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Table 1 Target prediction and degradome analysis of known miRNAs

From: microRNAs participate in gene expression regulation and phytohormone cross-talk in barley embryo during seed development and germination

miRNA

Target CDS_ID

Target annotation

Binding site on CDS

PARE_cut sites

miR156

AK356077

Squamosa promoter-binding protein

839–858

849

AK374598

Squamosa promoter-binding protein

860–879

870

MLOC_11199.2

Squamosa promoter-binding-like protein 11

1154–1173

1164

miR159

AK251726.1

MYB transcription factor

962–982

973

AK370348

Predicted protein

1009–1028

948 and 1019

miR160

MLOC_64795.1

Auxin response factor 17

1329–1349

1340

MLOC_69988.1

Auxin response factor 10

717–737

728

miR165

MLOC_44268.1

MATE efflux family protein

159–179

170

AK362009

Class III homeo domain-leucine zipper

578–598

589

AK364215

Class III homeo domain-leucine zipper

639–658

649

MLOC_58644.1

Class III homeo domain-leucine zipper

980–1000

991

miR166

AK362009

Class III homeo domain-leucine zipper

578–598

589

AK364215

Class III homeo domain-leucine zipper

638–658

649

AK364215

Class III homeo domain-leucine zipper

640–658

649

AK365312

Class III homeo domain-leucine zipper

563–583

574

MLOC_44268.1

MATE efflux family protein

159–179

170

MLOC_58644.1

Class III homeo domain-leucine zipper

980–1000

991

miR167

MLOC_51932.2

Auxin response factor 30

2343–2363

2354

MLOC_58330.2

Auxin response factor 18

2528–2549

2540

MLOC_63938.1

Auxin response factor 9

2402–2423

2414

miR171

AK371946

GRAS family transcription factor

1090–1109

1100

miR172

AK355002

AP2-like ethylene-responsive transcription factor

1214–1234

1225

miR319

AK370348

TCP family transcription factor containing protein

1009–1028

1019

MLOC_63989.1

TCP family transcription factor containing protein

976–995

986

miR360

MLOC_69988.1

Auxin response factor 19

717–737

728

miR393

AK355927

Auxin signaling F-box 2

1560–1580

1571

AK374984

Auxin signaling F-box 3

1974–1994

1985

miR396

MLOC_64055.4

Growth-regulating factor 2

375–395

386

AK250947.1

Growth-regulating factor 1

480–500

491

AK353813

Growth-regulating factor 1

387–407

398

AK376404

Growth-regulating factor 5

417–437

428

MLOC_67201.4

Growth-regulating factor 1

741–761

752

MLOC_80060.1

Growth-regulating factor 1-like

507–527

518

MLOC_12347.1

Pre-mRNA-processing protein 45

1438–1458

1449

AK375237

Nascent polypeptide-associated complex subunit alpha-like protein

184–204

195

miR444

MLOC_16182.1

RING finger protein

1035–1055

1046

miR5051

MLOC_57965.3

Serine/threonine protein kinase

595–615

606

miR7757

MLOC_17471.2

NBS-LRR disease resistance protein, putative

194–215

206

miR9863

MLOC_24045.1

Disease resistance protein

(CC-NBS-LRR class) family

1259–1280

1271