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Table 2 Correlation between miR399 and potential target genes

From: Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana

miRNA

Target

Function description of targeta

PCCb

Target scorec

Cluster IDd

miR399a

AtPT1

Inorganic phosphate transporter 1–1

-0.72

5

3

miR399a

SMXL5

Clp amino terminal domain-containing protein

-0.72

5

1

miR399a

ECT2

Physically interacts with CIPK1.

-0.71

4.5

3

miR399a

AtCS-C

Dehydratase epimerase/racemase deaminase

-0.70

4.8

2

miR399a

TIP4;1

Aquaporin TIP4-1, transporter

-0.68

4.8

3

miR399a

AtPT2

Inorganic phosphate transporter 1-2

-0.67

5

1

miR399a

SPPL5

Signal peptide peptidase-like 5, aspartic protease

-0.67

5

6

miR399a

AtSCAR4

Protein SCAR4

-0.62

5

6

miR399a

AtPP2-A5

Protein PHLOEM PROTEIN 2-LIKE A5

-0.59

4

6

miR399a

AT3G18620

DHHC-type zinc finger family protein

-0.59

4.8

3

miR399a

AtCFM2

Involved in group I and group II intron splicing.

-0.59

4.5

6

miR399a

AT1G61860

Protein kinase family protein

-0.58

4.8

3

miR399a

AT2G31150

ATP binding / ATPase

-0.58

5

6

miR399a

AT3G44820

Phototropic-responsive NPH3 family protein

-0.58

4.8

3

miR399a

IPGAM1

2,3-bisphosphoglycerate-independent phosphoglycerate mutase 1

-0.57

5

3

miR399a

AT2G25420

mRNA splicing factor esterase kinase inhibitor

-0.57

4

6

miR399a

AtOPR1

12-oxophytodienoate reductase 1

-0.57

4.8

3

miR399a

AT4G19520

TIR-NBS-LRR class disease resistance protein

-0.56

5

6

miR399a

OZS2

Pectinesterase/pectinesterase inhibitor 3

-0.55

4.8

3

miR399a

AT2G38740

Phosphatase

-0.55

4.5

2

miR399a

BLH1

BEL1-like homeodomain protein 1

-0.53

4.2

3

miR399a

TGA7

Transcription factor TGA7

-0.51

5

3

miR399a

AT1G61590

Protein kinase superfamily protein

-0.51

4.8

3

miR399a

CYP705A30

Cytochrome P450, family 705, subfamily A, polypeptide 30

-0.44

2

3

miR399a

PHO2

Mediates degradation of PHO1 and PHT1s

-0.37

0.8

/

miR399a

NF-YA10

Nuclear transcription factor Y subunit A-10

-0.10

2.5

1

miR399d

XLOC_001691

/

-0.74

5

1

miR399b

XLOC_026270

/

-0.68

5

6

miR399e

XLOC_013661

/

-0.64

5

2

miR399b

XLOC_013840

/

-0.63

4.5

6

miR399e

XLOC_026270

/

-0.62

4.5

6

miR399e

XLOC_003248

/

-0.60

5

3

miR399e

XLOC_001806

/

-0.59

4.8

5

miR399a

XLOC_018338

/

-0.58

4.5

5

miR399d

XLOC_027498

/

-0.58

4.8

6

miR399d

XLOC_010238

/

-0.57

4.8

3

miR399c-5p

XLOC_019368

/

-0.57

5

4

miR399c-3p

XLOC_016349

/

-0.53

4

6

miR399b

XLOC_020833

/

-0.53

5

3

miR399a

XLOC_008029

/

-0.51

5

6

miR399c-3p

XLOC_005358

/

-0.50

4.8

6

miR399f

XLOC_026270

/

-0.50

4.5

6

  1. Note:
  2. aColumn3 describes functions of targeted genes of miR399
  3. bPCC refers the expression correlation of miR399 and its target genes
  4. cTarget score is the target match score calculated by psRobot, and lower target score represents better base pair match between miRNA and targets
  5. dThe last column indicates the cluster that target genes or lncRNAs belonging to