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Table 3 Identified targets of known miRNAs in soybean

From: Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

miRNA Target gene Target annotation Class Abundance(TP10M) cleavage site(nt) target site location
gma-miR156 Glyma04g37390# SBP domain protein I 39 938 5'UTR
  Glyma06g17700# SBP domain protein I 39 1185 CDS
  Glyma05g00200* SBP domain protein I 42 1202 CDS
  Glyma04g32070* SBP domain protein II 42 130 3'UTR
  Glyma17g08840* SBP domain protein I 42 1011 CDS
  Glyma05g38180# SBP domain protein I 33 1356 CDS
  Glyma08g01450# SBP domain protein I 33 1154 CDS
  Glyma18g00890 SBP domain protein II 75 249 CDS
  Glyma12g27330 SBP domain protein II 17 621 5'UTR
  Glyma11g36980 SBP domain protein II 47 1223 CDS
  Glyma02g30670 SBP domain protein I 109 688/689 CDS
  Glyma18g36960 SBP domain protein I 14 723 CDS
  Glyma02g13370 SBP domain protein I 173 1219/1220 CDS
gma-miR159 Glyma15g35860# MYB family transcription factor II 27 937 CDS
  Glyma13g25720# MYB family transcription factor II 27 838 CDS
  Glyma20g11040 MYB family transcription factor I 17 918 CDS
gma-miR160 Glyma11g20490# Auxin response factor II 134 1510 CDS
  Glyma10g35480# Auxin response factor I 134 740 CDS
  Glyma12g08110# Auxin response factor II 134 1501 CDS
  Glyma13g20370* Auxin response factor I 177 1670 CDS
  Glyma10g06080* Auxin response factor I 177 1355 CDS
  Glyma13g02410 Auxin response factor I 74 1280 CDS
  Glyma14g33730 Auxin response factor I 29 1184 CDS
  Glyma19g36570 Auxin response factor II 807 652 CDS
  Glyma04g43350 Auxin response factor II 43 1337 5'UTR
  Glyma13g40030 Auxin response factor II 67 1277 CDS
  Glyma20g32040 Auxin response factor I 19 1313 CDS
  Glyma12g29720 Auxin response factor I 25 1626 CDS
gma-miR162 Glyma12g35400* embryo-related protein IV 13 995 CDS
  Glyma13g35110* embryo-related protein IV 13 963 CDS
gma-miR164 Glyma17g10970# NAC family transcription factor I 750 795 CDS
  Glyma05g00930# NAC family transcription factor II 750 751 CDS
  Glyma06g21020# NAC family transcription factor I 750 741 CDS
  Glyma04g33270# NAC family transcription factor I 750 634 CDS
  Glyma13g34950* NAC family transcription factor I 153 747 CDS
  Glyma12g35530* NAC family transcription factor II 153 712 CDS
  Glyma15g40510# NAC family transcription factor II 34 730 CDS
  Glyma08g18470# NAC family transcription factor II 34 731 CDS
  Glyma12g26190 NAC family transcription factor I 87 778 CDS
miRNA Target gene Target annotation Class Abundance(TP10M) cleavage site(nt) target site location
gma-miR164 Glyma06g35660 NAC family transcription factor I 24 811 CDS
gma-miR166 Glyma15g13640#b HD-ZIP transcription factor II 273 568/570 CDS
  Glyma08g21610#b HD-ZIP transcription factor II 235 898 CDS
  Glyma04g09000# HD-ZIP transcription factor II 273 93-95 CDS
  Glyma07g01950# HD-ZIP transcription factor II 273 618/620 CDS
  Glyma08g21620# HD-ZIP transcription factor II 273 789/791 CDS
  Glyma07g01940# HD-ZIP transcription factor II 273 919/921 CDS
  Glyma06g09100#b HD-ZIP transcription factor II 273 567/569 CDS
  Glyma05g30000* HD-ZIP transcription factor II 59 1041 CDS
  Glyma08g13110* HD-ZIP transcription factor II 59 571 CDS
  Glyma09g02750* HD-ZIP transcription factor II 59 568 CDS
  Glyma12g08080# HD-ZIP transcription factor II 160 1239 CDS
  Glyma11g20520# HD-ZIP transcription factor II 160 605/607 CDS
gma-miR167 Glyma15g09750* Auxin response factor II 159 2444 CDS
  Glyma13g29320* Auxin response factor II 159 3359 CDS
  Glyma05g27580# Auxin response factor II 86 2288 CDS
  Glyma08g10550# Auxin response factor II 86 2477 CDS
  Glyma18g05330 Auxin response factor II 54 2880 CDS
  Glyma15g00770 zinc finger family protein I 112 1815 5'UTR
  Glyma02g40650 Auxin response factor II 76 2924 CDS
gma-miR168 Glyma16g34300# AGO protein II 74 534 CDS
  Glyma09g29720# AGO protein II 74 409 CDS
gma-miR169 Glyma08g45030* NUCLEAR FACTORY II 31 1294 5'UTR
  Glyma18g07890* NUCLEAR FACTORY I 31 957 CDS
  Glyma17g05920# NUCLEAR FACTORY I 64 1262 5'UTR
  Glyma13g16770# NUCLEAR FACTORY II 64 1022 CDS
  Glyma09g07960* NUCLEAR FACTORY II 33 931 5'UTR
  Glyma15g18970* NUCLEAR FACTORY II 33 981 5'UTR
  Glyma19g38800 NUCLEAR FACTORY I 23 1385 5'UTR
gma-miR171 Glyma08g08590# polyubiquitin protein IV 13 195 CDS
  Glyma05g25610# polyubiquitin protein IV 13 187 CDS
  Glyma09g04950 TCP family transcription factor IV 19 39 3'UTR
gma-miR172 Glyma19g35560* heat shock cognate protein IV 47 282 CDS
  Glyma03g32850* heat shock cognate protein IV 47 480 CDS
  Glyma15g04930# AP2 transcription factor II 425 1279 CDS
  Glyma13g40470# AP2 transcription factor II 348 1798 CDS
  Glyma11g15650# AP2 transcription factor II 425 1811 5'UTR
  Glyma12g07800# AP2 transcription factor II 425 1763 CDS
  Glyma01g39520* AP2 transcription factor II 44 1709 CDS
  Glyma11g05720* AP2 transcription factor II 44 1777 CDS
  Glyma19g36200# AP2 transcription factor II 111 1447 CDS
  Glyma03g33470# AP2 transcription factor II 111 1243 CDS
miRNA Target gene Target annotation Class Abundance(TP10M) cleavage site(nt) target site location
gma-miR172 Glyma17g18640 AP2 transcription factor III 26 1973 CDS
  Glyma02g09600 AP2 transcription factor II 78 1469 CDS
  Glyma05g27370# TCP family transcription factor II 109 922 5'UTR
gma-miR319 Glyma13g29160# TCP family transcription factor II 112 2078 CDS
  Glyma08g10350# TCP family transcription factor II 109 1172 CDS
  Glyma15g09910# TCP family transcription factor II 112 959 CDS
  Glyma13g34690* TCP family transcription factor II 195 656 CDS
  Glyma12g35720* TCP family transcription factor II 195 1223 CDS
  Glyma14g06680# Plasma membrane intrinsic protein III 49 935 CDS
  Glyma02g42220# Plasma membrane intrinsic protein III 49 1029 5'UTR
  Glyma13g36840* TCP family transcription factor II 73 1220 CDS
  Glyma12g33640* TCP family transcription factor II 73 740 CDS
gma-miR390 Glyma15g14670 expressed protein IV 14 569 CDS
gma-miR393 Glyma03g36770# Auxin signaling F-BOX protein II 65 1750 CDS
  Glyma19g39420# Auxin signaling F-BOX protein II 65 1751 CDS
  Glyma16g05500* Auxin signaling F-BOX protein II 46 2279 CDS
  Glyma19g27280* Auxin signaling F-BOX protein II 46 2207 CDS
  Glyma10g02630# Auxin signaling F-BOX protein IV 14 2166 CDS
  Glyma02g17170# Auxin signaling F-BOX protein IV 14 1741 CDS
gma-miR394 Glyma01g06230* NADP+ IV 24 42 CDS
  Glyma06g01850* NADP+ IV 24 588 CDS
gma-miR396 Glyma03g02500# Growth regulating factor I 57 550 CDS
  Glyma01g34650# Growth regulating factor I 57 128 CDS
  Glyma09g34560* Growth regulating factor I 361 323 CDS
  Glyma01g35140* Growth regulating factor II 361 290 CDS
  Glyma07g04290# Growth regulating factor II 117 473 CDS
  Glyma16g00970# Growth regulating factor I 117 353 CDS
  Glyma13g16920* Growth regulating factor I 77 742 CDS
  Glyma17g05800* Growth regulating factor I 77 422 CDS
  Glyma09g07990* Growth regulating factor II 77 380 CDS
  Glyma11g11820# Growth regulating factor I 279 386 CDS
  Glyma11g01060# Growth regulating factor II 279 349 CDS
  Glyma12g01730# Growth regulating factor II 279 504 CDS
  Glyma01g44470# Growth regulating factor I 279 428 CDS
  Glyma17g35090* Growth regulating factor II 1007 913 CDS
  Glyma17g35100* Growth regulating factor II 1007 724 CDS
  Glyma14g10090* Growth regulating factor II 1007 704 CDS
  Glyma04g40880 Growth regulating factor I 46 233 CDS
  Glyma06g13960 Growth regulating factor II 46 831 CDS
  Glyma13g22840 Growth regulating factor IV 13 282 3'UTR
  Glyma14g10100 Growth regulating factor II 373 711 CDS
  Glyma15g19460 Growth regulating factor II 69 347 CDS
miRNA Target gene Target annotation Class Abundance(TP10M) cleavage site(nt) target site location
gma-miR398 Glyma15g13870 MtN19-like protein I 15 172 CDS
  Glyma14g39910 Serine-type endopeptidase II 87 1370 CDS
  Glyma19g42890 Copper/zinc superoxide dismutase III 30 174 CDS
gma-miR1509a Glyma05g24110 elongation factor IV 15 436 CDS
gma-miR1511a Glyma10g05580* 60S ribosomal protein II 28 1220 CDS
  Glyma13g19930* 60S ribosomal protein III 28 1318 CDS
gma-miR1514a Glyma11g35820# NSF attachment protein IV 13 651 CDS
  Glyma18g02590# NSF attachment protein IV 13 615 CDS
  Glyma07g05370 NAC family transcription factor II 19 832 CDS
  Glyma16g01940 NAC family transcription factor II 25 844 CDS
  Glyma16g01930 NAC family transcription factor I 47 742 CDS
gma-miR1515a Glyma12g00830 Autophagy protein III 17 889 CDS
gma-miR1516a Glyma04g42690 Disulfide isomerase III 33 1016 CDS
gma-miR1522a Glyma03g36390 FAD linked oxidase family protein III 45 1826 5'UTR
gma-miR1523a Glyma20g27950 polyubiquitinated protein IV 114 864 CDS
gma-miR1530a Glyma10g32330# Auxin inducible transcription factor III 24 79 3'UTR
  Glyma20g35280# Auxin inducible transcription factor III 24 445 CDS
  Glyma09g41100 expressed protein II 20 1324 5'UTR
  Glyma02g28890 transketolase III 104 67 CDS
gma-miR1536a Glyma19g06340# ribulose-1,5-bisphosphate carboxylase III 108 795 5'UTR
  Glyma19g06370# ribulose-1,5-bisphosphate carboxylase III 108 668 5'UTR
  Glyma13g07610 ribulose-1,5-bisphosphate carboxylase III 115 661 5'UTR
  1. CDS: coding sequence; UTR: untranslated region; TP10M: transcripts per 10 million; Cleavage site: nucleotide number from 5' end of cDNA; Adjacent target genes with same # or * were matched by identical reads; alegume or soybean specific miRNAs; bMiRNA targets validated by RLM-5' RACE.