CREP Browser

OsAffx.21897.5.S1_x_at

Description

gb:NM_195233.1
DB_XREF= gi:37531825
TID=OsAffx.21897.5
CNT=1
FEA=mRNA
TIER=ConsEnd
STK=0
NOTE=sequence(s) not in UniGene
DEF=Oryza sativa (japonica cultivar-group) putative gypsy-type retrotransposon (OSJNBb0086I08.2), mRNA.
PROD=putative gypsy-type retrotransposon
REP_ORG=O. sativa

Associated TIGR Gene Locus

TIGR Locus	Matching Probes	Description
LOC_Os06g33900	7/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os12g29200	7/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os12g33340	7/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os11g41750	6/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os06g50260	6/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os07g46250	6/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os05g04970	6/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os10g10840	6/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os08g27270	6/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os04g07030	6/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os04g49810	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os04g10840	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os10g31600	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os10g13390	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os12g17300	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os05g15980	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os08g08780	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os01g45220	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os07g47730	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os11g45230	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os08g15580	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os01g36150	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os08g13760	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os11g43380	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os04g07290	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os07g16490	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os02g38280	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os04g21150	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os01g09610	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os09g09250	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os03g26400	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os05g43020	4/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os06g32880	3/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os09g19600	3/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os10g12280	2/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os08g24640	2/11	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os06g14130	2/11	retrotransposon protein, putative, Ty3-gypsy subclass

Gene Context (flanking 25kb)

TIGR Locus	Matching Probeset	Matching Probes	Chr	Strand	Coordinates	Description
LOC_Os06g33870	NA	NA	6	+	19692895..19694181	transposon protein, putative, CACTA, En/Spm sub-class
LOC_Os06g33880	OsAffx.27921.1.S1_x_at	5/11	6	+	19700318..19700834	expressed protein
LOC_Os06g33890	NA	NA	6	+	19711500..19717595	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os06g33900	OsAffx.21897.5.S1_x_at	7/11	6	+	19717912..19720854	retrotransposon protein, putative, Ty3-gypsy subclass
LOC_Os06g33910	NA	NA	6	+	19723345..19723623	hypothetical protein
LOC_Os06g33920	Os.32493.1.S1_at	11/11	6	+	19729663..19734062	expressed protein
LOC_Os06g33930	OsAffx.15718.1.S1_at	11/11	6	+	19735568..19739290	Uncharacterized BCR, COG1963 family protein, expressed
LOC_Os06g33940	Os.4386.1.S1_s_at	11/11	6	+	19742868..19745340	expressed protein
LOC_Os06g33940	Os.54154.1.S1_at	10/11	6	+	19742868..19745340	expressed protein

Select all/Clear all

Gene Ontology Classification

GO id	Type	Name
NONE	NONE	NONE

Probe Info

Probe Name	Hit(s)	Location	Sequence	TIGR Locus
OsAffx.21897.5.S1_x_at--394--751	31	Chr11:26865954..26866049 (25 bp)	GTGGTTCATCAAAAGCGCAAGCCGC	LOC_Os11g45230
OsAffx.21897.5.S1_x_at--745--857	31	Chr11:26865955..26866050 (25 bp)	TGGTTCATCAAAAGCGCAAGCCGCC	LOC_Os11g45230
OsAffx.21897.5.S1_x_at--655--789	32	Chr11:26865956..26866051 (25 bp)	GGTTCATCAAAAGCGCAAGCCGCCA	LOC_Os11g45230
OsAffx.21897.5.S1_x_at--1032--673	32	Chr11:26865957..26866052 (25 bp)	GTTCATCAAAAGCGCAAGCCGCCAG	LOC_Os11g45230
OsAffx.21897.5.S1_x_at--483--983	2	Chr11:25681503..25681599 (25 bp)	TAAAGGAAGTCGAAGATCGCAAGAT	LOC_Os11g43380
OsAffx.21897.5.S1_x_at--503--231	7	Chr12:20137745..20137840 (24 bp)	AAAGGAAGTCGAAGATCGCAAGATC	LOC_Os12g33340
OsAffx.21897.5.S1_x_at--270--293	15	Chr11:24568727..24568823 (25 bp)	AAGGAAGTCGAAGATCGCAAGATCA	LOC_Os11g41750
OsAffx.21897.5.S1_x_at--214--95	16	Chr11:24568728..24568824 (25 bp)	AGGAAGTCGAAGATCGCAAGATCAA	LOC_Os11g41750

Target Sequence

GTGGTTCATCAAAAGCGCAAGCCGCCAGGATGGAACAGATGGCGAAGCAAATTGAAGCCCTGGAGAGGGACAAGACAGAA
CTGGCTGCACAAAGGGACTCAGCCTTAAAGGAAGTCGAAGATCGCAAGATCAA

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

Browse Element(s) Details