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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.