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Table 4 Criteria for verifying rice uORFs that are conserved in Arabidopsis

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)

 

AK101100

Yes

Yes

Yes

525

525

100

5.0e-287

Protein phosphatase 2A

[go:6470] protein dephosphorylation

[go:166] nucleotide binding

Yes

AK066952

Yes

Yes

Yes

860

694

99

0

WW domain containing protein

Not available

Yesd

AK119592

Yes

Yes

Yes

343

343

100

6.8e-187

Homeodomain leucine zipper protein

[go:6355] regulation of transcription

[go:3677] DNA binding

Yes

AK100589

Yes

Yes

Yes

398

398

100

1.1e-215

S-Adenosylmethionine decarboxylase

[go:6596] polyamine biosynthesis

[go:5694] chromosome

Yes

AK103391

Yes

Yes

Yes

371

371

100

3.3e-194

Trehalose-6-phosphate phosphatase

[go:5992] trehalose biosynthesis

[go:9507] chloroplast

Yes

AK069534

Yes

Yes

1066e

485

413

61

7.6e-117

Auxilin-like protein

Not available

Yesf

AK069526

Yes

Yes

Yes

483

483

83

5.8e-256

GAMYB-binding protein

[go:6468] protein phosphorylation

[go:5524] ATP binding

[go:16301] kinase activity

Yes

AK072868

Yes

Yes

Yes

443

443

100

3.5e-238

CBL-interacting kinase 15

[go:6468] protein phosphorylation

[go:5524] ATP binding

[go:16301] kinase activity

Yes

AK060523

No

Yes

Yes

166

166

99

8.2e-88

Ankyrin-3

[go:5515] protein binding

Yes

AK067412

Yes

Yes

Yes

353

353

72

1.2e-136

Protein kinase ATN1

[go:6468] protein phosphorylation

[go:5524] ATP binding

[go:16301] kinase activity

Yes

AK102277

Yes

Yes

Yes

338

338

99

4.9e-179

Hypothetical protein

Not available

Yes

AK100332

Yes

Yes

4092e

2192

872

30

5.3e-28

Helicase

[go:3676] nucleic acid binding

[go:6355] regulation of transcription

[go:5515] protein binding

Nog

AK059639

No

Yes

Yes

154

154

100

2.6e-77

40S ribosomal s15 protein

[go:3735] structural part of ribosome

[go:6412] protein biosynthesis

Noh

  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 protein data suggests that the main open reading frame predicted by uORFSCAN extends further upstream, but does not overlap the predicted uORFs and so the uORFs are still valid.
  5. e The genome annotation for the CDS is longer by the indicated number of base pairs.
  6. f A shorter protein was identified, but does not overlap the predicted uORFs and so the uORFs are still valid.
  7. g A longer protein was identified indicating the main open reading frame extends further upstream, and does overlap the predicted uORFs and so the uORFs are not valid.
  8. h Possibly not functional because pre-orf distance is less than 20 nucleotides that is thought to be required for translation initiation.