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Table 2 Criteria for verifying rice uORFs in 5 out of 5

From: Conserved upstream open reading frames in higher plants

Accession

FL- cDNAa

Upstream & In-frame stop codon

Agreement with genome annotationb

Alignment of uORFSCAN identified main proteins with UniProt proteinsc

uORF valid

    

UniProt protein length (AA)

Align length (AA)

Identities (%)

Expect

Annotation

GO classication (Arabidopsis thaliana)

 

AK106095

Yes

Yes

Yes

392

392

100

2.2e-217

Oxidoreductase

[go:19538] protein metabolism

[go:16706] oxidoreductase activity

Yes

AK103391

Yes

Yes

Yes

371

371

100

3.4e-194

Trehalose-6-phosphate phosphatase

[go:5992] trehalose biosynthesis

[go:9507] chloroplast

[go:4805] trehalose-phosphatase activity

Yes

AK100589

Yes

Yes

Yes

398

398

100

1.1e-215

AdoMetDC

[go:6596] polyamine biosynthesis

[go:5694] chromosome

Yes

AK073303

Yes

Yes

Yes

257

257

100

1.6e-141

Acyl-CoA independent ceramide synthase

[go:6672] ceramide metabolism

[go:16020] membrane

[go:3824] catalytic activity

[go:16811] hydrolase activity

Yes

AK072868

Yes

Yes

Yes

443

443

100

3.6e-238

uncharacterized protein (probable CBL-interacting serine/threonine-protein kinase 15)

[go:6468] protein phosphorylation

[go:7165] signal transduction

[go:5524] ATP binding

[go:4672] protein kinase activity

Yes

AK072649

Yes

Yes

Yes

480

488

76

9.6e-199

Ribosomal protein S6 Kinase

[go:45946] positive translation

[go:6468] protein phosphorylation

[go:9507] chloroplast

[go:16301] kinase activity

Yes

AK066145

No

Yes

Yes

119

119

100

1.3e-59

Membrane-anchored ubiquitin-fold protein

[go:6464] protein modification

Yes

AK064792

Yes

Yes

197d

109

108

57

8.4e-26

F9L1.29 protein

Not available

Yes

AK060523

Yes

Yes

Yes

166

166

100

1.9e-88

uncharacterized protein (probable ankyrin-3)

[go:9507] chloroplast

[go:5515] protein binding

Yes

  1. a Used rice cDNA in blastn search against "NCBI EST_Others" database (rice) to search for longer 5' ESTs.
  2. b Used rice cDNA in blastn search against "TIGR Rice Genome Annotation DB: Coding Sequences" database to verify the cDNA ORF.
  3. c Translated the rice cDNA in the same frame as the main open reading frame identified by uORFSCAN (include translations upstream of predicted start Methionine). The resulting protein sequence was used in a blastp search against "The UniProt Knowledgebase (UniProt)" database.
  4. d The genome annotation for the CDS is longer by the indicated number of base pairs.
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BMC Genomics

ISSN: 1471-2164

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