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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

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