Browse Element(s) Details


OsAffx.15220.1.S1_s_at

Description gb:NM_185342.1
DB_XREF= gi:34897769
TID=OsAffx.15220.1
CNT=4
FEA=mRNA
TIER=ConsEnd
STK=0
NOTE=sequence(s) not in UniGene
DEF=Oryza sativa (japonica cultivar-group) Similar to Arabidopsis thaliana chromosome II BAC F9O13 genomic sequence, putative non-LTR retroelement reverse transcriptase. (AC006248) (Gene), mRNA.
REP_ORG=O. sativa
Associated TIGR Gene Locus
TIGR LocusMatching ProbesDescription
LOC_Os06g0180011/11retrotransposon protein, putative, unclassified, expressed
LOC_Os04g4705911/11Helix-loop-helix DNA-binding domain containing protein, expressed
LOC_Os01g1931011/11retrotransposon protein, putative, LINE subclass
LOC_Os09g2381011/11hypothetical protein
LOC_Os02g0338011/11hypothetical protein
LOC_Os07g0249011/11retrotransposon protein, putative, unclassified
LOC_Os09g336907/11retrotransposon protein, putative, unclassified, expressed
LOC_Os07g484707/11retrotransposon protein, putative, unclassified
LOC_Os04g026004/11retrotransposon protein, putative, LINE subclass
LOC_Os04g043401/11retrotransposon protein, putative, unclassified
Gene Context (flanking 25kb)
TIGR LocusMatching ProbesetMatching ProbesChrStrandCoordinatesDescription
LOC_Os06g01740NANA6+429838..433798hypothetical protein
LOC_Os06g01750OsAffx.14351.1.S1_x_at2/116+436156..437133hypothetical protein
LOC_Os06g01760Os.12825.1.S1_at11/116+438061..440552expressed protein
LOC_Os06g01770Os.4441.1.S1_at11/116+443998..446785expressed protein
LOC_Os06g01780Os.52860.1.A1_at11/116+449988..452733expressed protein
LOC_Os06g01790Os.52389.1.S1_x_at11/116+453863..456206expressed protein
LOC_Os06g01800OsAffx.15220.1.S1_s_at11/116+457997..464513retrotransposon protein, putative, unclassified, expressed
LOC_Os06g01800Os.55780.1.S1_at10/116+457997..464513retrotransposon protein, putative, unclassified, expressed
LOC_Os06g01800OsAffx.15220.2.S1_s_at8/116+457997..464513retrotransposon protein, putative, unclassified, expressed
LOC_Os06g01800Os.48472.1.A1_at7/116+457997..464513retrotransposon protein, putative, unclassified, expressed
LOC_Os06g01800OsAffx.14814.1.S1_at1/116+457997..464513retrotransposon protein, putative, unclassified, expressed
LOC_Os06g01810NANA6+465385..466183hypothetical protein
LOC_Os06g01820OsAffx.10379.1.A1_at2/116+469319..470927hypothetical protein
LOC_Os06g01820Os.51646.1.S1_at1/116+469319..470927hypothetical protein
LOC_Os06g01830OsAffx.15222.1.S1_at9/116+472151..472577hypothetical protein
LOC_Os06g01840Os.12745.1.S1_at11/116+476099..478173Integral membrane protein DUF6 containing protein, expressed
LOC_Os06g01850Os.10696.1.S1_at11/116+478199..480658Ferredoxin-NADP reductase, leaf isozyme, chloroplast precursor, putative, expressed
LOC_Os06g01860Os.36672.1.S1_at11/116+483347..484309expressed protein
LOC_Os06g01860Os.36672.2.S1_x_at11/116+483347..484309expressed protein
LOC_Os06g01870NANA6+488917..489695hypothetical protein

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Gene Ontology Classification
GO idTypeName
GO:0001708biological_processcell fate specification
GO:0009813biological_processflavonoid biosynthesis
GO:0009957biological_processepidermal cell fate specification
GO:0045449biological_processregulation of transcription
GO:0005634cellular_componentnucleus
GO:0003677molecular_functionDNA binding
GO:0003700molecular_functiontranscription factor activity
GO:0005515molecular_functionprotein binding
Probe Info
Probe NameHit(s)LocationSequenceTIGR Locus
OsAffx.15220.1.S1_s_at--545--107713Chr11:26995686..26995709 (24 bp)
TTGGACGGGTGACCAGTGCTACTCA
NONE
OsAffx.15220.1.S1_s_at--750--91313Chr11:26995834..26995858 (25 bp)
TGCTGGACTGCCGATCTTCTCCAAA
NONE
OsAffx.15220.1.S1_s_at--1051--47112Chr11:26995835..26995859 (25 bp)
GCTGGACTGCCGATCTTCTCCAAAA
NONE
OsAffx.15220.1.S1_s_at--302--39113Chr11:26995836..26995860 (25 bp)
CTGGACTGCCGATCTTCTCCAAAAG
NONE
OsAffx.15220.1.S1_s_at--170--75116Chr11:26995862..26995886 (25 bp)
GTGGTATCGATAGCCACTCTGCTTG
NONE
OsAffx.15220.1.S1_s_at--833--78514Chr11:26995864..26995888 (25 bp)
GGTATCGATAGCCACTCTGCTTGCC
NONE
OsAffx.15220.1.S1_s_at--853--68915Chr11:26995865..26995889 (25 bp)
GTATCGATAGCCACTCTGCTTGCCC
NONE
OsAffx.15220.1.S1_s_at--123--35515Chr11:26995929..26995953 (25 bp)
CATCGATTGCGTGTTCGCTCGGCAG
NONE
OsAffx.15220.1.S1_s_at--566--5116Chr11:26995930..26995954 (25 bp)
ATCGATTGCGTGTTCGCTCGGCAGG
NONE
OsAffx.15220.1.S1_s_at--1085--516Chr11:26995934..26995958 (25 bp)
ATTGCGTGTTCGCTCGGCAGGTCTG
NONE
OsAffx.15220.1.S1_s_at--622--106120Chr11:26995935..26995959 (25 bp)
TTGCGTGTTCGCTCGGCAGGTCTGG
NONE
Target Sequence 
TTGGACGGGTGACCAGTGCTACTCANNGCNATCGNCGTATCNGGCGTTCTTCCTTGGCCAGCACTCTTTTGCCTGTGCCG
ACNTACTCTGGCACGCGAAGGGCCCTGNTAAATGCAAGTTCTTCCTTTGGTTTGCATTTCAGCNGCGCTGCTGGACTGCC
GATCTTCTCCAAAAGNGTGGTATCGATAGCCACTCTGCTTGCCCCTTTTGNGCTCAGNAGCTTGAGACNGCGAACCACAT
CCTCATCGATTGCGTGTTCGCTCGGCAGGTCTGG

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.15220.1.S1_s_at     

Putative homologies in rice

Putative homologies in arabidopsis