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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 Target Full Sequence	1.5	Zea mays clone 701961 mRNA sequence	NA	coding protein	psRNATarget
BT069961.2	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   ||||||||||||||||||=||||| targets:49   CAUGGAUUGGAUGAGAUUGGAAAA   72 Target Full Sequence	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 Target Full Sequence	1.5	Sequence 4974 from Patent EP2985353	NA	coding protein	psRNATarget
JB167310.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   =|||||||||||||||||=||||| targets:18   UAUGGAUUGGAUGAGAUUGGAAAA   41 Target Full Sequence	1.5	Sequence 4974 from Patent EP2559767	NA	coding protein	psRNATarget
HI406849.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   =|||||||||||||||||=||||| targets:18   UAUGGAUUGGAUGAGAUUGGAAAA   41 Target Full Sequence	1.5	Sequence 4974 from Patent EP2074227	NA	coding protein	psRNATarget
BT086633.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   =|||||||||||||||||=||||| targets:394   UAUGGAUUGGAUGAGAUUGGAAAA   417 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC100501429 (LOC100501429), mRNA	NA	coding protein	psRNATarget
XM_008678390.2	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   =|||||||||||||||||=||||| targets:1750   UAUGGAUUGGAUGAGAUUGGAAAA   1773 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	1.5	Zea mays clone 1581039 mRNA sequence	NA	coding protein	psRNATarget
EU957741.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   =|||||||||||||||||=||||| targets:1338   UAUGGAUUGGAUGAGAUUGGAAAA   1361 Target Full Sequence	1.5	Zea mays clone 1613489 mRNA sequence	NA	coding protein	psRNATarget
BT063416.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   =|||||||||||||||||=||||| targets:2019   UAUGGAUUGGAUGAGAUUGGAAAA   2042 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	1.0	Zea mays Flavonoid 3-monooxygenase (LOC100273153), mRNA	NA	coding protein	psRNATarget
XM_020552750.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   **|||||||||||||||||||||| targets:81   AUUGGAUUGGAUGAGAUUAGAAAA   104 Target Full Sequence	0.0	PREDICTED: Zea mays uncharacterized LOC103654238 (LOC103654238), mRNA	NA	coding protein	psRNATarget
JB166302.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   |||||||||*||||||||=||||| targets:28   CAUGGAUUGAAUGAGAUUGGAAAA   51 Target Full Sequence	2.5	Sequence 3966 from Patent EP2559767	NA	coding protein	psRNATarget
HI405841.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   |||||||||*||||||||=||||| targets:28   CAUGGAUUGAAUGAGAUUGGAAAA   51 Target Full Sequence	2.5	Sequence 3966 from Patent EP2074227	NA	coding protein	psRNATarget
LQ237971.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   |||||||||*||||||||=||||| targets:28   CAUGGAUUGAAUGAGAUUGGAAAA   51 Target Full Sequence	2.5	Sequence 3966 from Patent EP2985353	NA	coding protein	psRNATarget
XM_008674362.2	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   ||||||||*|||||||||=||||| targets:500   CAUGGAUUAGAUGAGAUUGGAAAA   523 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	1.5	TSA: Zea mays contig65216, mRNA sequence	NA	coding protein	psRNATarget
EU942657.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   ||||*|||||||||||||=||||| targets:177   CAUGAAUUGGAUGAGAUUGGAAAA   200 Target Full Sequence	1.5	Zea mays clone 1527578 mRNA sequence	NA	coding protein	psRNATarget
NM_001291558.2	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   ||||||||*|||||||||=||||| targets:641   CAUGGAUUAGAUGAGAUUGGAAAA   664 Target Full Sequence	2.5	Zea mays Membrane magnesium transporter (LOC100276290), mRNA	NA	coding protein	psRNATarget
EU964394.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   ||||||||*|||||||||=||||| targets:642   CAUGGAUUAGAUGAGAUUGGAAAA   665 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	1.5	Zea mays clone 447574 mRNA sequence	NA	coding protein	psRNATarget
XM_008651597.2	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   ||||*||||||||||||||||=|| targets:3251   CAUGAAUUGGAUGAGAUUAGAGAA   3274 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	2.0	Sequence 4002 from Patent EP2559767	NA	coding protein	psRNATarget
LQ238007.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   ||||||||*||||||||||||||* targets:26   CAUGGAUUAGAUGAGAUUAGAAAC   49 Target Full Sequence	2.0	Sequence 4002 from Patent EP2985353	NA	coding protein	psRNATarget
HI405877.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   ||||||||*||||||||||||||* targets:26   CAUGGAUUAGAUGAGAUUAGAAAC   49 Target Full Sequence	2.0	Sequence 4002 from Patent EP2074227	NA	coding protein	psRNATarget
LQ235150.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   =||||||||*|||=|||||||||| targets:37   UAUGGAUUGAAUGGGAUUAGAAAA   60 Target Full Sequence	2.5	Sequence 1145 from Patent EP2985353	NA	coding protein	psRNATarget
HI403020.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   =||||||||*|||=|||||||||| targets:37   UAUGGAUUGAAUGGGAUUAGAAAA   60 Target Full Sequence	2.5	Sequence 1145 from Patent EP2074227	NA	coding protein	psRNATarget
JB163481.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   =||||||||*|||=|||||||||| targets:37   UAUGGAUUGAAUGGGAUUAGAAAA   60 Target Full Sequence	2.5	Sequence 1145 from Patent EP2559767	NA	coding protein	psRNATarget
EZ108499.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   =||*||||||||||||||=||||| targets:710   UAUAGAUUGGAUGAGAUUGGAAAA   733 Target Full Sequence	1.5	TSA: Zea mays contig44158, mRNA sequence	NA	coding protein	psRNATarget
NM_001174368.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   =|||*|||||||||||||=||||| targets:1382   UAUGAAUUGGAUGAGAUUGGAAAA   1405 Target Full Sequence	1.5	Zea mays hypothetical protein (LOC100381539), mRNA	NA	coding protein	psRNATarget
BT061560.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   =|||*|||||||||||||=||||| targets:1382   UAUGAAUUGGAUGAGAUUGGAAAA   1405 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	2.5	Zea mays clone 390579 mRNA sequence	NA	coding protein	psRNATarget
XM_020546135.1	ncRNA:24   GUACCUAACCUACUCUAAUCUUUU   1   ==||||||*|||||||||=||||| targets:3056   UGUGGAUUAGAUGAGAUUGGAAAA   3079 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	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 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFb0044O07 mRNA, complete cds	NA	coding protein	psRNATarget