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Table 4 Non-conserved maize miRNA targets identified by degradome sequencing in this study

From: Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing

miRNAa

Target gene

Location of the target site

Repeat normalized read abundance (category)b

Target gene annotationc

Other degradome evidence

5′-RACE or genetic experiment

   

I

II

III

IV

   

miR2275

GRMZM2G044004

3′-UTR

0.33 (4)

   

nucleic acid binding protein

N

N

miR2275

GRMZM2G154532

5′-UTR/CDS

   

0.57 (2)

NAD dependent epimerase/dehydratase family protein

N

N

miR2275

GRMZM2G329532

CDS

   

1.00 (1)

unknown

N

N

miR2118

GRMZM2G066406

5′-UTR

  

16.00 (1)

2.00 (1)

unknown

N

N

miR2118

GRMZM2G031788

CDS

   

2.00 (1)

unknown

N

N

miRs4

GRMZM2G078124

CDS/3′-UTR

 

1.00 (2)

  

Molluscan rhodopsin C-terminal tail

N

N

miRs4

GRMZM5G829103

3′-UTR

 

1923.40 (0)

  

CCAAT-binding transcription factor#

[26, 28]

N

miRs4

GRMZM2G165488

3′-UTR

 

2804.25 (0)

  

CCAAT-binding transcription factor#

[26, 28]

N

miRs4

GRMZM2G000686

3′-UTR

 

21.80 (0)

  

CCAAT-binding transcription factor#

[26, 28]

N

miRs9

GRMZM2G467356

CDS

   

12.00 (0)

Ferredoxin

N

N

miRs14

GRMZM2G079683

3′-UTR

1.00 (4)

   

unknown

N

N

miRs15

GRMZM2G091189

3′-UTR

 

0.33 (4)

  

transcription factor

N

N

miRs17

GRMZM2G160041

CDS

0.25 (4)

  

1.75 (0)

DNA binding protein

N

N

miRs17

GRMZM2G085550

3′-UTR

  

5.00 (1)

 

unknown

N

N

  1. aMiRNA data from miRBase 19.0. bCalculation based on the method in Addo-Quaye et al. [47], cGene annotations fromB73 RefGen_v2 (release 5b. 60 in February 2011). #Predicted by Zhang et al. [17]. Abbreviation: tpm, transcripts per million; CDS, coding sequence; UTR, untranslated region; siRNA, small interfering RNA.