Browse Element(s) Details

Os.20204.2.S1_a_at

Description

gb:AF513384.1
DB_XREF= gi:31324096
TID=Os.20204.2
CNT=1
FEA=FLmRNA
TIER=FL
STK=1
UG=Os.20204 (NCBI UniGene Cluster)
DEF=Oryza sativa (japonica cultivar-group) histone deacetylase HDAC3 mRNA, complete cds; alternatively spliced.
PROD=histone deacetylase HDAC3
FL= gb:AF513384.1
REP_ORG=O. sativa

Associated TIGR Gene Locus

TIGR Locus	Matching Probes	Description
LOC_Os02g12350	11/11	histone deacetylase, putative, expressed

Gene Context (flanking 25kb)

TIGR Locus	Matching Probeset	Matching Probes	Chr	Strand	Coordinates	Description
LOC_Os02g12300	Os.53956.1.S1_at	11/11	2	+	6399412..6402186	Pectate lyase precursor, putative, expressed
LOC_Os02g12300	OsAffx.18481.1.S1_x_at	1/11	2	+	6399412..6402186	Pectate lyase precursor, putative, expressed
LOC_Os02g12310	Os.39041.1.S1_s_at	11/11	2	+	6404019..6405861	No apical meristem protein, expressed
LOC_Os02g12310	Os.10944.1.S1_at	10/11	2	+	6404019..6405861	No apical meristem protein, expressed
LOC_Os02g12320	NA	NA	2	+	6406853..6415392	retrotransposon protein, putative, Ty3-gypsy subclass, expressed
LOC_Os02g12330	OsAffx.12000.1.S1_at	11/11	2	+	6418378..6419378	hypothetical protein
LOC_Os02g12330	OsAffx.12000.1.S1_x_at	10/11	2	+	6418378..6419378	hypothetical protein
LOC_Os02g12340	OsAffx.12003.2.S1_at	11/11	2	+	6422491..6424004	hypothetical protein
LOC_Os02g12340	OsAffx.12003.2.S1_s_at	11/11	2	+	6422491..6424004	hypothetical protein
LOC_Os02g12340	OsAffx.12003.1.S1_at	9/11	2	+	6422491..6424004	hypothetical protein
LOC_Os02g12350	Os.20204.2.S1_a_at	11/11	2	+	6424581..6430587	histone deacetylase, putative, expressed
LOC_Os02g12350	Os.20204.1.S1_s_at	10/11	2	+	6424581..6430587	histone deacetylase, putative, expressed
LOC_Os02g12350	Os.20204.1.S1_x_at	3/11	2	+	6424581..6430587	histone deacetylase, putative, expressed
LOC_Os02g12350	Os.28463.1.S1_x_at	1/11	2	+	6424581..6430587	histone deacetylase, putative, expressed
LOC_Os02g12360	Os.53409.1.A1_at	11/11	2	+	6433220..6441415	nuclear protein ZAP, putative, expressed
LOC_Os02g12370	Os.53540.1.S1_at	11/11	2	+	6443131..6445361	expressed protein
LOC_Os02g12380	Os.20204.1.S1_at	11/11	2	+	6447083..6453145	histone deacetylase, putative, expressed
LOC_Os02g12380	Os.20204.3.S1_a_at	11/11	2	+	6447083..6453145	histone deacetylase, putative, expressed
LOC_Os02g12380	Os.20204.1.S1_s_at	10/11	2	+	6447083..6453145	histone deacetylase, putative, expressed
LOC_Os02g12380	Os.20204.1.S1_x_at	10/11	2	+	6447083..6453145	histone deacetylase, putative, expressed
LOC_Os02g12390	OsAffx.30226.4.S1_x_at	5/11	2	+	6454045..6458106	retrotransposon protein, putative, Ty1-copia subclass
LOC_Os02g12390	OsAffx.30226.2.S1_s_at	5/11	2	+	6454045..6458106	retrotransposon protein, putative, Ty1-copia subclass
LOC_Os02g12390	OsAffx.30226.4.S1_at	4/11	2	+	6454045..6458106	retrotransposon protein, putative, Ty1-copia subclass
LOC_Os02g12390	OsAffx.24587.1.S1_x_at	4/11	2	+	6454045..6458106	retrotransposon protein, putative, Ty1-copia subclass
LOC_Os02g12390	OsAffx.442.1.S1_x_at	4/11	2	+	6454045..6458106	retrotransposon protein, putative, Ty1-copia subclass
LOC_Os02g12390	OsAffx.30226.1.S1_x_at	3/11	2	+	6454045..6458106	retrotransposon protein, putative, Ty1-copia subclass
LOC_Os02g12390	OsAffx.30226.2.S1_x_at	3/11	2	+	6454045..6458106	retrotransposon protein, putative, Ty1-copia subclass
LOC_Os02g12390	OsAffx.30226.1.S1_at	2/11	2	+	6454045..6458106	retrotransposon protein, putative, Ty1-copia subclass
LOC_Os02g12390	OsAffx.19052.1.S1_at	1/11	2	+	6454045..6458106	retrotransposon protein, putative, Ty1-copia subclass
LOC_Os02g12390	OsAffx.442.1.S1_at	1/11	2	+	6454045..6458106	retrotransposon protein, putative, Ty1-copia subclass

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Gene Ontology Classification

GO id	Type	Name
GO:0007275	biological_process	development
GO:0009861	biological_process	jasmonic acid and ethylene-dependent systemic resistance
GO:0016441	biological_process	posttranscriptional gene silencing
GO:0016575	biological_process	histone deacetylation
GO:0005634	cellular_component	nucleus
GO:0004407	molecular_function	histone deacetylase activity

Probe Info

Probe Name	Hit(s)	Location	Sequence	TIGR Locus
Os.20204.2.S1_a_at--892--761	1	Chr02:6424939..6424963 (25 bp)	GGGAAGCTCACCCAAATGACCGAAC	LOC_Os02g12350
Os.20204.2.S1_a_at--540--433	1	Chr02:6424889..6424913 (25 bp)	CCATGATTTAGCTACCTTCAGGACA	LOC_Os02g12350
Os.20204.2.S1_a_at--463--1025	1	Chr02:6424883..6424907 (25 bp)	TTTAGCTACCTTCAGGACACGAGCT	LOC_Os02g12350
Os.20204.2.S1_a_at--4--875	1	Chr02:6424855..6424879 (25 bp)	TGTCAAGGTTTCCTGCATGCTCTTA	LOC_Os02g12350
Os.20204.2.S1_a_at--1147--683	1	Chr02:6424848..6424872 (25 bp)	GTTTCCTGCATGCTCTTAAGTTGGC	LOC_Os02g12350
Os.20204.2.S1_a_at--52--499	1	Chr02:6424841..6424865 (25 bp)	GCATGCTCTTAAGTTGGCAGAAACT	LOC_Os02g12350
Os.20204.2.S1_a_at--521--855	1	Chr02:6424817..6424841 (25 bp)	TGGAGTTGATCTGTATACTGCATCT	LOC_Os02g12350
Os.20204.2.S1_a_at--1137--197	1	Chr02:6424801..6424825 (25 bp)	ACTGCATCTTGACATTTCAAACTTA	LOC_Os02g12350
Os.20204.2.S1_a_at--383--533	1	Chr02:6424699..6424723 (25 bp)	GAAGTCCATAATGTTCAGGCAATAC	LOC_Os02g12350
Os.20204.2.S1_a_at--886--115	1	Chr02:6424658..6424682 (25 bp)	AGTCTGACTGACCAATGTAGTACAA	LOC_Os02g12350
Os.20204.2.S1_a_at--390--509	1	Chr02:6424613..6424637 (25 bp)	GCAAGTTAAAATGTACAGTCTGTTA	LOC_Os02g12350

Target Sequence

GGGAAGCTCACCCAAATGACCGAACCCACCAGCAGCTATGCACCAGAAGACCATGATTTAGCTACCTTCAGGACACGAGC
TCTCTGTCAAGGTTTCCTGCATGCTCTTAAGTTGGCAGAAACTGGAGTTGATCTGTATACTGCATCTTGACATTTCAAAC
TTAAAAATCGACACAAATCAAGAGCAAACACTGTTTGATTGTTTCTTCTGTAGGAGTTTACCATTGTTTCTTTTGTTGAA
GAAGTCCATAATGTTCAGGCAATACTGGACGTGGAGGCATTAGTCTGACTGACCAATGTAGTACAAAACAAAACATGTAA
CGTGAAGCAAGTTAAAATGTACAGTCTGTTA

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:

Putative homologies in rice

Putative homologies in arabidopsis