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Table 1 LincRNAs acting as miRNA targets validated using degradome data

From: Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize

zma-miRNAsa

Transcriptsb

start-endc

MFEratiod

Categorye

P-valuef

Degradome data fileg

zma-miR156e-3p

Li_TCONS_00080887

75-95

0.674311926605505

4

0.071329710792311

LN_root

zma-miR156e-3p

zhang_TCONS_00012690

489-511

0.768348623853211

4

0.020921336970078

LN_root

zma-miR156h-3p

zhang_TCONS_00012690

625-646

0.713936430317848

4/4/4

0.0514855197295749/0.046703544571294/0.0376430084254001

LN_root/LN_leaf/HN_root

zma-miR159d-3p:zma-miR159c-3p

Boerner_Z27kG1_14953

633-654

0.723192019950125

4

0.0382439063811821

HN_leaf

zma-miR159e-5p

Boerner_Z27kG1_09751

293-312

0.686602870813397

4/4

0.046703544571294/0.0376430084254001

LN_leaf/HN_root

zma-miR159e-5p

Boerner_Z27kG1_15115

817-837

0.657894736842105

4

0.0750252163870715

HN_leaf

zma-miR160b-3p:zma-miR160g-3p

Boerner_Z27kG1_08283

74-94

0.691588785046729

4

0.0302295095199341

HN_root

zma-miR160c-3p

Boerner_Z27kG1_16361

1423-1444

0.689156626506024

4

0.0824909413024753

LN_leaf

zma-miR160c-3p

Boerner_Z27kG1_23317

2302-2323

0.667469879518072

4/2/4

0.155614651330728/0.0297578023818319/0.117310766689232

LN_root/LN_leaf/HN_leaf

zma-miR162-5p

Boerner_Z27kG1_13892

28-48

0.659605911330049

4/4

0.155614651330728/0.115544761245953

LN_root/HN_root

zma-miR164b-3p

Boerner_Z27kG1_01046

97-117

0.67175572519084

1/0/0/0

0.0137287981463647/0.00691182420446057/0.00821020675558204/0.00827523084432658

LN_root/LN_leaf/HN_root/HN_leaf

zma-miR164d-3p

Boerner_Z27kG1_22106

573-593

0.693506493506494

4

0.181974073806857

LN_root

zma-miR164e-3p

Boerner_Z27kG1_03819

109-130

0.660831509846827

4

0.141916540983859

LN_leaf

zma-miR166h-5p

Boerner_Z27kG1_17085

280-301

0.688836104513064

4

0.0282897431510059

LN_leaf

zma-miR166i-5p

Boerner_Z27kG1_06707

85-104

0.757009345794392

4

0.0189498889103007

LN_leaf

zma-miR166i-5p

Boerner_Z27kG1_17308

553-572

0.77803738317757

4/2/4/3

0.0105159612050723/0.00188631556542906/0.00764459114629912/0.00047103572965379

LN_root/LN_leaf/HN_root/HN_leaf

zma-miR166n-5p

Boerner_Z27kG1_01291

759-780

0.65281173594132

4

0.262254475002389

HN_leaf

zma-miR169c-3p

Boerner_Z27kG1_22188

252-273

0.686635944700461

4

0.0312172902072148

LN_root

zma-miR169f-3p

Boerner_Z27kG1_15675

450-471

0.696517412935323

0

0.00163062708112194

LN_leaf

zma-miR169i-3p:zma-miR169j-3p:zma-miR169k-3p

Boerner_Z27kG1_23086

819-837

0.665753424657534

4

0.457851673892433

LN_leaf

zma-miR169l-3p

Boerner_Z27kG1_06005

556-575

0.661498708010336

4

0.0736720564421364

LN_leaf

zma-miR169m-3p

zhang_TCONS_00011169

341-360

0.660220994475138

2/3/3

0.04068724565891/0.0034421015727073/0.0103116935935227

LN_leaf/HN_root/HN_leaf

zma-miR171b-5p

Boerner_Z27kG1_16154

453-472

0.654285714285714

4

0.128405843607718

LN_root

zma-miR2118d

Boerner_Z27kG1_20838

4-26

0.660674157303371

4

0.0907587348469249

LN_root

zma-miR2275a-3p

Li_TCONS_00089775

205-227

0.669724770642202

4

0.108447036911749

LN_leaf

zma-miR394b-3p:zma-miR394a-3p

Boerner_Z27kG1_16154

1242-1260

0.691516709511568

4/2/4/4

0.0414049715995405/0.00752393997803091/0.0302295095199341/0.0307139613443539

LN_root/LN_leaf/HN_root/HN_leaf

zma-miR395o-3p

Boerner_Z27kG1_21671

386-406

0.67479674796748

4

0.00764459114629912

HN_root

zma-miR399e-5p

Boerner_Z27kG1_03819

175-196

0.652173913043478

4/4/4/2

0.301930016223076/0.277645717435721/0.22965334757042/0.0560077959605969

LN_root/LN_leaf/HN_root/HN_leaf

zma-miR399e-5p

Boerner_Z27kG1_15755

72-93

0.678743961352657

4

0.166191501641553

LN_leaf

zma-miR399e-5p

Boerner_Z27kG1_22850

800-821

0.70048309178744

4

0.0457153546791773

HN_leaf

zma-miR408b-3p:zma-miR408a

Boerner_Z27kG1_01046

94-115

0.655097613882863

2/0/2/0

0.0743714637805463/0.00893560703937002/0.0431631594963204/0.0106960643831452

LN_root/LN_leaf/HN_root/HN_leaf

zma-miR408b-5p

zhang_TCONS_00011169

185-204

0.675438596491228

4/4/3

0.108447036911749/0.0879746832508639/0.0056378079964241

LN_leaf/HN_root/HN_leaf

zma-miR444a:zma-miR444b

Boerner_Z27kG1_20838

5-25

0.728291316526611

4/0

0.0414049715995405/0.000941738699572037

LN_root/HN_root

zma-miR482-3p

Boerner_Z27kG1_08283

600-621

0.696022727272727

2

0.0781478318804442

HN_leaf

zma-miR482-3p

Boerner_Z27kG1_22204

94-112

0.735795454545454

4/4

0.207510626541854/0.155345100314279

LN_root/HN_root

zma-miR482-3p

Li_TCONS_00030374

285-304

0.732954545454545

4

0.170699850059004

HN_leaf

zma-miR482-3p

Li_TCONS_00055761

33-52

0.784090909090909

4

0.0531287606730582

HN_leaf

zma-miR528a-3p:zma-miR528b-3p

Boerner_Z27kG1_01046

97-118

0.68957345971564

1/0/0/0

0.0109982003430358/0.00610115440783998/0.00657357579419915/0.00730523957678519

LN_root/LN_leaf/HN_root/HN_leaf

zma-miR528a-3p:zma-miR528b-3p

Boerner_Z27kG1_08632

462-482

0.665876777251185

4

0.368800900766741

HN_leaf

zma-miR528a-3p:zma-miR528b-3p

Boerner_Z27kG1_23730

573-593

0.665876777251185

4

0.348799968161408

HN_leaf

zma-miR529-3p

Boerner_Z27kG1_17308

93-112

0.650872817955112

3

0.025580206396939

HN_leaf

zma-miR529-5p

zhang_TCONS_00077805

55-76

0.723785166240409

4

0.0312172902072148

LN_root

zma-miR827-5p

Boerner_Z27kG1_13480

1365-1385

0.654434250764526

4

0.249470323366813

LN_leaf

  1. amiRNA data from miRBase 21.0. bTargeted lincRNA genes for the miRNAs. cThe starting and terminating sites on the lincRNAs when it is bound by miRNAs. dMFEsite/MFEperfect, the calculation based on the method in Tafer et al.[50]. eClassification of the splicing signal of the alignments; the classifications corresponded to the degradome data files. f p-value for the degradome reads in different degradome data files. gThe evidence file for the alignments
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BMC Genomics

ISSN: 1471-2164

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