Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array

Kim, Sung-Hyun; Bhat, Prasanna R; Cui, Xinping; Walia, Harkamal; Xu, Jin; Wanamaker, Steve; Ismail, Abdelbagi M; Wilson, Clyde; Close, Timothy J

doi:10.1186/1471-2229-9-65

BMC Plant Biology

Table 1 Rice SFP probe sets in the Saltol region

From: Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array

Probe set name	Gene model ^a	Position of 5' end	Annotation ^b	E-value	IR29 ^c	Sequenced
Os.35495.1.S1_s_at	LOC_Os01g16030	9020854	Putative ADP-ribosylation factor protein	1.00E-101	+	NO
Os.455.1.S1_at	LOC_Os01g16240	9192919	Putative calmodulin protein	7.00E-81	+	YES
Os.37639.1.S1_at	LOC_Os01g16414	9320117	Actin family protein	0	+	YES
Os.37842.1.S1_at	LOC_Os01g16520	9374978	Glutamyl-tRNA synthetase family protein	0	+	YES
Os.247.1.S1_at	LOC_Os01g16650	9442463	Putative ubiquitin-conjugating enzyme X protein	1.00E-109	+	YES
Os.14702.1.S1_a_at	LOC_Os01g17020	9746901	Expressed protein	1.00E-136	+	YES
Os.7948.1.S1_a_at	LOC_Os01g17150	9856128	Expressed protein	2.00E-74	+	YES
Os.29809.2.S1_x_at	LOC_Os01g18280	10259724	SNF7 family protein	0	+	NO
Os.3655.1.S1_at	LOC_Os01g18744	10562090	Transferase family protein	0	+	YES
Os.55011.1.S1_x_at	LOC_Os01g20120	11427774	Expressed protein	0	-	YES
Os.45751.1.A1_x_at	LOC_Os01g20880	11637965	Protein kinase domain containing protein	1.00E-123	+	YES
Os.13500.2.S1_x_at	LOC_Os01g20940	11676292	Putative dual specificity protein phosphatase family protein	0	+	YES
Os.35123.1.S1_at	LOC_Os01g22230	12482404	Peroxidase family protein	0	+	YES
OsAffx.23355.1.S1_s_at	LOC_Os01g23630	13274139	Transcription initiation factor IID, 18kD subunit family protein	1.00E-104	+	NO
Os.24895.1.S1_at	LOC_Os01g24060	13543313	Putative Importin alpha-1b subunit protein	0	+	YES
Os.33510.1.S2_at	LOC_Os01g25320	14285672	TolA protein	0	+	YES
Os.25255.1.S1_at	LOC_Os01g25530	14454283	Putative PPR986-12 protein	0	+	YES
Os.18293.1.S1_at	LOC_Os01g26020	14734782	Expressed protein	1.00E-44	+	YES
Os.40545.1.S1_x_at	LOC_Os01g26160	14792157	Putative HASTY protein	0	+	YES
Os.12845.1.S1_at	LOC_Os01g26832	15177467	Hypothetical protein	1.00E-178	+	YES
Os.4023.1.S1_at	LOC_Os01g27020	15386316	Putative transposon protein, unclassified	0	+	YES

^a Rice gene models recorded from rice pseudomolecules, release 4 of the Institute of Genomic Research (TIGR).
^b Putative proteins were annotated by BLASTN search of TIGR rice pseudomolecules, release 4.
^c FL478 allele exactly matches the sequence of IR29 allele (+) or does not (-)

Back to article page

ISSN: 1471-2229

Contact us

General enquiries: journalsubmissions@springernature.com