Browse Element(s) Details


OsAffx.19953.5.S1_x_at

Description gb:AK059850.1
DB_XREF= gi:32969868
TID=OsAffx.19953.5
CNT=1
FEA=FLmRNA
TIER=FL
STK=1
NOTE=sequence(s) not in UniGene
DEF=Oryza sativa (japonica cultivar-group) cDNA clone:006-206-G02, full insert sequence.
FL= gb:AK059850.1
REP_ORG=O. sativa
Associated TIGR Gene Locus
TIGR LocusMatching ProbesDescription
LOC_Os05g4090011/11expressed protein
LOC_Os01g339604/11transposon protein, putative, CACTA, En/Spm sub-class
LOC_Os03g289604/11DNA-directed RNA polymerase III 130 kDa polypeptide, putative, expressed
Gene Context (flanking 25kb)
TIGR LocusMatching ProbesetMatching ProbesChrStrandCoordinatesDescription
LOC_Os05g40870NANA5+23882697..23888339retrotransposon protein, putative, unclassified
LOC_Os05g40880OsAffx.27266.1.S1_at10/115+23891210..23892247hypothetical protein
LOC_Os05g40880OsAffx.20993.1.S1_at1/115+23891210..23892247hypothetical protein
LOC_Os05g40890Os.10823.1.S1_x_at11/115+23895371..23896542expressed protein
LOC_Os05g40890Os.10823.2.S1_at11/115+23895371..23896542expressed protein
LOC_Os05g40900Os.26497.1.S1_at11/115+23907303..23911230expressed protein
LOC_Os05g40900OsAffx.4583.1.S1_s_at11/115+23907303..23911230expressed protein
LOC_Os05g40900OsAffx.19953.4.S1_s_at11/115+23907303..23911230expressed protein
LOC_Os05g40900OsAffx.19953.5.S1_x_at11/115+23907303..23911230expressed protein
LOC_Os05g40910Os.51274.1.S1_at9/115+23912941..23914408expressed protein
LOC_Os05g40920Os.56288.1.S1_at11/115+23917060..23919400expressed protein
LOC_Os05g40930NANA5+23923527..23924994retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os05g40940OsAffx.25819.2.S1_at11/115+23925218..23927091hypothetical protein
LOC_Os05g40940OsAffx.25819.3.S1_at3/115+23925218..23927091hypothetical protein
LOC_Os05g40940OsAffx.25819.1.S1_at1/115+23925218..23927091hypothetical protein
LOC_Os05g40940OsAffx.13875.1.S1_at1/115+23925218..23927091hypothetical protein
LOC_Os05g40950Os.56225.1.S1_at11/115+23930253..23931294expressed protein
LOC_Os05g40960OsAffx.27267.1.S1_at11/115+23932212..23934242myb-like DNA-binding domain, SHAQKYF class family protein, expressed

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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
OsAffx.19953.5.S1_x_at--1015--6191Chr05:23909652..23909676 (25 bp)
GATGGAACCACTCGGTGTGGCCAAA
LOC_Os05g40900
OsAffx.19953.5.S1_x_at--1072--1311Chr05:23909415..23909631 (25 bp)
AGAGGCTGTTGTGCAGGTCTTTGAA
LOC_Os05g40900
OsAffx.19953.5.S1_x_at--1155--411Chr05:23908258..23908282 (25 bp)
ATCTTTGAACAACGAAGCACGCCCG
LOC_Os05g40900
OsAffx.19953.5.S1_x_at--285--7474Chr12:20642643..20642667 (25 bp)
GTGTGCGTCTTTCACGACATGCTCT
NONE
OsAffx.19953.5.S1_x_at--748--3634Chr01:7301249..7301273 (25 bp)
CTTCCTGTGGTCTTCTAGCGTTAGA
NONE
OsAffx.19953.5.S1_x_at--609--10453Chr12:20642586..20642610 (25 bp)
TTAGAAGAAGTCGTGTCCGTCCCGG
NONE
OsAffx.19953.5.S1_x_at--80--5415Chr01:7301344..7301368 (25 bp)
GAACCCATTCGGTGACTTTCGCGGT
NONE
OsAffx.19953.5.S1_x_at--1116--5436Chr03:16379063..16379087 (25 bp)
GAACCGACTTGGATCTGAACTACGA
LOC_Os03g28960
OsAffx.19953.5.S1_x_at--219--5617Chr03:16379106..16379130 (25 bp)
GAAATTGGATTTCCTTTTCGTGCCA
LOC_Os03g28960
OsAffx.19953.5.S1_x_at--252--10318Chr11:10206550..10206574 (25 bp)
TTTCGTGCCATATGTCGCTTAGACT
NONE
OsAffx.19953.5.S1_x_at--1129--8696Chr12:13345500..13345524 (25 bp)
TGTCCTTTCCTCTATTTGTTCGATA
NONE
Target Sequence 
GATGGAACCACTCGGTGTGGCCAAATTCTGGAAGTTGATGGTGAAAGAGGCTGTTGTGCAGGTCTTTGAAGACACTTCAG
GAGTGGACAACAAATACACCATTGTGCAATTCACAGTACAAGGGTGGTGCAGCTGAGGGTGGCAGAAGACCAATCATCTG
GAACATCTTTGAACAACGAAGCACGCCCGCCCCGTGTGCGTCTTTCACGACATGCTCTGGTCCCGGGTTTCTTCCTGTGG
TCTTCTAGCGTTAGAAGAAGTCGTGTCCGTCCCGGACATCTGCAACGTCCTCTCACGCCTTTTTTTGGGGGGACAAACAA
AGATCAGGAAAAGACGGACCGAACCCATTCGGTGACTTTCGCGGTTGCCCTCACTGAACCGACTTGGATCTGAACTACGA
TTCAGATCAAGTCTTACCGAAATTGGATTTCCTTTTCGTGCCATATGTCGCTTAGACTTTACTTTTTCCCCTTTCTGTCC
TTTCCTCTATTTGTTCGATA

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 OsAffx.19953.5.S1_x_at     

Putative homologies in rice

Putative homologies in arabidopsis