Skip to main content

Table 3 Examples of expression ratios and putative functions of unannotated transcripts

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

shoot

      

Cufflinks_ID

NT_Length

RPKM_0

RPKM_1

Ratio

AA_Length

Description

Shoot_CUFF.273129.0

146

1.333

13.8

10.4

48

Indole-3-glycerol phosphate lyase

Shoot_CUFF.412372.0

372

3.871

14.33

3.7

122

Inter-alpha-trypsin inhibitor heavy chain-related

Shoot_CUFF.436239.0

1,376

2.744

7.23

2.6

320

Pleiotropic drug resistance protein 4

Shoot_CUFF.379980.0

692

2.137

5.398

2.5

118

HHP2 (heptahelical transmembrane protein2)

Shoot_CUFF.81865.0

2,068

17.504

37.286

2.1

591

Alcohol oxidase-related

root

      

Cufflinks_ID

NT_Length

RPKM_0

RPKM_1

Ratio

AA_Length

Description

Root_CUFF.327296.0

965

0

24.461

-

283

Gibberellin 2-beta-dioxygenase

Root_CUFF.298860.0

638

4.519

67.671

15.0

137

Putative lipoxygenase 5

Root_CUFF.439679.0

691

6.259

23.299

3.7

229

Probable pleiotropic drug resistance protein 1

Root_CUFF.168009.0

1,381

6.562

22.293

3.4

75

Phosphoinositide-specific phospholipase C

Root_CUFF.439685.0

1,382

3.8

12.555

3.3

336

Pleiotropic drug resistance protein 4

Root_CUFF.300686.0

473

1.415

4.607

3.3

157

Kinesin motor protein-related

Root_CUFF.177468.0

641

2.651

7.869

3.0

40

Phosphatidate cytidylyltransferase family protein

Root_CUFF.220154.0

636

1.7

4.695

2.8

212

Chromosome-associated kinesin, putative

Root_CUFF.365224.0

338

2.133

5.491

2.6

68

Binding/protein transporter

Root_CUFF.415910.0

372

6.228

14.968

2.4

122

Inter-alpha-trypsin inhibitor heavy chain-related

Root_CUFF.406739.0

669

1.462

3.317

2.3

48

VAD1 (vascular associated death1)

Root_CUFF.44438.0

639

2.256

4.736

2.1

118

Jacalin lectin family protein

Root_CUFF.450445.0

907

1.419

2.892

2.0

302

PDR11 (pleiotropic drug resistance 11)

  1. Cufflinks ID (Cufflinks_ID); total nucleotide length of each predicted transcript (NT_Length); RPKM without salinity stress (RPKM_0) or with salinity stress (RPKM_1); calculated ratio of RPKM (rpkm_1/rpkm_0; Ratio); number of amino acids encoded by putative ORF (AA_Length); and name of similar protein (Description) are listed. Differentially expressed Cufflinks transcripts were identified by the G-test with a 1% false discovery rate. Highly differentially expressed genes (ratio ≥2) derived from different loci that had ORFs predicted by BLASTX search are listed. "-" means a calculated ratio of infinity because the RPKM without salinity stress (RPKM_0) was 0. Detailed data for all unannotated transcripts are listed in Additional file 3: Table S3.