Browse Element(s) Details

Os.20204.3.S1_a_at

Description

gb:AK064000.1
DB_XREF= gi:32974018
TID=Os.20204.3
CNT=6
FEA=FLmRNA
TIER=FL
STK=1
UG=Os.20204 (NCBI UniGene Cluster)
UG_TITLE=(japonica cultivar-group) histone deacetylase HDAC3 mRNA, complete cds; alternatively spliced
DEF=Oryza sativa (japonica cultivar-group) cDNA clone:001-124-F07, full insert sequence.
FL= gb:AK064000.1
REP_ORG=O. sativa

Associated TIGR Gene Locus

TIGR Locus	Matching Probes	Description
LOC_Os02g12380	11/11	histone deacetylase, putative, expressed

Gene Context (flanking 25kb)

TIGR Locus	Matching Probeset	Matching Probes	Chr	Strand	Coordinates	Description
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
LOC_Os02g12400	Os.54164.1.S1_at	11/11	2	+	6468826..6472843	Leucine Rich Repeat family protein, expressed
LOC_Os02g12410	Os.53025.1.S1_at	1/11	2	+	6474514..6474992	U-box domain-containing protein, putative
LOC_Os02g12420	Os.53706.1.S1_at	11/11	2	+	6476683..6480097	Leucine Rich Repeat family protein, expressed

Select all/Clear all

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.20204.3.S1_a_at--217--199	1	Chr02:6452666..6452690 (25 bp)	ACTGCGGATGCAAATTCGATGGCCA	LOC_Os02g12380
Os.20204.3.S1_a_at--736--315	1	Chr02:6452678..6452702 (25 bp)	AATTCGATGGCCATCAACGCGCCAG	LOC_Os02g12380
Os.20204.3.S1_a_at--566--259	1	Chr02:6452718..6452742 (25 bp)	AACCGGGAAGCTCACTATGAACTAA	LOC_Os02g12380
Os.20204.3.S1_a_at--381--1009	1	Chr02:6452733..6452757 (25 bp)	TATGAACTAACCCACTTCAGGCCAC	LOC_Os02g12380
Os.20204.3.S1_a_at--791--441	1	Chr02:6452753..6452777 (25 bp)	GCCACCAGCTCTTATGCCACGGATT	LOC_Os02g12380
Os.20204.3.S1_a_at--332--441	1	Chr02:6452768..6452792 (25 bp)	GCCACGGATTCCTGCATGCTATTAG	LOC_Os02g12380
Os.20204.3.S1_a_at--724--63	1	Chr02:6452783..6452807 (25 bp)	ATGCTATTAGTTACTTACTCCGAGG	LOC_Os02g12380
Os.20204.3.S1_a_at--740--203	1	Chr02:6452795..6452819 (25 bp)	ACTTACTCCGAGGTGTTGTATGACT	LOC_Os02g12380
Os.20204.3.S1_a_at--85--665	1	Chr02:6452809..6452833 (25 bp)	GTTGTATGACTGTTTCTTCTGTAGG	LOC_Os02g12380
Os.20204.3.S1_a_at--339--519	1	Chr02:6452867..6452891 (25 bp)	GAATTCCAAAGTGTCCAGGCAATAC	LOC_Os02g12380
Os.20204.3.S1_a_at--655--359	1	Chr02:6452904..6452928 (25 bp)	CATTAGTCTGATCAATGTACTGCAG	LOC_Os02g12380

Target Sequence

ACTGCGGATGCAAATTCGATGGCCATCAACGCGCCAGGCAACGCCAAGAATGAACCGGGAAGCTCACTATGAACTAACCC
ACTTCAGGCCACCAGCTCTTATGCCACGGATTCCTGCATGCTATTAGTTACTTACTCCGAGGTGTTGTATGACTGTTTCT
TCTGTAGGAGTTTACAAATTACAACTGTTTCTTTTGTTGAAGAATTCCAAAGTGTCCAGGCAATACTGGACGTGGAGACA
TTAGTCTGATCAATGTACTGCAG

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