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BaseInfo

ncRNA ID	novel_zma_miR3539
Species	Zea mays
Class	miRNA
Genome position	Chr6:7133507-7133688 [-]
Reference genome	RefGen_v4
Source	SRR2287031
Length	24
Mature sequence(if miRNA)	159 - AGAGGGUGUUUGGUUUGUAGGGAC - 182
Stem-loop(if miRNA)	--  A             G                  A    A       U          UU        -  AA    A          C   AG GGGUGUUUGGUUU UAGGGACUAAUUUUUAGU CCUC AUUUUAU UUAUUUUAGU  CUAAAUUG CA  AUAC GAAACUAAAA U   || ||||||||||||| |||||||||||||||||| |||| ||||||| ||||||||||  |||||||| ||  |||| |||||||||| C   UC CCCACAAACCGAA AUCCUUGAUUAAAAAUCA GGAG UAAAAUA GAUAAAAUUA  GAUUUAAC GU  UAUG CUUUGAUUUU U AU  -             A                  A    A       U          GG        A  -A    C          A
Stem-loop sequence	AGAGGGUGUUUGGUUUGUAGGGACUAAUUUUUAGUACCUCAAUUUUAUUUUAUUUUAGUUUCUAAAUUGCAAAAUACAGAAACUAAAACUCUAUUUUAGUUUCCGUAUAUGACAAUUUAGGGAUUAAAAUAGUAUAAAAUAGAGGAACUAAAAAUUAGUUCCUAAAAGCCAAACACCCCUUA

Targets Info

Target Acc	Alignment	Exception	Target Description	Target Gene Name	Target Type	Method
XM_020553397.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||||||||||||||||||||*|| targets:704   GUCCCUACAAACCAAACACCCCCU   727 Target Full Sequence	1.5	PREDICTED: Zea mays SANT/MYB protein (LOC100284980), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_020542840.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||||||||||||||||||||*|| targets:1124   GUCCCUACAAACCAAACACCCCCU   1147 Target Full Sequence	1.5	PREDICTED: Zea mays hypothetical protein (LOC103636172), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008676281.2	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||||||||||||||||||||*|| targets:44   GUCCCUACAAACCAAACACCCCCU   67 Target Full Sequence	1.5	PREDICTED: Zea mays U-box domain-containing protein 14 (LOC103650716), mRNA	NA	coding protein	psRNATarget
BT085047.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||||||=|||||||||||||*|| targets:1345   GUCCCUAUAAACCAAACACCCCCU   1368 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0232J05 mRNA, complete cds	NA	coding protein	psRNATarget
XM_020543841.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||||||*|||||||||||||*|| targets:1071   GUCCCUAGAAACCAAACACCCCCU   1094 Target Full Sequence	2.5	PREDICTED: Zea mays lo1 pI allergen homolog 1 (lop1), transcript variant X1, mRNA	NA	coding protein	psRNATarget
BT065747.2	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||||||*|||||||||||||*|| targets:916   GUCCCUAGAAACCAAACACCCCCU   939 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFc0062G24 mRNA, complete cds	NA	coding protein	psRNATarget
XM_008674294.2	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||||||*|||||||||||||*|| targets:22   GUCCCUAAAAACCAAACACCCCCU   45 Target Full Sequence	2.5	PREDICTED: Zea mays OSJNBa0059D20.8-like protein (LOC100274149), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008674295.2	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||||||*|||||||||||||*|| targets:22   GUCCCUAAAAACCAAACACCCCCU   45 Target Full Sequence	2.5	PREDICTED: Zea mays OSJNBa0059D20.8-like protein (LOC100274149), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_008674147.2	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||||||*|||||||||||||*|| targets:29   GUCCCUAGAAACCAAACACCCCCU   52 Target Full Sequence	2.5	PREDICTED: Zea mays uncharacterized LOC100272682 (TIDP2766), transcript variant X8, mRNA	NA	coding protein	psRNATarget
BT053999.2	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||||||*|||||||||||||*|| targets:2086   GUCCCUAGAAACCAAACACCCCCU   2109 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFc0109O10 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001152323.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||||||*|||||||||||||*|| targets:2086   GUCCCUAGAAACCAAACACCCCCU   2109 Target Full Sequence	2.5	Zea mays uncharacterized LOC100279302 (LOC100279302), mRNA	NA	coding protein	psRNATarget
HI406713.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   ||||*||=|||||||||||||*|| targets:294   GUCCAUAUAAACCAAACACCCCCU   317 Target Full Sequence	2.5	Sequence 4838 from Patent EP2074227	NA	coding protein	psRNATarget
LQ238843.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   ||||*||=|||||||||||||*|| targets:294   GUCCAUAUAAACCAAACACCCCCU   317 Target Full Sequence	2.5	Sequence 4838 from Patent EP2985353	NA	coding protein	psRNATarget
JB167174.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   ||||*||=|||||||||||||*|| targets:294   GUCCAUAUAAACCAAACACCCCCU   317 Target Full Sequence	2.5	Sequence 4838 from Patent EP2559767	NA	coding protein	psRNATarget
BT019141.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   ||||*||=|||||||||||||*|| targets:419   GUCCAUAUAAACCAAACACCCCCU   442 Target Full Sequence	2.5	Zea mays clone Contig786.F mRNA sequence	NA	coding protein	psRNATarget
NM_001153051.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||=|||*|||||||||||||*|| targets:939   GUCUCUAGAAACCAAACACCCCCU   962 Target Full Sequence	2.5	Zea mays NAD(P)-binding Rossmann-fold superfamily protein (LOC100280114), mRNA	NA	coding protein	psRNATarget
BT055601.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||=|||*|||||||||||||*|| targets:939   GUCUCUAGAAACCAAACACCCCCU   962 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFc0063A22 mRNA, complete cds	NA	coding protein	psRNATarget
XM_008680551.2	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||*|||*|||||||||||||*|| targets:963   GUCACUAGAAACCAAACACCCCCU   986 Target Full Sequence	2.5	PREDICTED: Zea mays Plant-specific domain TIGR01589 family protein (pco120805), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_020547858.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||*|||*|||||||||||||*|| targets:1693   GUCACUAGAAACCAAACACCCCCU   1716 Target Full Sequence	2.5	PREDICTED: Zea mays uncharacterized LOC100382535 (LOC100382535), transcript variant X3, mRNA	NA	coding protein	psRNATarget
EU957896.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   |||*=||*|||||||||||||*|| targets:1395   GUCGUUAGAAACCAAACACCCCCU   1418 Target Full Sequence	2.5	Zea mays clone 1630391 mRNA sequence	NA	coding protein	psRNATarget
BT019277.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   **|**||=|||||||||||=|||| targets:744   AGCGAUAUAAACCAAACACUCUCU   767 Target Full Sequence	2.5	Zea mays clone Contig950.F mRNA sequence	NA	coding protein	psRNATarget
EZ107034.1	ncRNA:24   CAGGGAUGUUUGGUUUGUGGGAGA   1   **|**||=|||||||||||=|||| targets:803   AGCGAUAUAAACCAAACACUCUCU   826 Target Full Sequence	2.5	TSA: Zea mays contig42692, mRNA sequence	NA	coding protein	psRNATarget