Browse Element(s) Details


OsAffx.1647.1.S1_at

Description gb:NM_184699.1
DB_XREF= gi:34896487
GEN=OSJNBa0057E11.13
TID=OsAffx.1647.1
CNT=1
FEA=mRNA
TIER=ConsEnd
STK=0
NOTE=sequence(s) not in UniGene
DEF=Oryza sativa (japonica cultivar-group) putative gypsy-type retrotransposon RIRE2 (OSJNBa0057E11.13), mRNA.
PROD=putative gypsy-type retrotransposon RIRE2
REP_ORG=O. sativa
Associated TIGR Gene Locus
TIGR LocusMatching ProbesDescription
LOC_Os03g3572011/11retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os04g011903/11retrotransposon protein, putative, unclassified
LOC_Os12g235402/11retrotransposon protein, putative, unclassified
LOC_Os08g135002/11retrotransposon protein, putative, unclassified
LOC_Os11g356902/11retrotransposon protein, putative, unclassified
LOC_Os09g072502/11retrotransposon protein, putative, unclassified
LOC_Os05g232801/11retrotransposon protein, putative, unclassified
LOC_Os05g178701/11retrotransposon protein, putative, unclassified
LOC_Os09g082401/11retrotransposon protein, putative, unclassified
LOC_Os04g148701/11retrotransposon protein, putative, unclassified
LOC_Os11g287901/11retrotransposon protein, putative, unclassified
LOC_Os12g055001/11retrotransposon protein, putative, unclassified
LOC_Os09g231301/11retrotransposon protein, putative, unclassified
LOC_Os08g332501/11retrotransposon protein, putative, unclassified
Gene Context (flanking 25kb)
TIGR LocusMatching ProbesetMatching ProbesChrStrandCoordinatesDescription
LOC_Os03g35670NANA3+19711240..19713776retrotransposon protein, putative, unclassified
LOC_Os03g35690OsAffx.1646.1.S1_x_at1/113+19721635..19724601retrotransposon protein, putative, Ty3-gypsy subclass, expressed
LOC_Os03g35700OsAffx.22722.1.S1_x_at11/113+19728264..19729481retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os03g35700OsAffx.22722.1.S1_at11/113+19728264..19729481retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os03g35710OsAffx.10496.1.S1_at11/113+19731268..19735740retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os03g35710OsAffx.20628.2.S1_at2/113+19731268..19735740retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os03g35710OsAffx.20628.2.S1_x_at2/113+19731268..19735740retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os03g35710OsAffx.30582.1.S1_s_at2/113+19731268..19735740retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os03g35720OsAffx.1647.1.S1_at11/113+19738530..19741290retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os03g35720OsAffx.29148.1.S1_at2/113+19738530..19741290retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os03g35730NANA3+19749058..19751728hypothetical protein
LOC_Os03g35740OsAffx.22699.1.S1_x_at3/113+19753467..19758173retrotransposon protein, putative, unclassified
LOC_Os03g35740Os.45161.1.A1_x_at1/113+19753467..19758173retrotransposon protein, putative, unclassified
LOC_Os03g35750OsAffx.25368.1.S1_at11/113+19762222..19762578hypothetical protein

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Gene Ontology Classification
GO idTypeName
NONENONENONE
Probe Info
Probe NameHit(s)LocationSequenceTIGR Locus
OsAffx.1647.1.S1_at--133--1012Chr04:132610..132634 (25 bp)
AGGTTGGCACACGAACTGGTTCTAT
LOC_Os04g01190
OsAffx.1647.1.S1_at--454--6733Chr11:20424110..20424134 (25 bp)
GTTCTATGTGCAAAACCCTGAGCCA
LOC_Os11g35690
OsAffx.1647.1.S1_at--661--7155Chr09:3556243..3556267 (25 bp)
GTCTATCGCGATACCTGGAACTCAC
LOC_Os09g07250
OsAffx.1647.1.S1_at--1074--5352Chr08:20585497..20585516 (20 bp)
GAAGAGGCCGCCCAAGCACTCGACT
LOC_Os08g33250
OsAffx.1647.1.S1_at--113--5112Chr12:13323494..13323518 (25 bp)
GCACTCGACTTGTTGGATCGCATGC
LOC_Os12g23540
OsAffx.1647.1.S1_at--996--5811Chr03:19740586..19740610 (25 bp)
GACCCGGCTGGCACTAATCAAGGAA
LOC_Os03g35720
OsAffx.1647.1.S1_at--113--551Chr03:19740559..19740583 (25 bp)
ATCCAGAACGGCCTTTCAGTTTGAC
LOC_Os03g35720
OsAffx.1647.1.S1_at--440--3451Chr03:19740543..19740567 (25 bp)
CAGTTTGACAGCAAGCATGACCCCA
LOC_Os03g35720
OsAffx.1647.1.S1_at--379--52710Chr11:20424426..20424450 (25 bp)
GAATGCCATCGTGGTCAGCTATTCA
LOC_Os11g35690
OsAffx.1647.1.S1_at--980--10512Chr08:8026727..8026751 (25 bp)
TTCACATTTATTGCCAGTTGTGCCA
LOC_Os08g13500
OsAffx.1647.1.S1_at--539--6631Chr03:19740417..19740441 (25 bp)
GTTGTGCCATACAACTCCTTCAACC
LOC_Os03g35720
Target Sequence 
AGGTTGGCACACGAACTGGTTCTATGTGCAAAACCCTGAGCCAGCGCTTCCCGGATACTCCTGTCTTCCCCCAGTCTATC
GCGATACCTGGAACTCACTGCCGATGGGAGAAGAGGCCGCCCAAGCACTCGACTTGTTGGATCGCATGCTGAAGCTGAAA
GAACAAGGTCTGCAGGGGAAACAAATCACCCGGCACTTCATCAAGACCCGGCTGGCACTAATCAAGGAAAGATCCAGAAC
GGCCTTTCAGTTTGACAGCAAGCATGACCCCAACCGAGAGAACCCAGAATCTCTTGAGTTCAAAATTATGCAGGAGAGGA
TGTACAAAATCTTCTCGAATGCCATCGTGGTCAGCTATTCACATTTATTGCCAGTTGTGCCATACAACTCCTTCAACC

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.1647.1.S1_at     

Putative homologies in rice

Putative homologies in arabidopsis