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BaseInfo

ncRNA ID	novel_osa_miR3541
Species	Oryza sativa
Class	miRNA
Genome position	Chr1:10878223-10878357 [+]
Reference genome	IRGSP-1.0
Source	SRR2040391;SRR2040411;SRR5351737;SRR1460507
Length	24
Mature sequence(if miRNA)	1 - AUCCAGAUUCGUAGUAUUAGAAUG - 24
Stem-loop(if miRNA)	--A                   A               C        C      UAA    CG        UCCAGAUUCGUAGUAUUAG AUGUGUCACAUCCCU CGAAAUUC UUAUAU   AAGA  GAUGG    ||||||||||||||||||| ||||||||||||||| |||||||| ||||||   ||||  ||||A    AGGUCUAAGCAUCAUAAUC UACACAGUGUAGGGA GUUUUAGG AAUAUA   UUCU  UUAUG GAC                   C               A        A      UAG    CA
Stem-loop sequence	AUCCAGAUUCGUAGUAUUAGAAUGUGUCACAUCCCUCCGAAAUUCCUUAUAUUAAAAGACGGAUGGAGUAUUACUCUUGAUAUAUAAAGGAUUUUGAAGGGAUGUGACACAUCCUAAUACUACGAAUCUGGACAG

Targets Info

Target Acc	Alignment	Exception	Target Description	Target Gene Name	Target Type	Method
AK288631.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||||||=|||||||||||||||| targets:4123   CAUUCUAGUACUACGAAUCUGGAU   4146 Target Full Sequence	1.0	Oryza sativa Japonica Group cDNA, clone: J090055C12, full insert sequence	NA	coding protein	psRNATarget
CT829763.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   =||||||||||||||||||||||* targets:973   UAUUCUAAUACUACGAAUCUGGAC   996 Target Full Sequence	1.0	Oryza sativa (indica cultivar-group) cDNA clone:OSIGCRA105M10, full insert sequence	NA	coding protein	psRNATarget
AK066512.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   =||||||||||||||||||||||* targets:976   UAUUCUAAUACUACGAAUCUGGAA   999 Target Full Sequence	1.0	Oryza sativa Japonica Group cDNA clone:J013068C19, full insert sequence	NA	coding protein	psRNATarget
AK107495.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   =||||||=|||||=|||||||||| targets:930   UAUUCUAGUACUAUGAAUCUGGAU   953 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:002-129-D07, full insert sequence	NA	coding protein	psRNATarget
AK241555.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   ||||=||=|||||||||||||||* targets:154   CAUUUUAGUACUACGAAUCUGGAC   177 Target Full Sequence	2.0	Oryza sativa Japonica Group cDNA, clone: J065178B07, full insert sequence	NA	coding protein	psRNATarget
CT830398.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   =|||=||=||=||||||||||||| targets:355   UAUUUUAGUAUUACGAAUCUGGAU   378 Target Full Sequence	2.0	Oryza sativa (indica cultivar-group) cDNA clone:OSIGCSA041E02, full insert sequence	NA	coding protein	psRNATarget
XM_015758227.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   =|||||||||||||||||||*||| targets:1705   UAUUCUAAUACUACGAAUCUAGAU   1728 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group uncharacterized LOC9272131 (LOC9272131), transcript variant X4, mRNA	uncharacterized LOC9272131(Os01g0200175)	coding protein	psRNATarget
AK064924.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||*=||||||||||||||||||| targets:2014   CAUCUUAAUACUACGAAUCUGGAU   2037 Target Full Sequence	0.0	Oryza sativa Japonica Group cDNA clone:J013000N15, full insert sequence	NA	coding protein	psRNATarget
AK119748.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||*=||||||||||||||||||| targets:2191   CAUCUUAAUACUACGAAUCUGGAU   2214 Target Full Sequence	0.0	Oryza sativa Japonica Group cDNA clone:002-165-F11, full insert sequence	NA	coding protein	psRNATarget
XM_015758220.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   =|||||||||||||||||||*||| targets:2082   UAUUCUAAUACUACGAAUCUAGAU   2105 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group uncharacterized LOC9272131 (LOC9272131), transcript variant X3, mRNA	uncharacterized LOC9272131(Os01g0200175)	coding protein	psRNATarget
XM_015785327.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||*=||||||||||||||||||| targets:2247   CAUCUUAAUACUACGAAUCUGGAU   2270 Target Full Sequence	0.0	PREDICTED: Oryza sativa Japonica Group phosphoinositide phospholipase C 2 (LOC4337686), mRNA	phosphoinositide phospholipase C 2(LOC4337686)	coding protein	psRNATarget
XM_015758212.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   =|||||||||||||||||||*||| targets:2157   UAUUCUAAUACUACGAAUCUAGAU   2180 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group uncharacterized LOC9272131 (LOC9272131), transcript variant X2, mRNA	uncharacterized LOC9272131(Os01g0200175)	coding protein	psRNATarget
XM_015758208.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   =|||||||||||||||||||*||| targets:2455   UAUUCUAAUACUACGAAUCUAGAU   2478 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group uncharacterized LOC9272131 (LOC9272131), transcript variant X1, mRNA	uncharacterized LOC9272131(Os01g0200175)	coding protein	psRNATarget
AK072141.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||*=||||||||||||||||||| targets:2814   CAUCUUAAUACUACGAAUCUGGAU   2837 Target Full Sequence	0.0	Oryza sativa Japonica Group cDNA clone:J013122I07, full insert sequence	NA	coding protein	psRNATarget
JB164009.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||*|||||||||||||||||||* targets:151   CAUCCUAAUACUACGAAUCUGGAC   174 Target Full Sequence	1.0	Sequence 1673 from Patent EP2559767	NA	coding protein	psRNATarget
JB164009.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||**|||||||||||||=||||* targets:9   CAUCAUAAUACUACGAAUUUGGAC   32 Target Full Sequence	2.5	Sequence 1673 from Patent EP2559767	NA	coding protein	psRNATarget
HI403548.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||*|||||||||||||||||||* targets:151   CAUCCUAAUACUACGAAUCUGGAC   174 Target Full Sequence	1.0	Sequence 1673 from Patent EP2074227	NA	coding protein	psRNATarget
HI403548.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||**|||||||||||||=||||* targets:9   CAUCAUAAUACUACGAAUUUGGAC   32 Target Full Sequence	2.5	Sequence 1673 from Patent EP2074227	NA	coding protein	psRNATarget
LQ235678.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||*|||||||||||||||||||* targets:151   CAUCCUAAUACUACGAAUCUGGAC   174 Target Full Sequence	1.0	Sequence 1673 from Patent EP2985353	NA	coding protein	psRNATarget
LQ235678.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||**|||||||||||||=||||* targets:9   CAUCAUAAUACUACGAAUUUGGAC   32 Target Full Sequence	2.5	Sequence 1673 from Patent EP2985353	NA	coding protein	psRNATarget
AK288418.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||*|||||||||||||||||||* targets:886   CAUCCUAAUACUACGAAUCUGGAC   909 Target Full Sequence	1.0	Oryza sativa Japonica Group cDNA, clone: J090031L18, full insert sequence	NA	coding protein	psRNATarget
AK288418.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||**|||||||||||||=||||* targets:744   CAUCAUAAUACUACGAAUUUGGAC   767 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA, clone: J090031L18, full insert sequence	NA	coding protein	psRNATarget
CT833051.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||*=||||||||=|||||||||| targets:603   CAUCUUAAUACUAUGAAUCUGGAU   626 Target Full Sequence	1.5	Oryza sativa (indica cultivar-group) cDNA clone:OSIGCSN042I02, full insert sequence	NA	coding protein	psRNATarget
XM_015775668.1	ncRNA:24   GUAA--GAUUAUGAUGCUUAGACCUA   1   ||||--|||=|||||||||||||||* targets:1583   CAUUUCCUAGUACUACGAAUCUGGAC   1608 Target Full Sequence	2.0	PREDICTED: Oryza sativa Japonica Group RNA pseudouridine synthase 5 (LOC4332490), mRNA	RNA pseudouridine synthase 5(LOC4332490)	coding protein	psRNATarget
AK063452.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   =||*|||=|||||=|||||||||| targets:119   UAUCCUAGUACUAUGAAUCUGGAU   142 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:001-115-G03, full insert sequence	NA	coding protein	psRNATarget
AK242875.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   =|||=||=|||*|||||||||||| targets:1780   UAUUUUAGUACCACGAAUCUGGAU   1803 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA, clone: J090077K21, full insert sequence	NA	coding protein	psRNATarget
AK107672.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   =||*|||=|||||||||||||||* targets:877   UAUCCUAGUACUACGAAUCUGGAC   900 Target Full Sequence	2.0	Oryza sativa Japonica Group cDNA clone:002-131-H10, full insert sequence	NA	coding protein	psRNATarget
AK071898.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   ||||*||=|||*|||||||||||| targets:2685   CAUUAUAGUACAACGAAUCUGGAU   2708 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:J013059B05, full insert sequence	NA	coding protein	psRNATarget
XM_015764610.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   ||||*||=|||*|||||||||||| targets:2701   CAUUAUAGUACAACGAAUCUGGAU   2724 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group BTB/POZ domain-containing protein NPY4 (LOC4352652), mRNA	BTB/POZ domain-containing protein NPY4(LOC4352652)	coding protein	psRNATarget
XM_015780460.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   ||||-||=*|*||||||||||||| targets:1676   CAUU-UAGAAAUACGAAUCUGGAU   1698 Target Full Sequence	3.0	PREDICTED: Oryza sativa Japonica Group probable carboxylesterase Os04g0669600 (LOC4337345), transcript variant X4, mRNA	probable carboxylesterase Os04g0669600(LOC4337345)	coding protein	psRNATarget
XM_015780461.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   ||||-||=*|*||||||||||||| targets:1761   CAUU-UAGAAAUACGAAUCUGGAU   1783 Target Full Sequence	3.0	PREDICTED: Oryza sativa Japonica Group probable carboxylesterase Os04g0669600 (LOC4337345), transcript variant X5, mRNA	probable carboxylesterase Os04g0669600(LOC4337345)	coding protein	psRNATarget
AK072439.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||**|||||=||=|||||||||| targets:2673   CAUCGUAAUAUUAUGAAUCUGGAU   2696 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:J023111C14, full insert sequence	NA	coding protein	psRNATarget
AK288602.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   =*|||||||||*|||||||||||* targets:777   UUUUCUAAUACAACGAAUCUGGAC   800 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA, clone: J090052H23, full insert sequence	NA	coding protein	psRNATarget
HI403955.1	ncRNA:24   GUAA--GAUUAUGAUGCUUAGACCUA   1   |||*--|||=|||*|||||||||||| targets:32   CAUAACCUAGUACAACGAAUCUGGAU   57 Target Full Sequence	2.5	Sequence 2080 from Patent EP2074227	NA	coding protein	psRNATarget
LQ236085.1	ncRNA:24   GUAA--GAUUAUGAUGCUUAGACCUA   1   |||*--|||=|||*|||||||||||| targets:32   CAUAACCUAGUACAACGAAUCUGGAU   57 Target Full Sequence	2.5	Sequence 2080 from Patent EP2985353	NA	coding protein	psRNATarget
JB164416.1	ncRNA:24   GUAA--GAUUAUGAUGCUUAGACCUA   1   |||*--|||=|||*|||||||||||| targets:32   CAUAACCUAGUACAACGAAUCUGGAU   57 Target Full Sequence	2.5	Sequence 2080 from Patent EP2559767	NA	coding protein	psRNATarget
AK288866.1	ncRNA:24   GUAAGAUUAUGAUGCUUAGACCUA   1   |||*=||=||*||||||||||||* targets:1900   CAUCUUAGUAGUACGAAUCUGGAC   1923 Target Full Sequence	3.0	Oryza sativa Japonica Group cDNA, clone: J090078B06, full insert sequence	NA	coding protein	psRNATarget
XM_015784597.1	ncRNA:24   GUAA--GAUUAUGAUGCUUAGACCUA   1   |||*--|||=|||*|||||||||||| targets:2386   CAUAACCUAGUACAACGAAUCUGGAU   2411 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group pentatricopeptide repeat-containing protein At3g62470, mitochondrial (LOC4338514), transcript variant X4, mRNA	pentatricopeptide repeat-containing protein At3g62470, mitochondrial(LOC4338514)	coding protein	psRNATarget
XM_015784596.1	ncRNA:24   GUAA--GAUUAUGAUGCUUAGACCUA   1   |||*--|||=|||*|||||||||||| targets:2386   CAUAACCUAGUACAACGAAUCUGGAU   2411 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group pentatricopeptide repeat-containing protein At3g62470, mitochondrial (LOC4338514), transcript variant X3, mRNA	pentatricopeptide repeat-containing protein At3g62470, mitochondrial(LOC4338514)	coding protein	psRNATarget
XM_015784593.1	ncRNA:24   GUAA--GAUUAUGAUGCUUAGACCUA   1   |||*--|||=|||*|||||||||||| targets:2386   CAUAACCUAGUACAACGAAUCUGGAU   2411 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group pentatricopeptide repeat-containing protein At3g62470, mitochondrial (LOC4338514), transcript variant X1, mRNA	pentatricopeptide repeat-containing protein At3g62470, mitochondrial(LOC4338514)	coding protein	psRNATarget
XM_015784595.1	ncRNA:24   GUAA--GAUUAUGAUGCUUAGACCUA   1   |||*--|||=|||*|||||||||||| targets:2386   CAUAACCUAGUACAACGAAUCUGGAU   2411 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group pentatricopeptide repeat-containing protein At3g62470, mitochondrial (LOC4338514), transcript variant X2, mRNA	pentatricopeptide repeat-containing protein At3g62470, mitochondrial(LOC4338514)	coding protein	psRNATarget
AK109615.1	ncRNA:24   GUA--A--GAUUAUGAUGCUUAGACCUA   1   |=|--|--|||=||||||||||||*||| targets:1510   CGUCCUAGCUAGUACUACGAAUCUAGAU   1537 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:002-137-G12, full insert sequence	NA	coding protein	psRNATarget
XM_015760168.1	ncRNA:24   GUA--A--GAUUAUGAUGCUUAGACCUA   1   |=|--|--|||=||||||||||||*||| targets:1510   CGUCCUAGCUAGUACUACGAAUCUAGAU   1537 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group uncharacterized LOC4350559 (LOC4350559), mRNA	uncharacterized LOC4350559(LOC4350559)	coding protein	psRNATarget