Browse Element(s) Details


Os.3407.1.S1_a_at

Description gb:AB005290.1
DB_XREF= gi:2780745
TID=Os.3407.1
CNT=15
FEA=FLmRNA
TIER=FL
STK=5
UG=Os.3407 (NCBI UniGene Cluster)
UG_TITLE=(japonica cultivar-group) plastid RNA polymerase sigma factor (OJ9990_A01.9), mRNA
DEF=Oryza sativa (japonica cultivar-group) mRNA for plastid RNA polymerase sigma factor, complete cds.
FL= gb:AB005290.1
REP_ORG=O. sativa
Associated TIGR Gene Locus
TIGR LocusMatching ProbesDescription
LOC_Os08g0663010/11Sigma-70 region 2 family protein, expressed
Gene Context (flanking 25kb)
TIGR LocusMatching ProbesetMatching ProbesChrStrandCoordinatesDescription
LOC_Os08g06570NANA8+3701705..3707845retrotransposon protein, putative, unclassified
LOC_Os08g06580Os.28943.1.S1_x_at1/118+3708558..3711635retrotransposon protein, putative, unclassified
LOC_Os08g06590OsAffx.5724.1.S1_x_at11/118+3713914..3714991hypothetical protein
LOC_Os08g06590OsAffx.5724.2.S1_at11/118+3713914..3714991hypothetical protein
LOC_Os08g06590OsAffx.5724.1.S1_at8/118+3713914..3714991hypothetical protein
LOC_Os08g06600Os.36139.1.S1_at11/118+3716022..3719897Nuf2 family protein, expressed
LOC_Os08g06610Os.12047.1.S1_a_at11/118+3720558..3721117Mps one binder kinase activator-like 1A, putative
LOC_Os08g06620OsAffx.16857.1.S1_s_at11/118+3721757..3722500expressed protein
LOC_Os08g06630Os.3407.1.S1_a_at10/118+3726171..3730177Sigma-70 region 2 family protein, expressed
LOC_Os08g06640OsAffx.9796.1.S1_x_at11/118+3733845..3739068expressed protein
LOC_Os08g06640Os.17547.1.S1_at9/118+3733845..3739068expressed protein
LOC_Os08g06659Os.31625.1.S1_at11/118+3741880..3743529expressed protein
LOC_Os08g06659OsAffx.29067.1.S1_s_at11/118+3741880..3743529expressed protein
LOC_Os08g06659Os.31625.2.S1_x_at11/118+3741880..3743529expressed protein
LOC_Os08g06680OsAffx.5725.1.S1_at11/118+3744313..3744615hypothetical protein
LOC_Os08g06690OsAffx.21982.1.S1_x_at11/118+3746663..3748451hypothetical protein
LOC_Os08g06690OsAffx.1199.1.S1_at1/118+3746663..3748451hypothetical protein
LOC_Os08g06700Os.31736.1.S1_at11/118+3750972..3754484expressed protein
LOC_Os08g06700OsAffx.21982.1.S1_x_at5/118+3750972..3754484expressed protein

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Gene Ontology Classification
GO idTypeName
GO:0006352biological_processtranscription initiation
GO:0006355biological_processregulation of transcription, DNA-dependent
GO:0019685biological_processphotosynthesis, dark reaction
GO:0045941biological_processpositive regulation of transcription
GO:0009507cellular_componentchloroplast
GO:0003677molecular_functionDNA binding
GO:0003700molecular_functiontranscription factor activity
GO:0003899molecular_functionDNA-directed RNA polymerase activity
GO:0016987molecular_functionsigma factor activity
Probe Info
Probe NameHit(s)LocationSequenceTIGR Locus
Os.3407.1.S1_a_at--431--5631NONE
GACACTGCACAGTTACATAGAGGAT
NONE
Os.3407.1.S1_a_at--587--772Chr08:3728789..3728813 (25 bp)
ATGTCGCAAATGATCCATGGCATGG
LOC_Os08g06630
Os.3407.1.S1_a_at--341--2611Chr08:3729113..3729137 (25 bp)
AAGCTTTTAAACTCAACTCTCAACG
LOC_Os08g06630
Os.3407.1.S1_a_at--525--3591Chr08:3729151..3729175 (25 bp)
CATTATCCGGTTATATCATGGCATA
LOC_Os08g06630
Os.3407.1.S1_a_at--309--8231Chr08:3729418..3729442 (25 bp)
GGCAAGTAGGACTCATCGCAATGGA
LOC_Os08g06630
Os.3407.1.S1_a_at--452--7591Chr08:3729507..3729531 (25 bp)
GGGCTTTTTGTTTGAGTCAGATCCA
LOC_Os08g06630
Os.3407.1.S1_a_at--814--7111Chr08:3729522..3729546 (25 bp)
GTCAGATCCACAAACACAGCGGTTG
LOC_Os08g06630
Os.3407.1.S1_a_at--78--2191Chr08:3729535..3729559 (25 bp)
ACACAGCGGTTGTATATACTCAGAA
LOC_Os08g06630
Os.3407.1.S1_a_at--747--7691Chr08:3729566..3729590 (25 bp)
GGGTACATCCTTCAAAAGGCGTACT
LOC_Os08g06630
Os.3407.1.S1_a_at--210--911Chr08:3729582..3729606 (25 bp)
AGGCGTACTGCCACTCACATGAAAG
LOC_Os08g06630
Os.3407.1.S1_a_at--1091--451Chr08:3729654..3729678 (25 bp)
ATCTCTATGCCTGTGTTATGACCAA
LOC_Os08g06630
Target Sequence 
GACACTGCACAGTTACATAGAGGATCAAAATGTCGCAAATGATCCATGGCATGGATTTGAGGAGTGGTATCTCAAGGAAG
AAGTCAACAAGCTTTTAAACTCAACTCTCAACGAGCGTGAGAGGGACATTATCCGGTTATATCATGGCATAGGAAAACAA
TGCCATACATGGGAGGATATTAGCAGACAATTCGGGTTGTCGAGGGAGAGGGTGAGGCAAGTAGGACTCATCGCAATGGA
GAAGCTGAAGCATGCTGCGAGGAGGAAAAATTTGGAGGCATTGCTTGAGGATTATTGAGTTGAGGGGCTTTTTGTTTGAG
TCAGATCCACAAACACAGCGGTTGTATATACTCAGAAAACATAGGGTACATCCTTCAAAAGGCGTACTGCCACTCACATG
AAAGTAATTATACGTGTACATTTTGTGACATTAGGGAGATGCATGATCAAAATCTCTATGCCTGTGTTATGACCAA

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.3407.1.S1_a_at     

Putative homologies in rice

Putative homologies in arabidopsis