Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.)

Table 2 Numbers and ORF predictions of transcripts

		shoot	root
No. of transcripts mapped on RAP2 annotated loci		48,506	51,409
No. of transcripts mapped on unannotated region		2,795	3,082
	--ORFs detected by BLASTX	(995)	(1,052)
	--ORFs ≥ 20 a.a., no BLASTX hits	(1,670)	(1,873)
	--no ORFs or ORFs < 20 a.a.	(130)	(157)
Total		51,301	54,491

Transcripts were predicted on the basis of the piling up of mapped reads by the Cufflinks program (RPKM ≥ 2, length ≥ 100 bp). ORF prediction was conducted by BLASTX search against UniProt (Swiss-Prot) and RefSeq (reviewed and validated). ORF: open reading frame; a.a: amino acids.

ISSN: 1471-2164