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BaseInfo

ncRNA ID	novel_osa_miR3549
Species	Oryza sativa
Class	miRNA
Genome position	Chr5:17259406-17259521 [-]
Reference genome	IRGSP-1.0
Source	SRR2040391
Length	24
Mature sequence(if miRNA)	1 - ACGAACCGGGACUAAAGAUCGAUC - 24
Stem-loop(if miRNA)	--C                  G  AAC  A                -  U UG    GC    CGAUCUUUAGUCCCGGUU GU   AC AACCGGGACUAAAGAU GG U  GCCG  C    |||||||||||||||||| ||   || |||||||||||||||| || |  ||||    GCUAGAAAUCAGGGCCAA CA   UG UUGGCCUUGAUUUCUA CC A  CGGU  A CUA                  G  CAA  G                G  - GU    GC
Stem-loop sequence	CCGAUCUUUAGUCCCGGUUGGUAACACAAACCGGGACUAAAGAUGGUUUGGCCGGCCACGUGGCUGACCGAUCUUUAGUUCCGGUUGGUAACACGAACCGGGACUAAAGAUCGAUC

Targets Info

Target Acc	Alignment	Exception	Target Description	Target Gene Name	Target Type	Method
AK288796.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   |||||||||||||||||||||*|| targets:1826   GAUCGAUCUUUAGUCCCGGUUGGU   1849 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA, clone: J090070F05, full insert sequence	NA	coding protein	psRNATarget
AK288377.1	ncRNA:24   CUA--GCUAGAAAUCAGGGCCAAGCA   1   |||--||||||||||||||||||*|| targets:1370   GAUAGCGAUCUUUAGUCCCGGUUGGU   1395 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA, clone: J090026K06, full insert sequence	NA	coding protein	psRNATarget
XM_015759968.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   ||||-|||||||||||||||||*| targets:3366   GAUC-AUCUUUAGUCCCGGUUCAU   3388 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group F-box/LRR-repeat protein At3g58930 (LOC9269963), transcript variant X1, mRNA	F-box/LRR-repeat protein At3g58930(LOC9269963)	coding protein	psRNATarget
AK121178.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   ||-||||||||||||||||||*|| targets:1905   GA-CGAUCUUUAGUCCCGGUUGGU   1927 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA clone:J023083G22, full insert sequence	NA	coding protein	psRNATarget
XM_015759969.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   ||||-|||||||||||||||||*| targets:1868   GAUC-AUCUUUAGUCCCGGUUCAU   1890 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group F-box/LRR-repeat protein At3g58930 (LOC9269963), transcript variant X3, mRNA	F-box/LRR-repeat protein At3g58930(LOC9269963)	coding protein	psRNATarget
XM_015774887.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   ||||-|||||||||||||||||*| targets:1444   GAUC-AUCUUUAGUCCCGGUUCUU   1466 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group metacaspase-1 (LOC4333012), transcript variant X2, mRNA	metacaspase-1(LOC4333012)	coding protein	psRNATarget
XM_015774888.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   ||||-|||||||||||||||||*| targets:1438   GAUC-AUCUUUAGUCCCGGUUCUU   1460 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group metacaspase-1 (LOC4333012), transcript variant X3, mRNA	metacaspase-1(LOC4333012)	coding protein	psRNATarget
AK288153.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   ||||-|||||||||||||||||*| targets:37   GAUC-AUCUUUAGUCCCGGUUCUU   59 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA, clone: J080319C04, full insert sequence	NA	coding protein	psRNATarget
AK288734.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   **|=|||||||||||||||||*|| targets:43   AUUUGAUCUUUAGUCCCGGUUGGU   66 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA, clone: J090063I24, full insert sequence	NA	coding protein	psRNATarget
AK289098.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   *||*|||||||||||||||||*|| targets:143   AAUAGAUCUUUAGUCCCGGUUGGU   166 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA, clone: J090096E23, full insert sequence	NA	coding protein	psRNATarget
AK289098.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   *||*|||||||||||||||||*|| targets:234   AAUAGAUCUUUAGUCCCGGUUGGU   257 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA, clone: J090096E23, full insert sequence	NA	coding protein	psRNATarget
AK066662.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   *||**||||||||||||||||||| targets:651   AAUGUAUCUUUAGUCCCGGUUCGU   674 Target Full Sequence	0.0	Oryza sativa Japonica Group cDNA clone:J013071A17, full insert sequence	NA	coding protein	psRNATarget
AK288598.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   ***||||||||||||||||||*|| targets:966   UUACGAUCUUUAGUCCCGGUUGGU   989 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA, clone: J090051P05, full insert sequence	NA	coding protein	psRNATarget
AK288463.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   *=**|||||||||||||||||*|| targets:551   CGAGGAUCUUUAGUCCCGGUUGGU   574 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA, clone: J090036E20, full insert sequence	NA	coding protein	psRNATarget
AK288424.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   *||-|||||||||||||||||*|| targets:2378   AAU-GAUCUUUAGUCCCGGUUAGU   2400 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA, clone: J090032J12, full insert sequence	NA	coding protein	psRNATarget
AK288438.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   **|**||||||||||||||||*|| targets:2359   ACUAAAUCUUUAGUCCCGGUUGGU   2382 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA, clone: J090034C21, full insert sequence	NA	coding protein	psRNATarget
AK288438.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   *|**||*|*||||||||||||||* targets:2322   AAAAGAGCAUUAGUCCCGGUUCGG   2345 Target Full Sequence	3.0	Oryza sativa Japonica Group cDNA, clone: J090034C21, full insert sequence	NA	coding protein	psRNATarget
XM_015755256.1	ncRNA:24   CUA--GCUAGAAAUCAGGGCCAAGCA   1   *||--=|||||||||||||||||*|| targets:137   AAUAAUGAUCUUUAGUCCCGGUUGGU   162 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group uncharacterized LOC4346665 (LOC4346665), transcript variant X2, mRNA	uncharacterized LOC4346665(LOC4346665)	coding protein	psRNATarget
XM_015755884.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   *||=-||||||||||||||||*|| targets:1371   AAUU-AUCUUUAGUCCCGGUUGGU   1393 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group S-norcoclaurine synthase 1 (LOC4346830), mRNA	S-norcoclaurine synthase 1(LOC4346830)	coding protein	psRNATarget
LQ236416.1	ncRNA:24   CUAG-----CUAGAAAUCAGGGCCAAGCA   1   *|||-----|||||||||||||||||*|| targets:33   UAUCUGCAUGAUCUUUAGUCCCGGUUAGU   61 Target Full Sequence	1.5	Sequence 2411 from Patent EP2985353	NA	coding protein	psRNATarget
HI404286.1	ncRNA:24   CUAG-----CUAGAAAUCAGGGCCAAGCA   1   *|||-----|||||||||||||||||*|| targets:33   UAUCUGCAUGAUCUUUAGUCCCGGUUAGU   61 Target Full Sequence	1.5	Sequence 2411 from Patent EP2074227	NA	coding protein	psRNATarget
JB164747.1	ncRNA:24   CUAG-----CUAGAAAUCAGGGCCAAGCA   1   *|||-----|||||||||||||||||*|| targets:33   UAUCUGCAUGAUCUUUAGUCCCGGUUAGU   61 Target Full Sequence	1.5	Sequence 2411 from Patent EP2559767	NA	coding protein	psRNATarget
XM_015779829.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   *|||-|||||||||||||||||*| targets:1646   AAUC-AUCUUUAGUCCCGGUUCAU   1668 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group uncharacterized LOC4335182 (LOC4335182), mRNA	uncharacterized LOC4335182(LOC4335182)	coding protein	psRNATarget
XM_015779829.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   *=**|||||||||||||||||*|| targets:1696   CGAGGAUCUUUAGUCCCGGUUGGU   1719 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group uncharacterized LOC4335182 (LOC4335182), mRNA	uncharacterized LOC4335182(LOC4335182)	coding protein	psRNATarget
AK105552.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   *||*|||||||||||||||||*|* targets:1269   AAUAGAUCUUUAGUCCCGGUUAGC   1292 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:001-128-A12, full insert sequence	NA	coding protein	psRNATarget
XM_015790121.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   **|=*||||||||||||||||*|| targets:925   UUUUAAUCUUUAGUCCCGGUUGGU   948 Target Full Sequence	1.5	PREDICTED: Oryza sativa Japonica Group putative disease resistance protein RGA4 (LOC107281518), transcript variant X2, mRNA	putative disease resistance protein RGA4(LOC107281518)	coding protein	psRNATarget
XM_015790121.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   *=*=|||||||||||||||||*|* targets:969   UGCUGAUCUUUAGUCCCGGUUGGA   992 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group putative disease resistance protein RGA4 (LOC107281518), transcript variant X2, mRNA	putative disease resistance protein RGA4(LOC107281518)	coding protein	psRNATarget
AK065811.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   **|**||||||||||||||||*|| targets:1901   ACUAAAUCUUUAGUCCCGGUUGGU   1924 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA clone:J013039F07, full insert sequence	NA	coding protein	psRNATarget
LQ236051.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   |*|=*||||||||||||||||*|* targets:45   GUUUUAUCUUUAGUCCCGGUUGGG   68 Target Full Sequence	2.5	Sequence 2046 from Patent EP2985353	NA	coding protein	psRNATarget
HI403921.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   |*|=*||||||||||||||||*|* targets:45   GUUUUAUCUUUAGUCCCGGUUGGG   68 Target Full Sequence	2.5	Sequence 2046 from Patent EP2074227	NA	coding protein	psRNATarget
JB164382.1	ncRNA:24   CUAGCUAGAAAUCAGGGCCAAGCA   1   |*|=*||||||||||||||||*|* targets:45   GUUUUAUCUUUAGUCCCGGUUGGG   68 Target Full Sequence	2.5	Sequence 2046 from Patent EP2559767	NA	coding protein	psRNATarget