Browse Element(s) Details


Os.4601.1.S1_a_at

Description gb:AB109892.1
DB_XREF= gi:30578177
GEN=PHYB
TID=Os.4601.1
CNT=15
FEA=FLmRNA
TIER=FL
STK=3
UG=Os.4601 (NCBI UniGene Cluster)
DEF=Oryza sativa (japonica cultivar-group) PHYB mRNA for phytochrome B, complete cds.
PROD=phytochrome B
FL= gb:AB109892.1 gb:AK063814.1
REP_ORG=O. sativa
Associated TIGR Gene Locus
TIGR LocusMatching ProbesDescription
LOC_Os03g1959011/11Phytochrome B, putative, expressed
Gene Context (flanking 25kb)
TIGR LocusMatching ProbesetMatching ProbesChrStrandCoordinatesDescription
LOC_Os03g19560Os.19474.1.S1_a_at11/113+10971683..10976387TPR Domain containing protein, expressed
LOC_Os03g19570OsAffx.12938.1.S1_at11/113+10977833..10985302Fip1 motif family protein, expressed
LOC_Os03g19570Os.7345.1.S1_x_at11/113+10977833..10985302Fip1 motif family protein, expressed
LOC_Os03g19580Os.6884.1.S1_at11/113+10986381..10990714expressed protein
LOC_Os03g19590Os.4601.1.S1_a_at11/113+10998964..11007022Phytochrome B, putative, expressed
LOC_Os03g19600Os.11065.1.A1_at11/113+11009669..11011712retrotransposon protein, putative, Ty3-gypsy subclass, expressed
LOC_Os03g19600Os.8570.3.S1_s_at11/113+11009669..11011712retrotransposon protein, putative, Ty3-gypsy subclass, expressed
LOC_Os03g19610Os.18212.1.S1_at11/113+11012355..11014375Pectinesterase family protein, expressed
LOC_Os03g19620OsAffx.12939.2.S1_at11/113+11015747..11016130hypothetical protein
LOC_Os03g19630OsAffx.27626.1.S1_at11/113+11018627..11019196Myb-like DNA-binding domain containing protein
LOC_Os03g19640OsAffx.12941.1.S1_at11/113+11024800..11025308hypothetical protein
LOC_Os03g19650Os.26818.2.S1_at11/113+11027321..11032298PPR2, putative, expressed
LOC_Os03g19650Os.26818.1.S1_a_at11/113+11027321..11032298PPR2, putative, expressed
LOC_Os03g19650Os.26818.2.S2_at11/113+11027321..11032298PPR2, putative, expressed

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Gene Ontology Classification
GO idTypeName
GO:0006355biological_processregulation of transcription, DNA-dependent
GO:0009630biological_processgravitropism
GO:0009638biological_processphototropism
GO:0009649biological_processentrainment of circadian clock
GO:0010017biological_processred or far red light signaling pathway
GO:0010201biological_processresponse to high irradiance
GO:0010202biological_processresponse to low fluence red light
GO:0010203biological_processresponse to very low fluence red light
GO:0010218biological_processresponse to far red light
GO:0005634cellular_componentnucleus
GO:0005737cellular_componentcytoplasm
GO:0004673molecular_functionprotein histidine kinase activity
GO:0004871molecular_functionsignal transducer activity
GO:0008020molecular_functionG-protein coupled photoreceptor activity
GO:0009883molecular_functionred or far-red light photoreceptor activity
Probe Info
Probe NameHit(s)LocationSequenceTIGR Locus
Os.4601.1.S1_a_at--491--6091Chr03:11006455..11006479 (25 bp)
GAGTCGGAGCGGAGTTTCTTCCATA
LOC_Os03g19590
Os.4601.1.S1_a_at--619--10552Chr03:11006470..11006494 (25 bp)
TTCTTCCATATCGTACTTGAGCTGC
LOC_Os03g19590
Os.4601.1.S1_a_at--187--6511Chr03:11006531..11006555 (25 bp)
GATATGGTGTATGCTCGTCGCTAAC
LOC_Os03g19590
Os.4601.1.S1_a_at--555--3792Chr04:8749198..8749242 (24 bp)
CTCGCATAACTATTCGGTCAACCAG
NONE
Os.4601.1.S1_a_at--165--1051Chr03:11006579..11006603 (25 bp)
AGGTGACCTGGGATCTTCTGATGGA
LOC_Os03g19590
Os.4601.1.S1_a_at--421--3271Chr03:11006632..11006656 (25 bp)
CAACATTTCGTCCACTCTGATGAAG
LOC_Os03g19590
Os.4601.1.S1_a_at--1067--5111Chr03:11006656..11006680 (25 bp)
GCACATCTGAACTTTGGAACGGCAT
LOC_Os03g19590
Os.4601.1.S1_a_at--875--2571Chr03:11006673..11006697 (25 bp)
AACGGCATCGGTGATTCTCGGTGTC
LOC_Os03g19590
Os.4601.1.S1_a_at--925--8471Chr03:11006726..11006750 (25 bp)
TGGCATGCCCGACTGTAAGTTCAGC
LOC_Os03g19590
Os.4601.1.S1_a_at--531--8231Chr03:11006785..11006809 (25 bp)
GGCAAGCAATGCACACTGACGGTCA
LOC_Os03g19590
Os.4601.1.S1_a_at--804--731Chr03:11006809..11006833 (25 bp)
ATGTAACTCGTAGCATAGGCCCACT
LOC_Os03g19590
Target Sequence 
GAGTCGGAGCGGAGTTTCTTCCATATCGTACTTGAGCTGCCCCAGCCTCAGCAAGCAGCAAGTAGGGGGACAAGCTGATA
TGGTGTATGCTCGTCGCTAACCTCGCATAACTATTCGGTCAACCAGGTGACCTGGGATCTTCTGATGGAGAACCCAGTTT
ATGAGAGTTCCAGAAACCAACATTTCGTCCACTCTGATGAAGCACATCTGAACTTTGGAACGGCATCGGTGATTCTCGGT
GTCGAGGTGGTCCCTCCAGTCTCCTGATTCCTGGCATGCCCGACTGTAAGTTCAGCTTTGGACGATGTTGTTCTATTAGA
GTTCTATGGCGGCAAGCAATGCACACTGACGGTCATGTAACTCGTAGCATAGGCCCACT

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 Os.4601.1.S1_a_at     

Putative homologies in rice

Putative homologies in arabidopsis