LOC_Os08g07480
Os.54855.1.S1_at--1005--9811Chr08:4185326..4185350 (25 bp)
TAAAACCTGTATTGGGATATTATCC
LOC_Os08g07480
Os.54855.1.S1_at--828--7599Chr11:5234661..5234770 (25 bp)
GGGCAATTGTGTTCTTACCCCTACT
NONE
Os.54855.1.S1_at--219--3672Chr06:18819351..18819375 (25 bp)
CTTACCCCTACTTTCATATCTAATT
NONE
Target Sequence 
ACCGAGCTCATCTAGAGTAGACTCTCAGCTTTGGACGGGAAACATCATGATTTATTCTTTTAAAAATGGGATTTTTATCA
TTTTTTAAGAACATTTTTAAGGACATTTTAGTCTGGTGAGGAGAGTTGACAATTTACTCCATTCATTTTATATTATAAGA
CGCTTTGGATTTGTCGTAATAAGTCTCTTGAATGTCATTAAAACCTGTATTGGGATATTATCCAATTGGGGCAATTGTGT
TCTTACCCCTACTTTCATATCTAATT

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.54855.1.S1_at     

Putative homologies in rice

Putative homologies in arabidopsis