Browse Element(s) Details


OsAffx.5954.1.S1_x_at

Description tigr:9637.m00479
TID=OsAffx.5954.1
CNT=8
FEA=mRNA
TIER=ConsEnd
STK=0
NOTE=sequence(s) not in UniGene
DEF=Putative gag-pol polyprotein
REP_ORG=O. sativa
Associated TIGR Gene Locus
TIGR LocusMatching ProbesDescription
LOC_Os09g0722011/11Zinc knuckle family protein
LOC_Os09g080208/11retrotransposon protein, putative, unclassified
LOC_Os03g611807/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os10g010207/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os08g397607/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os07g112407/11retrotransposon protein, putative, unclassified
LOC_Os03g136806/11retrotransposon protein, putative, Ty1-copia subclass, expressed
LOC_Os02g491206/11retrotransposon protein, putative, unclassified
LOC_Os02g346605/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os01g334604/11retrotransposon protein, putative, unclassified
LOC_Os03g335304/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os05g088804/11Zinc knuckle family protein
LOC_Os04g173204/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os06g391603/11Zinc knuckle family protein
LOC_Os06g217803/11retrotransposon protein, putative, unclassified
LOC_Os04g087723/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os09g014003/11retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os04g187703/11retrotransposon protein, putative, unclassified
LOC_Os10g053803/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os07g188902/11retrotransposon protein, putative, unclassified
LOC_Os06g238902/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os01g161602/11retrotransposon protein, putative, unclassified
LOC_Os12g259902/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os09g103902/11hypothetical protein
LOC_Os07g055402/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os03g357882/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os04g124101/11Zinc knuckle family protein
LOC_Os08g297001/11Zinc knuckle family protein
LOC_Os02g397801/11retrotransposon protein, putative, unclassified
LOC_Os03g365701/11retrotransposon protein, putative, unclassified
LOC_Os02g196201/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os03g365901/11retrotransposon protein, putative, Ty1-copia subclass
Gene Context (flanking 25kb)
TIGR LocusMatching ProbesetMatching ProbesChrStrandCoordinatesDescription
LOC_Os09g07170OsAffx.12204.1.S1_at2/119+3508853..3517481retrotransposon protein, putative, unclassified
LOC_Os09g07170OsAffx.448.1.S1_x_at1/119+3508853..3517481retrotransposon protein, putative, unclassified
LOC_Os09g07180OsAffx.17587.1.S1_at11/119+3517951..3521519retrotransposon, putative, centromere-specific
LOC_Os09g07180Os.24648.1.A1_at1/119+3517951..3521519retrotransposon, putative, centromere-specific
LOC_Os09g07190NANA9+3522247..3523032retrotransposon protein, putative, unclassified
LOC_Os09g07200OsAffx.29742.4.S1_x_at11/119+3524023..3525519transposon protein, putative, unclassified
LOC_Os09g07210OsAffx.29742.5.S1_at11/119+3528931..3529529hypothetical protein
LOC_Os09g07210OsAffx.29742.5.S1_s_at11/119+3528931..3529529hypothetical protein
LOC_Os09g07220OsAffx.5954.1.S1_x_at11/119+3531749..3533473Zinc knuckle family protein
LOC_Os09g07220OsAffx.5954.3.S1_x_at3/119+3531749..3533473Zinc knuckle family protein
LOC_Os09g07220OsAffx.5954.2.S1_at1/119+3531749..3533473Zinc knuckle family protein
LOC_Os09g07230OsAffx.5954.5.S1_x_at8/119+3534759..3542841retrotransposon protein, putative, unclassified
LOC_Os09g07230OsAffx.29791.1.S1_x_at4/119+3534759..3542841retrotransposon protein, putative, unclassified
LOC_Os09g07230OsAffx.29791.2.S1_s_at3/119+3534759..3542841retrotransposon protein, putative, unclassified
LOC_Os09g07230OsAffx.29791.2.S1_x_at2/119+3534759..3542841retrotransposon protein, putative, unclassified
LOC_Os09g07230Os.47114.1.S1_x_at2/119+3534759..3542841retrotransposon protein, putative, unclassified
LOC_Os09g07230OsAffx.29791.1.S1_at1/119+3534759..3542841retrotransposon protein, putative, unclassified
LOC_Os09g07230OsAffx.576.1.A1_at1/119+3534759..3542841retrotransposon protein, putative, unclassified
LOC_Os09g07240NANA9+3548186..3549582retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os09g07250OsAffx.1647.1.S1_at2/119+3555766..3558573retrotransposon protein, putative, unclassified
LOC_Os09g07250OsAffx.20565.1.S1_at2/119+3555766..3558573retrotransposon protein, putative, unclassified
LOC_Os09g07250OsAffx.1412.2.S1_at1/119+3555766..3558573retrotransposon protein, putative, unclassified

Select all/Clear all

Gene Ontology Classification
GO idTypeName
NONENONENONE
Probe Info
Probe NameHit(s)LocationSequenceTIGR Locus
OsAffx.5954.1.S1_x_at--890--9312Chr09:3532941..3532965 (25 bp)
AGGAATCCCTACCACACTTGAGTGA
LOC_Os09g07220
OsAffx.5954.1.S1_x_at--182--107519Chr12:15089480..15089504 (25 bp)
TTGGTACGGCTTTACAAGCAAACCA
LOC_Os12g25990
OsAffx.5954.1.S1_x_at--661--6094Chr09:3533120..3533144 (25 bp)
GAGTCTCATGCTAATCTTGATGTGG
LOC_Os09g07220
OsAffx.5954.1.S1_x_at--308--8159Chr09:3533179..3533203 (25 bp)
GGACAAAGCATACCTCACTCTTGAA
LOC_Os09g07220
OsAffx.5954.1.S1_x_at--199--31124Chr12:15089612..15089635 (24 bp)
AATAGTGTCTCTCTCCCTAGCGAGC
LOC_Os12g25990
OsAffx.5954.1.S1_x_at--696--36914Chr09:3533241..3533265 (25 bp)
CTAGCGAGCCATCTTGTTCCAAAAT
LOC_Os09g07220
OsAffx.5954.1.S1_x_at--846--87113Chr09:3533266..3533290 (25 bp)
TGTCCCAAGCAATGAACCATGTGTG
LOC_Os09g07220
OsAffx.5954.1.S1_x_at--90--26120Chr09:3533312..3533336 (25 bp)
AACGCTTGTGCTACTAACTCTATTG
LOC_Os09g07220
OsAffx.5954.1.S1_x_at--536--2011Chr09:3533328..3533352 (25 bp)
ACTCTATTGCCTTGAGTGGTTTGCA
LOC_Os09g07220
OsAffx.5954.1.S1_x_at--758--56919Chr09:3533376..3533400 (25 bp)
GACTCCTTCACAATGGCCTACTTAA
LOC_Os09g07220
OsAffx.5954.1.S1_x_at--30--1131Chr09:3533414..3533438 (25 bp)
AGTAAGGCCCTAAATGTCGCGACCG
LOC_Os09g07220
Target Sequence 
AGGAATCCCTACCACACTTGAGTGANTTNCTTGGNAGAATTGAGGACCAATATGCAANTCTTGAGAGGCAAGAGNCTTTG
CTCATTCGTGAGAAAGAGNGNNNNNNNGANNTNNNGANTNNNNNNNNNNNGNANAGNNNNNNNNNNNANNNATTGGTACG
GCTTTACAAGCAAACCAAAGAGTCTCATGCTAATCTTGATGTGGCGAACGCTCAACTTCAAGAGAGAGTGGATGGCTTGG
ACAAAGCATACCTCACTCTTGAAGAAAAGTTCGAAACCTTAAAGAATAGTGTCTCTCTCCCTAGCGAGCCATCTTGTTCC
AAAATTGTCCCAAGCAATGAACCATGTGTGAGATGCAAAGATATTGATATTAACGCTTGTGCTACTAACTCTATTGCCTT
GAGTGGTTTGCAAAAGCAAAATGAGAAGCTTACGGGACTCCTTCACAATGGCCTACTTAAGTGCTATATGGGTAGTAAGG
CCCTAAATGTCGCGACCG

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.5954.1.S1_x_at     

Putative homologies in rice

Putative homologies in arabidopsis