Browse Element(s) Details


OsAffx.5954.4.S1_x_at

Description gb:NM_194469.1
DB_XREF= gi:37530297
TID=OsAffx.5954.4
CNT=1
FEA=mRNA
TIER=ConsEnd
STK=0
NOTE=sequence(s) not in UniGene
DEF=Oryza sativa (japonica cultivar-group) putative copia-type pol polyprotein (OJ1136E01.16), mRNA.
PROD=putative copia-type pol polyprotein
REP_ORG=O. sativa
Associated TIGR Gene Locus
TIGR LocusMatching ProbesDescription
LOC_Os10g0102011/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os09g0801010/11hypothetical protein
LOC_Os07g112409/11retrotransposon protein, putative, unclassified
LOC_Os08g397607/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os05g138907/11hypothetical protein
LOC_Os02g491107/11hypothetical protein
LOC_Os03g335307/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os07g224305/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os07g055404/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os03g136703/11retrotransposon protein, putative, unclassified
LOC_Os08g296903/11retrotransposon protein, putative, Ty1-copia subclass
LOC_Os01g334702/11hypothetical protein
Gene Context (flanking 25kb)
TIGR LocusMatching ProbesetMatching ProbesChrStrandCoordinatesDescription
LOC_Os10g01010OsAffx.8589.1.S1_at3/1110+6385..6747transposon protein, putative, Ac/Ds sub-class
LOC_Os10g01020OsAffx.5954.4.S1_x_at11/1110+12860..20923retrotransposon protein, putative, Ty1-copia subclass
LOC_Os10g01020OsAffx.5954.1.S1_x_at7/1110+12860..20923retrotransposon protein, putative, Ty1-copia subclass
LOC_Os10g01020OsAffx.5954.5.S1_x_at4/1110+12860..20923retrotransposon protein, putative, Ty1-copia subclass
LOC_Os10g01020OsAffx.5954.3.S1_x_at4/1110+12860..20923retrotransposon protein, putative, Ty1-copia subclass
LOC_Os10g01020OsAffx.5954.2.S1_at1/1110+12860..20923retrotransposon protein, putative, Ty1-copia subclass
LOC_Os10g01030OsAffx.6537.1.S1_at11/1110+22819..24231hypothetical protein
LOC_Os10g01030OsAffx.20927.1.S1_x_at1/1110+22819..24231hypothetical protein
LOC_Os10g01044Os.17906.1.S1_at10/1110+30118..42506Tic62 protein, putative, expressed
LOC_Os10g01044OsAffx.6538.1.S1_x_at7/1110+30118..42506Tic62 protein, putative, expressed
LOC_Os10g01044OsAffx.6538.1.S1_at1/1110+30118..42506Tic62 protein, putative, expressed

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Gene Ontology Classification
GO idTypeName
NONENONENONE
Probe Info
Probe NameHit(s)LocationSequenceTIGR Locus
OsAffx.5954.4.S1_x_at--671--3516Chr07:6192072..6192096 (25 bp)
CATGTCTATCACTTTGTGTGGGAGG
LOC_Os07g11240
OsAffx.5954.4.S1_x_at--901--8557Chr07:6192157..6192180 (24 bp)
TGGATGATCGAGACTGTGACTCAGC
LOC_Os07g11240
OsAffx.5954.4.S1_x_at--1034--1397Chr07:6192166..6192190 (25 bp)
AGACTGTGACTCAGCTCCAGTTTCG
LOC_Os07g11240
OsAffx.5954.4.S1_x_at--450--43511Chr07:6192182..6192206 (25 bp)
CCAGTTTCGCCATGATGTGACTCAT
LOC_Os07g11240
OsAffx.5954.4.S1_x_at--714--88711Chr07:6192194..6192217 (24 bp)
TGATGTGACTCATTCTCAGCTTCAG
LOC_Os07g11240
OsAffx.5954.4.S1_x_at--770--5411Chr10:13109..13133 (25 bp)
GAACCACCGATTGCGGAATTCGGCA
LOC_Os10g01020
OsAffx.5954.4.S1_x_at--1106--2376Chr07:6192418..6192442 (25 bp)
AAACGGCTCGTGATGTCAAGTTCCT
LOC_Os07g11240
OsAffx.5954.4.S1_x_at--576--9717Chr07:6192433..6192457 (25 bp)
TCAAGTTCCTCAAGGCAAGGTATTA
LOC_Os07g11240
OsAffx.5954.4.S1_x_at--850--5157Chr07:6192447..6192471 (25 bp)
GCAAGGTATTATGAGGACCACCACA
LOC_Os07g11240
OsAffx.5954.4.S1_x_at--362--3636Chr05:7696243..7696267 (25 bp)
CTTCCGACTTCGACTTCTTTGGATA
LOC_Os05g13890
OsAffx.5954.4.S1_x_at--171--2058Chr07:6192565..6192589 (25 bp)
ACTTCGACTTCTTTGGATATGGCCA
LOC_Os07g11240
Target Sequence 
CATGTCTATCACTTTGTGTGGGAGGAGATCCGCATGGCTTCAATTCAGTACAAGAAGGGGTTGGTCTATGCCCCTCACAT
TATGTGGATGATCGAGACTGTGACTCAGCTCCAGTTTCGCCATGATGTGACTCATTCTCAGCTTCAGTTGCGCCTTCTTA
AGGCCCCCCGCTCCTCAGCTGCTCGGGACATACCCTCCTCTTCCACTCAGCCGCCTCCTGCTCCTGAGCGCCCTGCCTCT
GTGGCTCGTCGTGAGCCGTCTCCCTTATTCCGCATTTTGCGGAGTCTTTTTGGTCTTTGCTCCACGGAGGCCAAAAAGAA
CCACCGATTGCGGAATTCGGCAAAGAAAACGGCTCGTGATGTCAAGTTCCTCAAGGCAAGGTATTATGAGGACCACCACA
TTGATATCCCTCCTTCTCCTCCAGGTTTCGAGGCCGAGCCCGATGAGCCAGAGGATGAAGAGATTGAGGATCCTTTTGCC
GGGTTGCCTTCCGACTTCGACTTCTTTGGATATGGCCA

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.5954.4.S1_x_at     

Putative homologies in rice

Putative homologies in arabidopsis