Browse Element(s) Details


OsAffx.20517.1.S1_at

Description gb:NM_187699.1
DB_XREF= gi:34902483
GEN=OJ1743A09.21
TID=OsAffx.20517.1
CNT=1
FEA=mRNA
TIER=ConsEnd
STK=0
NOTE=sequence(s) not in UniGene
DEF=Oryza sativa (japonica cultivar-group) Putative non-LTR retroelement reverse transcriptase (OJ1743A09.21), mRNA.
PROD=Putative non-LTR retroelement reversetranscriptase
REP_ORG=O. sativa
Associated TIGR Gene Locus
TIGR LocusMatching ProbesDescription
LOC_Os03g1231011/11retrotransposon protein, putative, unclassified
LOC_Os06g200902/11non-repetitive/WGA-negative nucleoporin family protein, putative, expressed
Gene Context (flanking 25kb)
TIGR LocusMatching ProbesetMatching ProbesChrStrandCoordinatesDescription
LOC_Os03g12270Os.45954.1.S1_at11/113+6432197..6434699mannitol dehydrogenase, putative, expressed
LOC_Os03g12280NANA3+6435583..6436190hypothetical protein
LOC_Os03g12290Os.12728.1.S1_at11/113+6437026..6441842Glutamine synthetase root isozyme 5, putative, expressed
LOC_Os03g12300Os.11686.2.S1_x_at11/113+6447427..6455524HEAT repeat family protein, expressed
LOC_Os03g12300Os.11686.1.S1_at11/113+6447427..6455524HEAT repeat family protein, expressed
LOC_Os03g12300Os.52150.1.S1_at2/113+6447427..6455524HEAT repeat family protein, expressed
LOC_Os03g12300Os.52150.1.S1_x_at1/113+6447427..6455524HEAT repeat family protein, expressed
LOC_Os03g12310OsAffx.20517.1.S1_at11/113+6459539..6466629retrotransposon protein, putative, unclassified
LOC_Os03g12310OsAffx.20517.2.S1_x_at7/113+6459539..6466629retrotransposon protein, putative, unclassified
LOC_Os03g12320Os.38092.1.S1_at11/113+6473023..6478089UDP-3-0-acyl N-acetylglucosamine deacetylase family protein, expressed
LOC_Os03g12330NANA3+6484157..6484597hypothetical protein
LOC_Os03g12340Os.47130.4.A1_x_at5/113+6485933..6486190retrotransposon protein, putative, unclassified

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Gene Ontology Classification
GO idTypeName
GO:0006913biological_processnucleocytoplasmic transport
GO:0005643cellular_componentnuclear pore
GO:0005487molecular_functionnucleocytoplasmic transporter activity
Probe Info
Probe NameHit(s)LocationSequenceTIGR Locus
OsAffx.20517.1.S1_at--403--4892Chr06:11522103..11522126 (24 bp)
GCTTTCATAAGGTCCATGTGTCATA
LOC_Os06g20090
OsAffx.20517.1.S1_at--15--3571Chr03:6465099..6465123 (25 bp)
CATATGGAATGAGACCTACTTTTTT
LOC_Os03g12310
OsAffx.20517.1.S1_at--1007--10392Chr06:11522145..11522169 (25 bp)
TTTTGCATCCAGGTATCAATATCTG
LOC_Os06g20090
OsAffx.20517.1.S1_at--1022--9071Chr03:6465151..6465175 (25 bp)
TGCTGCGGTTCAGGGCAAAAGTGAA
LOC_Os03g12310
OsAffx.20517.1.S1_at--1025--6551Chr03:6465178..6465202 (25 bp)
GATTACTGCAGATTCCTCGAGGAAC
LOC_Os03g12310
OsAffx.20517.1.S1_at--590--6191Chr03:6465196..6465220 (25 bp)
GAGGAACCCTATTGATAGCAGCGCA
LOC_Os03g12310
OsAffx.20517.1.S1_at--815--10011Chr03:6465211..6465235 (25 bp)
TAGCAGCGCAGTAGATCGACTTGAA
LOC_Os03g12310
OsAffx.20517.1.S1_at--601--3011Chr03:6465262..6465393 (25 bp)
AATGCAAATCAAATGTCCCATGGAC
LOC_Os03g12310
OsAffx.20517.1.S1_at--1085--10131Chr03:6465448..6465472 (25 bp)
TATGCTGTTCCTTTTAATCTTTGGG
LOC_Os03g12310
OsAffx.20517.1.S1_at--538--1411Chr03:6466346..6466370 (25 bp)
AGAAATTTGGGCCAGGCTCCTTGGC
LOC_Os03g12310
OsAffx.20517.1.S1_at--139--911Chr03:6466359..6466383 (25 bp)
AGGCTCCTTGGCCAGTACAAGAGGT
LOC_Os03g12310
Target Sequence 
GCTTTCATAAGGTCCATGTGTCATATGGAATGAGACCTACTTTTTTTGCATCCAGGTATCAATATCTGAGCAGTGCTGCG
GTTCAGGGCAAAAGTGAAGGGATTACTGCAGATTCCTCGAGGAACCCTATTGATAGCAGCGCAGTAGATCGACTTGAAGG
CAAACTTGCAGTTCTTCAGTTCCAAATGCAAATCAAATGTCCCATGGACAAGGCTAAAGAGCTTTCACTGAATCTCAAGA
GTATTACTCAACTTTTCAACAATTATGCTGTTCCTTTTAATCTTTGGGAGATGCTGACAGTAAAATTATTTGAGAAATTT
GGGCCAGGCTCCTTGGCCAGTACAAGAGGT

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.20517.1.S1_at     

Putative homologies in rice

Putative homologies in arabidopsis