Agri-SNPs – MyRiceBase

Search for SNPs in genes related to agronomical traits:

Trait :

Category :

SNP effect :

Chr :

Trait	Category	Gene ID	SNP ID	SNP effect	Chr	Pos	Allele	Gene name	Gene description	Bali	PH9	MRM16	MRQ100	MR297	MRQ76	OsID
drawf	Agronomical	Os01g0286900	chr01_10312477	5_prime_UTR_variant	chr01	10,312,477	C/A	OsIAA4,IAA4	Similar to Auxin-responsive protein IAA31 (Indoleacetic acid-induced protein 31).	CC	CC	CA	CC	CC	CC	Os01g0286900
lodging drawf	Abiotic Stress	Os01g0286900	chr01_10312477	5_prime_UTR_variant	chr01	10,312,477	C/A	OsIAA4,IAA4	Similar to Auxin-responsive protein IAA31 (Indoleacetic acid-induced protein 31).	CC	CC	CA	CC	CC	CC	Os01g0286900
absisic acid	Biochemical	Os01g0286900	chr01_10312477	5_prime_UTR_variant	chr01	10,312,477	C/A	OsIAA4,IAA4	Similar to Auxin-responsive protein IAA31 (Indoleacetic acid-induced protein 31).	CC	CC	CA	CC	CC	CC	Os01g0286900
absisic acid	Biochemical	Os01g0286900	chr01_10312516	5_prime_UTR_variant	chr01	10,312,516	G/A	OsIAA4,IAA4	Similar to Auxin-responsive protein IAA31 (Indoleacetic acid-induced protein 31).	GA	GG	GG	GA	GA	GA	Os01g0286900
drawf	Agronomical	Os01g0286900	chr01_10312516	5_prime_UTR_variant	chr01	10,312,516	G/A	OsIAA4,IAA4	Similar to Auxin-responsive protein IAA31 (Indoleacetic acid-induced protein 31).	GA	GG	GG	GA	GA	GA	Os01g0286900
lodging drawf	Abiotic Stress	Os01g0286900	chr01_10312516	5_prime_UTR_variant	chr01	10,312,516	G/A	OsIAA4,IAA4	Similar to Auxin-responsive protein IAA31 (Indoleacetic acid-induced protein 31).	GA	GG	GG	GA	GA	GA	Os01g0286900
lodging drawf	Abiotic Stress	Os01g0286900	chr01_10313534	intron_variant	chr01	10,313,534	C/A	OsIAA4,IAA4	Similar to Auxin-responsive protein IAA31 (Indoleacetic acid-induced protein 31).	CA	CC	CA	CA	CA	CA	Os01g0286900
absisic acid	Biochemical	Os01g0286900	chr01_10313534	intron_variant	chr01	10,313,534	C/A	OsIAA4,IAA4	Similar to Auxin-responsive protein IAA31 (Indoleacetic acid-induced protein 31).	CA	CC	CA	CA	CA	CA	Os01g0286900
drawf	Agronomical	Os01g0286900	chr01_10313534	intron_variant	chr01	10,313,534	C/A	OsIAA4,IAA4	Similar to Auxin-responsive protein IAA31 (Indoleacetic acid-induced protein 31).	CA	CC	CA	CA	CA	CA	Os01g0286900
lodging drawf	Abiotic Stress	Os01g0286900	chr01_10313901	intron_variant	chr01	10,313,901	T/C	OsIAA4,IAA4	Similar to Auxin-responsive protein IAA31 (Indoleacetic acid-induced protein 31).	TC	TT	TC	TC	TC	TC	Os01g0286900
Trait	Category			SNP effect	Chr

Search SNPs with deleterious effect in genes related to agronomical traits:

Traits :

Class :

Chr :

SIFT score :

Traits	Class	OsID	LocID	R498ID	Gene name	Gene description	SNP ID	Chr	Pos	Allele	SIFT score	Transcript ID	Amino acid allele	Amino acid pos	dbsnp	Bali	PH9	MRM16	MRQ100	MR297	MRQ76
salicylic acid	Biochemical	Os01g0358400	LOC_Os01g25610	OsR498G0100935300.01	RPS4	40S ribosomal protein S4, putative, expressed	chr01_14514480	chr01	14,514,480	A/G	0.04	OS01T0358400-01	I/V	92	novel	AG	AA	AA	AA	AA	AA
drought tolerance	Abiotic Stress	Os01g0358400	LOC_Os01g25610	OsR498G0100935300.01	RPS4	40S ribosomal protein S4, putative, expressed	chr01_14514480	chr01	14,514,480	A/G	0.04	OS01T0358400-01	I/V	92	novel	AG	AA	AA	AA	AA	AA
BLB	Biotic stress	Os01g0383900	LOC_Os01g28690	OsR498G0101004300.01	APIP12	nucleoporin autopeptidase domain containing protein, expressed	chr01_16062855	chr01	16,062,855	A/G	0.04	OS01T0383900-01	S/G	3	rs18634483	AG	AA	AG	AG	AG	AG
shoot	Morphology	Os01g0142800	LOC_Os01g04950	OsR498G0100152900.01	OsPTR7,PTR7	peptide transporter PTR2, putative, expressed	chr01_2296920	chr01	2,296,920	C/T	0.00	OS01T0142800-02	R/W	223	novel	CT	CT	CT	CT	CT	CC
grain	Agronomical	Os01g0142800	LOC_Os01g04950	OsR498G0100152900.01	OsPTR7,PTR7	peptide transporter PTR2, putative, expressed	chr01_2296920	chr01	2,296,920	C/T	0.00	OS01T0142800-02	R/W	223	novel	CT	CT	CT	CT	CT	CC
transporter	Biochemical	Os01g0142800	LOC_Os01g04950	OsR498G0100152900.01	OsPTR7,PTR7	peptide transporter PTR2, putative, expressed	chr01_2296920	chr01	2,296,920	C/T	0.00	OS01T0142800-02	R/W	223	novel	CT	CT	CT	CT	CT	CC
endosperm	Morphology	Os01g0601000	LOC_Os01g41720	OsR498G0101477000.01	OsEnS-10	expressed protein	chr01_23611397	chr01	23,611,397	A/G	0.01	OS01T0601000-00	S/P	461	novel	AA	AG	AA	AA	AA	AA
endosperm	Morphology	Os01g0601000	LOC_Os01g41720	OsR498G0101477000.01	OsEnS-10	expressed protein	chr01_23611652	chr01	23,611,652	T/G	0.01	OS01T0601000-00	Q/P	433	novel	TG	TT	TG	TT	TT	TG
culm	Morphology	Os01g0612700	LOC_Os01g42710	OsR498G0101532700.01	OsLOL5,OsLSD5,LOL5,LOL2,OsLOL2	retrotransposon protein, putative, unclassified, expressed	chr01_24294974	chr01	24,294,974	C/T	0.01	OS01T0612700-01	P/L	228	novel	CT	CC	CT	CT	CT	CT
lodging drawf	Abiotic Stress	Os01g0612700	LOC_Os01g42710	OsR498G0101532700.01	OsLOL5,OsLSD5,LOL5,LOL2,OsLOL2	retrotransposon protein, putative, unclassified, expressed	chr01_24294974	chr01	24,294,974	C/T	0.01	OS01T0612700-01	P/L	228	novel	CT	CC	CT	CT	CT	CT
Traits	Class							Chr			SIFT score