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BaseInfo

ncRNA ID novel_zma_miR5643
Species Zea mays
Class miRNA
Genome position Chr2:34714133-34714214 [+]
Reference genome RefGen_v4
Source SRR2638137;SRR2647385;SRR2647390
Length 24
Mature sequence(if miRNA) 59 - UUUUCUAAUCUCAUCCAAUCCAUG - 82
Stem-loop(if miRNA) --       AG          -------   GUUUAAAUCUCAA
  UGGAUUG  UGAGAUUGGA       UGA             U
  |||||||  ||||||||||       |||             C
  ACCUAAC  ACUCUAAUCU       UUC             A
GU       CU          UUUUUAA   UUUUGCCAACUGA
Stem-loop sequence UGGAUUGAGUGAGAUUGGAUGAGUUUAAAUCUCAAUCAAGUCAACCGUUUUCUUAAUUUUUUCUAAUCUCAUCCAAUCCAUG

Targets Info

Target Acc Alignment Exception Target Description Target Gene Name Target Type Method
EU951448.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||||||||||||||||=|||||
targets:684   CAUGGAUUGGAUGAGAUUGGAAAA   707

1.5 Zea mays clone 701961 mRNA sequence NA coding protein psRNATarget
BT069961.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||||||||||||||||=|||||
targets:49   CAUGGAUUGGAUGAGAUUGGAAAA   72

1.5 Zea mays full-length cDNA clone ZM_BFb0347H16 mRNA, complete cds NA coding protein psRNATarget
LQ238979.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:18   UAUGGAUUGGAUGAGAUUGGAAAA   41

1.5 Sequence 4974 from Patent EP2985353 NA coding protein psRNATarget
JB167310.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:18   UAUGGAUUGGAUGAGAUUGGAAAA   41

1.5 Sequence 4974 from Patent EP2559767 NA coding protein psRNATarget
HI406849.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:18   UAUGGAUUGGAUGAGAUUGGAAAA   41

1.5 Sequence 4974 from Patent EP2074227 NA coding protein psRNATarget
BT086633.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:394   UAUGGAUUGGAUGAGAUUGGAAAA   417

1.5 Zea mays full-length cDNA clone ZM_BFa0068P14 mRNA, complete cds NA coding protein psRNATarget
BT062183.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:185   UAUGGAUUGGAUGAGAUUGGAAAA   208

1.5 Zea mays full-length cDNA clone ZM_BFb0224O15 mRNA, complete cds NA coding protein psRNATarget
XM_008667120.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:887   UAUGGAUUGGAUGAGAUUGGAAAA   910

1.5 PREDICTED: Zea mays uncharacterized LOC100501429 (LOC100501429), mRNA NA coding protein psRNATarget
XM_008678390.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:1750   UAUGGAUUGGAUGAGAUUGGAAAA   1773

1.5 PREDICTED: Zea mays RNA-binding motif protein, X-linked 2 (LOC100282627), transcript variant X2, mRNA NA coding protein psRNATarget
XM_008678388.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:1766   UAUGGAUUGGAUGAGAUUGGAAAA   1789

1.5 PREDICTED: Zea mays RNA-binding motif protein, X-linked 2 (LOC100282627), transcript variant X1, mRNA NA coding protein psRNATarget
EU957033.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:1337   UAUGGAUUGGAUGAGAUUGGAAAA   1360

1.5 Zea mays clone 1581039 mRNA sequence NA coding protein psRNATarget
EU957741.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:1338   UAUGGAUUGGAUGAGAUUGGAAAA   1361

1.5 Zea mays clone 1613489 mRNA sequence NA coding protein psRNATarget
BT063416.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:2019   UAUGGAUUGGAUGAGAUUGGAAAA   2042

1.5 Zea mays full-length cDNA clone ZM_BFc0061L20 mRNA, complete cds NA coding protein psRNATarget
XM_008674604.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:2220   UAUGGAUUGGAUGAGAUUGGAAAA   2243

1.5 PREDICTED: Zea mays protein kinase domain containing protein (LOC100281444), transcript variant X3, mRNA NA coding protein psRNATarget
XM_020549704.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:2227   UAUGGAUUGGAUGAGAUUGGAAAA   2250

1.5 PREDICTED: Zea mays protein kinase domain containing protein (LOC100281444), transcript variant X2, mRNA NA coding protein psRNATarget
XM_020549703.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||||||||||||=|||||
targets:2287   UAUGGAUUGGAUGAGAUUGGAAAA   2310

1.5 PREDICTED: Zea mays protein kinase domain containing protein (LOC100281444), transcript variant X1, mRNA NA coding protein psRNATarget
BT040331.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  |||||||||*||||||||||||||
targets:1737   CAUGGAUUGAAUGAGAUUAGAAAA   1760

1.0 Zea mays full-length cDNA clone ZM_BFc0083E04 mRNA, complete cds NA coding protein psRNATarget
NM_001157801.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  |||||||||*||||||||||||||
targets:1774   CAUGGAUUGAAUGAGAUUAGAAAA   1797

1.0 Zea mays Flavonoid 3-monooxygenase (LOC100273153), mRNA NA coding protein psRNATarget
XM_020552750.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  **||||||||||||||||||||||
targets:81   AUUGGAUUGGAUGAGAUUAGAAAA   104

0.0 PREDICTED: Zea mays uncharacterized LOC103654238 (LOC103654238), mRNA NA coding protein psRNATarget
JB166302.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  |||||||||*||||||||=|||||
targets:28   CAUGGAUUGAAUGAGAUUGGAAAA   51

2.5 Sequence 3966 from Patent EP2559767 NA coding protein psRNATarget
HI405841.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  |||||||||*||||||||=|||||
targets:28   CAUGGAUUGAAUGAGAUUGGAAAA   51

2.5 Sequence 3966 from Patent EP2074227 NA coding protein psRNATarget
LQ237971.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  |||||||||*||||||||=|||||
targets:28   CAUGGAUUGAAUGAGAUUGGAAAA   51

2.5 Sequence 3966 from Patent EP2985353 NA coding protein psRNATarget
XM_008674362.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||||||*|||||||||=|||||
targets:500   CAUGGAUUAGAUGAGAUUGGAAAA   523

2.5 PREDICTED: Zea mays Membrane magnesium transporter (LOC100276290), transcript variant X1, mRNA NA coding protein psRNATarget
EU975230.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||||||*|||||||||=|||||
targets:505   CAUGGAUUAGAUGAGAUUGGAAAA   528

2.5 Zea mays clone 485079 hypothetical protein mRNA, complete cds NA coding protein psRNATarget
EU973494.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||||||*|||||||||=|||||
targets:517   CAUGGAUUAGAUGAGAUUGGAAAA   540

2.5 Zea mays clone 399694 hypothetical protein mRNA, complete cds NA coding protein psRNATarget
EZ064093.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||*|||||||||||||=|||||
targets:127   CAUGAAUUGGAUGAGAUUGGAAAA   150

1.5 TSA: Zea mays contig65216, mRNA sequence NA coding protein psRNATarget
EU942657.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||*|||||||||||||=|||||
targets:177   CAUGAAUUGGAUGAGAUUGGAAAA   200

1.5 Zea mays clone 1527578 mRNA sequence NA coding protein psRNATarget
NM_001291558.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||||||*|||||||||=|||||
targets:641   CAUGGAUUAGAUGAGAUUGGAAAA   664

2.5 Zea mays Membrane magnesium transporter (LOC100276290), mRNA NA coding protein psRNATarget
EU964394.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||||||*|||||||||=|||||
targets:642   CAUGGAUUAGAUGAGAUUGGAAAA   665

2.5 Zea mays clone 278539 hypothetical protein mRNA, complete cds NA coding protein psRNATarget
EU976922.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||||||*|||||||||=|||||
targets:678   CAUGGAUUAGAUGAGAUUGGAAAA   701

2.5 Zea mays clone 993749 hypothetical protein mRNA, complete cds NA coding protein psRNATarget
BT069115.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  |||||||||*||||||||=|||||
targets:466   CAUGGAUUGAAUGAGAUUGGAAAA   489

2.5 Zea mays full-length cDNA clone ZM_BFb0186N21 mRNA, complete cds NA coding protein psRNATarget
EU949831.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||*|||||||||||||=|||||
targets:955   CAUGAAUUGGAUGAGAUUGGAAAA   978

1.5 Zea mays clone 447574 mRNA sequence NA coding protein psRNATarget
XM_008651597.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||*||||||||||||||||=||
targets:3251   CAUGAAUUGGAUGAGAUUAGAGAA   3274

1.5 PREDICTED: Zea mays probable calcium-transporting ATPase 6, plasma membrane-type (LOC103630548), transcript variant X1, mRNA NA coding protein psRNATarget
XM_008666493.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||*|||||||||||||=|||||
targets:3422   CAUGAAUUGGAUGAGAUUGGAAAA   3445

1.5 PREDICTED: Zea mays uncharacterized LOC103643333 (LOC103643333), transcript variant X3, mRNA NA coding protein psRNATarget
XM_020546709.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||*|||||||||||||=|||||
targets:3408   CAUGAAUUGGAUGAGAUUGGAAAA   3431

1.5 PREDICTED: Zea mays uncharacterized LOC103643333 (LOC103643333), transcript variant X4, mRNA NA coding protein psRNATarget
XM_008651599.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||*||||||||||||||||=||
targets:3897   CAUGAAUUGGAUGAGAUUAGAGAA   3920

1.5 PREDICTED: Zea mays probable calcium-transporting ATPase 6, plasma membrane-type (LOC103630548), transcript variant X3, mRNA NA coding protein psRNATarget
XM_008651598.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||*||||||||||||||||=||
targets:3921   CAUGAAUUGGAUGAGAUUAGAGAA   3944

1.5 PREDICTED: Zea mays probable calcium-transporting ATPase 6, plasma membrane-type (LOC103630548), transcript variant X2, mRNA NA coding protein psRNATarget
XM_008666491.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||*|||||||||||||=|||||
targets:3690   CAUGAAUUGGAUGAGAUUGGAAAA   3713

1.5 PREDICTED: Zea mays uncharacterized LOC103643333 (LOC103643333), transcript variant X1, mRNA NA coding protein psRNATarget
XM_008666492.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||*|||||||||||||=|||||
targets:3695   CAUGAAUUGGAUGAGAUUGGAAAA   3718

1.5 PREDICTED: Zea mays uncharacterized LOC103643333 (LOC103643333), transcript variant X2, mRNA NA coding protein psRNATarget
JB166338.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||||||*||||||||||||||*
targets:26   CAUGGAUUAGAUGAGAUUAGAAAC   49

2.0 Sequence 4002 from Patent EP2559767 NA coding protein psRNATarget
LQ238007.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||||||*||||||||||||||*
targets:26   CAUGGAUUAGAUGAGAUUAGAAAC   49

2.0 Sequence 4002 from Patent EP2985353 NA coding protein psRNATarget
HI405877.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ||||||||*||||||||||||||*
targets:26   CAUGGAUUAGAUGAGAUUAGAAAC   49

2.0 Sequence 4002 from Patent EP2074227 NA coding protein psRNATarget
LQ235150.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =||||||||*|||=||||||||||
targets:37   UAUGGAUUGAAUGGGAUUAGAAAA   60

2.5 Sequence 1145 from Patent EP2985353 NA coding protein psRNATarget
HI403020.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =||||||||*|||=||||||||||
targets:37   UAUGGAUUGAAUGGGAUUAGAAAA   60

2.5 Sequence 1145 from Patent EP2074227 NA coding protein psRNATarget
JB163481.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =||||||||*|||=||||||||||
targets:37   UAUGGAUUGAAUGGGAUUAGAAAA   60

2.5 Sequence 1145 from Patent EP2559767 NA coding protein psRNATarget
EZ108499.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =||*||||||||||||||=|||||
targets:710   UAUAGAUUGGAUGAGAUUGGAAAA   733

1.5 TSA: Zea mays contig44158, mRNA sequence NA coding protein psRNATarget
NM_001174368.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||*|||||||||||||=|||||
targets:1382   UAUGAAUUGGAUGAGAUUGGAAAA   1405

1.5 Zea mays hypothetical protein (LOC100381539), mRNA NA coding protein psRNATarget
BT061560.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||*|||||||||||||=|||||
targets:1382   UAUGAAUUGGAUGAGAUUGGAAAA   1405

1.5 Zea mays full-length cDNA clone ZM_BFb0158C09 mRNA, complete cds NA coding protein psRNATarget
XM_020542014.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||||||*|||||||||=|||||
targets:114   UAUGGAUUAGAUGAGAUUGGAAAA   137

2.5 PREDICTED: Zea mays uncharacterized LOC100277104 (LOC100277104), transcript variant X1, mRNA NA coding protein psRNATarget
EU948930.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ==||||||*|||||||||=|||||
targets:344   UGUGGAUUAGAUGAGAUUGGAAAA   367

2.5 Zea mays clone 390579 mRNA sequence NA coding protein psRNATarget
XM_020546135.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ==||||||*|||||||||=|||||
targets:3056   UGUGGAUUAGAUGAGAUUGGAAAA   3079

2.5 PREDICTED: Zea mays protein FAR1-RELATED SEQUENCE 6 (LOC103642139), transcript variant X1, mRNA NA coding protein psRNATarget
XM_020546136.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ==||||||*|||||||||=|||||
targets:3203   UGUGGAUUAGAUGAGAUUGGAAAA   3226

2.5 PREDICTED: Zea mays protein FAR1-RELATED SEQUENCE 6 (LOC103642139), transcript variant X2, mRNA NA coding protein psRNATarget
XM_020538633.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ==||||||*|||||||||=|||||
targets:3892   UGUGGAUUAGAUGAGAUUGGAAAA   3915

2.5 PREDICTED: Zea mays transcription factor TFIIIB component B'' homolog (LOC100304161), transcript variant X5, mRNA NA coding protein psRNATarget
XM_008647808.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ==||||||*|||||||||=|||||
targets:4005   UGUGGAUUAGAUGAGAUUGGAAAA   4028

2.5 PREDICTED: Zea mays transcription factor TFIIIB component B'' homolog (LOC100304161), transcript variant X2, mRNA NA coding protein psRNATarget
XM_020538630.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ==||||||*|||||||||=|||||
targets:4044   UGUGGAUUAGAUGAGAUUGGAAAA   4067

2.5 PREDICTED: Zea mays transcription factor TFIIIB component B'' homolog (LOC100304161), transcript variant X1, mRNA NA coding protein psRNATarget
XM_020538631.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ==||||||*|||||||||=|||||
targets:4792   UGUGGAUUAGAUGAGAUUGGAAAA   4815

2.5 PREDICTED: Zea mays transcription factor TFIIIB component B'' homolog (LOC100304161), transcript variant X3, mRNA NA coding protein psRNATarget
XM_020538632.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ==||||||*|||||||||=|||||
targets:4793   UGUGGAUUAGAUGAGAUUGGAAAA   4816

2.5 PREDICTED: Zea mays transcription factor TFIIIB component B'' homolog (LOC100304161), transcript variant X4, mRNA NA coding protein psRNATarget
NM_001350089.1
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  ==||||||*|||||||||=|||||
targets:5855   UGUGGAUUAGAUGAGAUUGGAAAA   5878

2.5 Zea mays transcription factor TFIIIB component B'' homolog (LOC100304161), mRNA NA coding protein psRNATarget
BT083841.2
ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1
  =|||*||||||||||||||*||||
targets:510   UAUGAAUUGGAUGAGAUUAAAAAA   533

1.5 Zea mays full-length cDNA clone ZM_BFb0044O07 mRNA, complete cds NA coding protein psRNATarget