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BaseInfo

ncRNA ID novel_zma_miR3993
Species Zea mays
Class miRNA
Genome position Chr1:225267312-225267432 [-]
Reference genome RefGen_v4
Source SRR1583944
Length 24
Mature sequence(if miRNA) 98 - AGGGCUAGUUUGGAAACACCAAUU - 121
Stem-loop(if miRNA) --             A   A  A     -G    A    CC                 AUG
  AGGGCUAGUUUGG AAC CC AUUUU  UAAG GAUU  UAUUUUUCCAAGGGAAA   A
  ||||||||||||| ||| || |||||  |||| ||||  |||||||||||||||||   A
  UCCCGAUCAAACC UUG GG UAAAA  GUUC CUAA  GUAAAAGGGUUUCCUUU   C
AA             C   -  A     AG    A    AA                 AAU
Stem-loop sequence AGGGCUAGUUUGGAAACACCAAUUUUGUAAGAGAUUCCUAUUUUUCCAAGGGAAAAUGAACUAAUUUCCUUUGGGAAAAUGAAAAUCACUUGGAAAAAUAGGGUUCCCAAACUAGCCCUAA

Targets Info

Target Acc Alignment Exception Target Description Target Gene Name Target Type Method
HI406263.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||||||*|||||||||||||
targets:105   AAAUGGUGUUCCCAAACUAGCCCU   128

1.0 Sequence 4388 from Patent EP2074227 NA coding protein psRNATarget
LQ238393.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||||||*|||||||||||||
targets:105   AAAUGGUGUUCCCAAACUAGCCCU   128

1.0 Sequence 4388 from Patent EP2985353 NA coding protein psRNATarget
JB166724.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||||||*|||||||||||||
targets:105   AAAUGGUGUUCCCAAACUAGCCCU   128

1.0 Sequence 4388 from Patent EP2559767 NA coding protein psRNATarget
EU951374.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||*|||||||||||||||||
targets:414   AAAUGGGGUUUCCAAACUAGCCCU   437

1.0 Zea mays clone 697858 mRNA sequence NA coding protein psRNATarget
EU947368.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||||||*|||||||||||||
targets:324   AAAUGGUGUUACCAAACUAGCCCU   347

1.0 Zea mays clone 341178 mRNA sequence NA coding protein psRNATarget
EU973119.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||||||*|||||||||||||
targets:1447   AAAUGGUGUUCCCAAACUAGCCCU   1470

1.0 Zea mays clone 393646 mRNA sequence NA coding protein psRNATarget
NM_001196460.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||||||*|||||||||||||
targets:1449   AAAUGGUGUUCCCAAACUAGCCCU   1472

1.0 Zea mays Mosaic virus helicase domain-binding protein (LOC100501804), mRNA NA coding protein psRNATarget
BT086269.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||||||*|||||||||||||
targets:1449   AAAUGGUGUUCCCAAACUAGCCCU   1472

1.0 Zea mays full-length cDNA clone ZM_BFc0140P03 mRNA, complete cds NA coding protein psRNATarget
XM_020544943.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||||*|||||*|||||||||||||
targets:1471   AAUUAGUGUUCCCAAACUAGCCCU   1494

1.0 PREDICTED: Zea mays uncharacterized LOC100273625 (IDP475), transcript variant X5, mRNA NA coding protein psRNATarget
XM_020544942.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||||*|||||*|||||||||||||
targets:1514   AAUUAGUGUUCCCAAACUAGCCCU   1537

1.0 PREDICTED: Zea mays uncharacterized LOC100273625 (IDP475), transcript variant X4, mRNA NA coding protein psRNATarget
XM_020544940.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||||*|||||*|||||||||||||
targets:1515   AAUUAGUGUUCCCAAACUAGCCCU   1538

1.0 PREDICTED: Zea mays uncharacterized LOC100273625 (IDP475), transcript variant X2, mRNA NA coding protein psRNATarget
XM_020544939.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||||*|||||*|||||||||||||
targets:1558   AAUUAGUGUUCCCAAACUAGCCCU   1581

1.0 PREDICTED: Zea mays uncharacterized LOC100273625 (IDP475), transcript variant X1, mRNA NA coding protein psRNATarget
XM_020544941.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||||*|||||*|||||||||||||
targets:1644   AAUUAGUGUUCCCAAACUAGCCCU   1667

1.0 PREDICTED: Zea mays uncharacterized LOC100273625 (IDP475), transcript variant X3, mRNA NA coding protein psRNATarget
XM_008665186.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||||*|||||*|||||||||||||
targets:2   AAUUAGUGUUCCCAAACUAGCCCU   25

1.0 PREDICTED: Zea mays probable galacturonosyltransferase-like 3 (LOC103641870), mRNA NA coding protein psRNATarget
EZ069159.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  =|||*|*|||||||||||||||||
targets:88   GAUUUGAGUUUCCAAACUAGCCCU   111

1.0 TSA: Zea mays contig04794, mRNA sequence NA coding protein psRNATarget
HI407023.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||||||*|||||||||||=|
targets:102   AAAUGGUGUUGCCAAACUAGCCUU   125

2.5 Sequence 5148 from Patent EP2074227 NA coding protein psRNATarget
JB167484.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||||||*|||||||||||=|
targets:102   AAAUGGUGUUGCCAAACUAGCCUU   125

2.5 Sequence 5148 from Patent EP2559767 NA coding protein psRNATarget
LQ239153.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||||||*|||||||||||=|
targets:102   AAAUGGUGUUGCCAAACUAGCCUU   125

2.5 Sequence 5148 from Patent EP2985353 NA coding protein psRNATarget
NM_001137966.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||**|||||||=||||||||||||
targets:1479   AAACGGUGUUUUCAAACUAGCCCU   1502

1.5 Zea mays uncharacterized LOC100192770 (pco077380), mRNA NA coding protein psRNATarget
BT034838.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||**|||||||=||||||||||||
targets:1479   AAACGGUGUUUUCAAACUAGCCCU   1502

1.5 Zea mays full-length cDNA clone ZM_BFb0022H04 mRNA, complete cds NA coding protein psRNATarget
XM_008679616.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  =|||*|*|||||||||||||||||
targets:1220   GAUUUGAGUUUCCAAACUAGCCCU   1243

1.0 PREDICTED: Zea mays uncharacterized LOC103652675 (LOC103652675), mRNA NA coding protein psRNATarget
EU957492.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||||||*|||*||||||||||||*
targets:1779   AAUUGGGGUUCCCAAACUAGCCCK   1802

3.0 Zea mays clone 1594874 mRNA sequence NA coding protein psRNATarget
XM_020550081.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||||*|*||||||||||||||=||
targets:2430   AAUUUGAGUUUCCAAACUAGCUCU   2453

2.5 PREDICTED: Zea mays uncharacterized LOC109944788 (LOC109944788), mRNA NA coding protein psRNATarget
XM_008659899.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  =|||*|*||||||=||||||||||
targets:2352   GAUUUGAGUUUCCGAACUAGCCCU   2375

2.5 PREDICTED: Zea mays carotene epsilon-monooxygenase, chloroplastic (LOC103637620), mRNA NA coding protein psRNATarget
XM_008671736.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  =|||*|*||||=||||||||||||
targets:2517   GAUUUGAGUUUUCAAACUAGCCCU   2540

2.5 PREDICTED: Zea mays probable serine/threonine-protein kinase PBL28 (LOC103647166), mRNA NA coding protein psRNATarget
XM_008676336.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  =|||*|*||||||||||||||=||
targets:4377   GAUUUGAGUUUCCAAACUAGCUCU   4400

2.5 PREDICTED: Zea mays Serine/arginine repetitive matrix protein 2 isoform 4 (LOC103650763), transcript variant X3, mRNA NA coding protein psRNATarget
XM_008676333.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  =|||*|*||||||||||||||=||
targets:4391   GAUUUGAGUUUCCAAACUAGCUCU   4414

2.5 PREDICTED: Zea mays Serine/arginine repetitive matrix protein 2 isoform 4 (LOC103650763), transcript variant X1, mRNA NA coding protein psRNATarget
XM_008676335.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  =|||*|*||||||||||||||=||
targets:4404   GAUUUGAGUUUCCAAACUAGCUCU   4427

2.5 PREDICTED: Zea mays Serine/arginine repetitive matrix protein 2 isoform 4 (LOC103650763), transcript variant X2, mRNA NA coding protein psRNATarget
EZ069250.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||||*|*|*|||||||||||||||
targets:156   AAUUUGGGGUUCCAAACUAGCCCU   179

2.0 TSA: Zea mays contig04885, mRNA sequence NA coding protein psRNATarget
AY110835.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||||||*|*|||||||||||
targets:38   AAAUGGUGUUGCAAAACUAGCCCU   61

2.5 Zea mays CL46086_1 mRNA sequence NA coding protein psRNATarget
BT069551.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  |||||**|||*|||||||||||||
targets:321   AAUUGAGGUUCCCAAACUAGCCCU   344

3.0 Zea mays full-length cDNA clone ZM_BFb0167A20 mRNA, complete cds NA coding protein psRNATarget
XM_008660198.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||||*|*|*|||||||||||||||
targets:1003   AAUUUGGGGUUCCAAACUAGCCCU   1026

2.0 PREDICTED: Zea mays ER membrane protein complex subunit 7-like protein (LOC100277198), transcript variant X1, mRNA NA coding protein psRNATarget
BT065747.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||*||*||||||||||||||
targets:7   AAAUGGAGUCUCCAAACUAGCCCU   30

2.0 Zea mays full-length cDNA clone ZM_BFc0062G24 mRNA, complete cds NA coding protein psRNATarget
XM_008680878.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|*|||||*|||||||||||||
targets:1604   AAAUAGUGUUGCCAAACUAGCCCU   1627

1.0 PREDICTED: Zea mays E3 ubiquitin protein ligase RIE1 (LOC103654076), mRNA NA coding protein psRNATarget
XM_020544055.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||**||||||||||||||||
targets:1888   AAAUGGGAUUUCCAAACUAGCCCU   1911

2.0 PREDICTED: Zea mays probable mitochondrial adenine nucleotide transporter BTL3 (LOC103639491), transcript variant X1, mRNA NA coding protein psRNATarget
XM_008662239.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||**||||||||||||||||
targets:1908   AAAUGGGAUUUCCAAACUAGCCCU   1931

2.0 PREDICTED: Zea mays probable mitochondrial adenine nucleotide transporter BTL3 (LOC103639491), transcript variant X3, mRNA NA coding protein psRNATarget
EU956611.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||*|||*|||||||||||||
targets:1503   AAAUGGGGUUGCCAAACUAGCCCU   1526

2.0 Zea mays clone 1568093 mRNA sequence NA coding protein psRNATarget
XM_008675357.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||||*|||||*|||||||||*|||
targets:205   AAUUAGUGUUCCCAAACUAGGCCU   228

2.5 PREDICTED: Zea mays UNE1 (LOC103649618), mRNA NA coding protein psRNATarget
NM_001152323.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||*||*||||||||||||||
targets:1177   AAAUGGAGUCUCCAAACUAGCCCU   1200

2.0 Zea mays uncharacterized LOC100279302 (LOC100279302), mRNA NA coding protein psRNATarget
BT053999.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||*||*||||||||||||||
targets:1177   AAAUGGAGUCUCCAAACUAGCCCU   1200

2.0 Zea mays full-length cDNA clone ZM_BFc0109O10 mRNA, complete cds NA coding protein psRNATarget
XM_020542483.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*||*||||*|||||||||||||
targets:3186   AAAUGCUGUUGCCAAACUAGCCCU   3209

2.0 PREDICTED: Zea mays protein TPR1-like (LOC103634695), transcript variant X4, mRNA NA coding protein psRNATarget
XM_020552563.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||*|||*|||||||||||||
targets:455   AAAUGGAGUUCCCAAACUAGCCCU   478

2.0 PREDICTED: Zea mays probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 10 (LOC103653427), transcript variant X2, mRNA NA coding protein psRNATarget
XM_020542482.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*||*||||*|||||||||||||
targets:3675   AAAUGCUGUUGCCAAACUAGCCCU   3698

2.0 PREDICTED: Zea mays protein TPR1-like (LOC103634695), transcript variant X3, mRNA NA coding protein psRNATarget
XM_020542481.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*||*||||*|||||||||||||
targets:3687   AAAUGCUGUUGCCAAACUAGCCCU   3710

2.0 PREDICTED: Zea mays protein TPR1-like (LOC103634695), transcript variant X2, mRNA NA coding protein psRNATarget
XM_020542480.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*||*||||*|||||||||||||
targets:3723   AAAUGCUGUUGCCAAACUAGCCCU   3746

2.0 PREDICTED: Zea mays protein TPR1-like (LOC103634695), transcript variant X1, mRNA NA coding protein psRNATarget
NM_001350811.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||*|||*|||||||||||||
targets:2559   AAAUGGAGUUCCCAAACUAGCCCU   2582

2.0 Zea mays uncharacterized LOC100278071 (LOC100278071), mRNA NA coding protein psRNATarget
XM_020547541.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||*|||*|||||||||||||
targets:1964   AAAUGGGGUUCCCAAACUAGCCCU   1987

2.0 PREDICTED: Zea mays uncharacterized LOC100273682 (LOC100273682), transcript variant X1, mRNA NA coding protein psRNATarget
LQ239236.1
ncRNA:24   UUAACCA--CAAAGGUUUGAUCGGGA   1
  =||--||--|||||||||||||||||
targets:93   GAU--GUAAGUUUCCAAACUAGCCCU   116

2.5 Sequence 5231 from Patent EP2985353 NA coding protein psRNATarget
HI407106.1
ncRNA:24   UUAACCA--CAAAGGUUUGAUCGGGA   1
  =||--||--|||||||||||||||||
targets:93   GAU--GUAAGUUUCCAAACUAGCCCU   116

2.5 Sequence 5231 from Patent EP2074227 NA coding protein psRNATarget
JB167567.1
ncRNA:24   UUAACCA--CAAAGGUUUGAUCGGGA   1
  =||--||--|||||||||||||||||
targets:93   GAU--GUAAGUUUCCAAACUAGCCCU   116

2.5 Sequence 5231 from Patent EP2559767 NA coding protein psRNATarget
BT017648.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  =|||*|*|||||||||||||||*|
targets:309   GAUUUGAGUUUCCAAACUAGCCAU   332

2.5 Zea mays clone EL01N0439D04.c mRNA sequence NA coding protein psRNATarget
NM_001154017.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  *||--|*|||||||||||||||||
targets:2158   UAU--GAGUUUCCAAACUAGCCCU   2179

1.0 Zea mays kelch motif family protein (LOC100281098), mRNA NA coding protein psRNATarget
EU955577.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  *||--|*|||||||||||||||||
targets:2159   UAU--GAGUUUCCAAACUAGCCCU   2180

1.0 Zea mays clone 1537616 kelch motif family protein mRNA, complete cds NA coding protein psRNATarget
XM_008666284.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  =||--|*|||||||||||||||||
targets:3310   GAU--GAGUUUCCAAACUAGCCCU   3331

1.0 PREDICTED: Zea mays protein indeterminate-domain 16 (LOC103643131), transcript variant X2, mRNA NA coding protein psRNATarget
XM_008666283.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  =||--|*|||||||||||||||||
targets:3393   GAU--GAGUUUCCAAACUAGCCCU   3414

1.0 PREDICTED: Zea mays protein indeterminate-domain 16 (LOC103643131), transcript variant X1, mRNA NA coding protein psRNATarget
EZ111591.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  *|||*|*|||||||||||||||*|
targets:104   CAUUUGAGUUUCCAAACUAGCCAU   127

2.5 TSA: Zea mays contig47252, mRNA sequence NA coding protein psRNATarget
XM_008652590.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*||**||||||||||||||||*
targets:972   AAAUGAGGUUUCCAAACUAGCCCC   995

3.0 PREDICTED: Zea mays Chaperone DnaJ-domain superfamily protein (LOC100191793), transcript variant X4, mRNA NA coding protein psRNATarget
XM_008652589.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*||**||||||||||||||||*
targets:999   AAAUGAGGUUUCCAAACUAGCCCC   1022

3.0 PREDICTED: Zea mays Chaperone DnaJ-domain superfamily protein (LOC100191793), transcript variant X3, mRNA NA coding protein psRNATarget
NM_001137218.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*||**||||||||||||||||*
targets:1017   AAAUGAGGUUUCCAAACUAGCCCC   1040

3.0 Zea mays Chaperone DnaJ-domain superfamily protein (LOC100191793), mRNA NA coding protein psRNATarget
BT034002.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*||**||||||||||||||||*
targets:1017   AAAUGAGGUUUCCAAACUAGCCCC   1040

3.0 Zea mays full-length cDNA clone ZM_BFc0044B05 mRNA, complete cds NA coding protein psRNATarget
XM_008652587.2
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*||**||||||||||||||||*
targets:1077   AAAUGAGGUUUCCAAACUAGCCCC   1100

3.0 PREDICTED: Zea mays Chaperone DnaJ-domain superfamily protein (LOC100191793), transcript variant X1, mRNA NA coding protein psRNATarget
AF023159.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  ||*|||*|||*||||||||||||*
targets:5579   AAAUGGGGUUCCCAAACUAGCCCG   5602

3.0 Zea mays starch synthase DULL1 (dull1) mRNA, complete cds NA coding protein psRNATarget
XM_020539411.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  *||||**|||*|||||||||||||
targets:3522   UAUUGUGGUUCCCAAACUAGCCCU   3545

3.0 PREDICTED: Zea mays Protein kinase superfamily protein (LOC100502407), transcript variant X7, mRNA NA coding protein psRNATarget
XM_020539397.1
ncRNA:24   UUAACCACAAAGGUUUGAUCGGGA   1
  *||||**|||*|||||||||||||
targets:3557   UAUUGUGGUUCCCAAACUAGCCCU   3580

3.0 PREDICTED: Zea mays Protein kinase superfamily protein (LOC100502407), transcript variant X3, mRNA NA coding protein psRNATarget