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Table 2 Arabidopsis loci with conserved peptide uORFs identified from Arabidopsis-rice comparison

From: Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes

Homology group

Locus

Gene Name

mORF description

Gene ontology molecular function

Recent duplicate

1

At2g18160.1

GBF5, AtbZIP2

Basic leucine zipper (bZIP)

Transcription factor

At4g34590

1

At4g34590.1

GBF6, ATB2, AtbZIP11

bZIP

Transcription factor

At2g18160

1

At3g62420.1a

AtbZIP53

bZIP

Transcription factor

Not found

1

At5g49450.1

AtbZIP1

bZIP

Transcription factor

Not found

1

At1g75390.1

AtbZIP44

bZIP

Transcription factor

Not found

2

At2g27230.1

AtBHLH156 b

Basic helix-loop-helix (bHLH)

Transcription factor

Not found

2

At2g31280.1

AtBHLH155 b

bHLH

Transcription factor

At1g06150

2

At1g06150.1

 

bHLH

Transcription factor

At2g31280

3

At3g02470.1

AdoMetDC1

AdoMetDC

AdoMetDC

At5g15950

3

At5g15950.1

AdoMetDC2

AdoMetDC

AdoMetDC

At3g02470

3

At3g25570.1

AdoMetDC3

AdoMetDC

AdoMetDC

Not found

4

At4g25670.1

 

Expressed transcript

Unknown

At5g52550

4

At4g25690.1

 

Expressed transcript

Unknown

At5g52550c

4

At5g52550.1

 

Expressed transcript

Unknown

At4g25670

5

At5g61230.1

 

Ankyrin repeat

Protein binding

At5g07840

5

At5g07840.1

 

Ankyrin repeat

Protein binding

At5g61230

6

At2g43020.1

 

Amine oxidase

Oxidoreductase

At3g59050

6

At3g59050.1

 

Amine oxidase

Oxidoreductase

At2g43020

7

At1g36730.1

 

Putative eIF-5

Translation initiation factor

Not found

8

At3g12010.1a

 

Similar to Mic-1

Unknown

Not found

9

At5g09670.1 and .2

 

Expressed transcript

Unknown

At5g64550

9

At5g64550.1

 

Expressed transcript

Unknown

At5g09670

9

At1g64140.1

 

Expressed transcript

Unknown

Not found

10

At5g45430.1

AtMPK23 d

MAP kinase, PPC family 4.5.1

ATP binding, protein kinase

At4g19110e

10

At4g19110.1

AtMPK22 d

MAP kinase, PPC family 4.5.1

ATP binding, protein kinase

At5g45430e

11

At4g12430.1

 

TPPase

Catalytic activity

At4g22590

11

At4g22590.1

 

TPPase

Catalytic activity

At4g12430

12

At1g70780.1

 

Expressed transcript

Unknown

At1g23150

12

At1g23150.1

 

Expressed transcript

Unknown

At1g70780

13

At3g18000.1

XPL1, NMT1, PEAMT1

Phosphoethanolamine N-methyltransferase

Methyltransferase

At1g48600

13

At1g48600.2

NMT2

Methyltransferase

Methyltransferase

At3g18000

13

At1g73600.1

NMT3

Methyltransferase

Methyltransferase

Not found

14

At3g01470.1

HAT5, HB-1, HD-ZIP-1, ATHB1

Homeobox

DNA binding, transcription factor, transcriptional activator

Not found

15

At1g29950.2

AtBHLH144 b

bHLH

Transcription factor

Not found

15

At5g50010.1

AtBHLH145 b

bHLH

Transcription factor

Not found

15

At5g64340.1

AtBHLH142 b, SAC51

bHLH

Transcription factor

At5g09460

15

At5g09460.1a

AtBHLH143 b

bHLH

Transcription factor

At5g64340

16

At3g51630.1

ZIK1, WNK5

MAP kinase, PPC family 4.1.5

Protein kinase

Not found

17

At1g58120.1

 

Expressed transcript

Unknown

Not found

17

At3g53400.1

 

Expressed transcript

Unknown

Not found

17

At5g03190.1

 

Expressed transcript

Unknown

Not found

17

At5g01710.1

 

Expressed transcript

Unknown

Not found

18

At4g36990.1

AT-HSFB1, ATHSF4

Heat shock factor

Transcription factor

Not found

19

At5g53590.1

 

SAUR Auxin responsive

Unknown

Not found

  1. AdoMetDC, S-Adenosylmethionine decarboxylase; PPC, PlantsP protein kinase classification; TPPase, Trehalose-6-phosphate phosphatase.
  2. auORF found upstream of annotated mORF-containing locus (within 2 kb).
  3. bAs designated by Bailey et al [68], nomenclature agreed upon by both Heim et al [69] and Toledo-Ortiz et al [67].
  4. cAt4g25670 and At4g25690 (tandem duplicates) have the same recent retained duplicate (not reported by Blanc and Wolfe).
  5. dAs designated by the PlantsP database [99].
  6. eNot found in Blanc and Wolfe's initial analysis of ohnologs, but synteny and homology suggest they are retained recent duplicates.
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BMC Biology

ISSN: 1741-7007

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