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BaseInfo

ncRNA ID	novel_osa_miR3353
Species	Oryza sativa
Class	miRNA
Genome position	Chr1:26049191-26049333 [-]
Reference genome	IRGSP-1.0
Source	SRR1555747;SRR3123648;SRR1556020;SRR1738235
Length	24
Mature sequence(if miRNA)	1 - AAGACGAACGGUCAAAUGUUGAAC - 24
Stem-loop(if miRNA)	--C              C          -----AAAAAAUUUA     AUUUAGUCACACAUAAAGUAUUAUUC    UAAUAUUUGACCGU CGUCUUAUUU               AAAAU                          A    |||||||||||||| ||||||||||               |||||    GUUGUAAACUGGCA GCAGAAUAAA               AUUAU                          U CAA              A          CUUAAAAAAAAUCUA     AAAAAUAACGAUAAUCUACUAUUUUG
Stem-loop sequence	CUAAUAUUUGACCGUCCGUCUUAUUUAAAAAAUUUAAAAAUAUUUAGUCACACAUAAAGUAUUAUUCAUGUUUUAUCAUCUAAUAGCAAUAAAAAUAUUAAUCUAAAAAAAAUUCAAAUAAGACGAACGGUCAAAUGUUGAAC

Targets Info

Target Acc	Alignment	Exception	Target Description	Target Gene Name	Target Type	Method
AK288230.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   |||||||=|||||||||||||||| targets:5284   GUUCAACGUUUGACCGUUCGUCUU   5307 Target Full Sequence	1.0	Oryza sativa Japonica Group cDNA, clone: J090012M14, full insert sequence	NA	coding protein	psRNATarget
AK288670.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   |||=|||=|||||||||||||||| targets:934   GUUUAACGUUUGACCGUUCGUCUU   957 Target Full Sequence	1.0	Oryza sativa Japonica Group cDNA, clone: J090058O04, full insert sequence	NA	coding protein	psRNATarget
XM_015779567.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*||||||||||||||||||||| targets:1946   GUCCAACAUUUGACCGUUCGUCUU   1969 Target Full Sequence	0.0	PREDICTED: Oryza sativa Japonica Group beta-fructofuranosidase, insoluble isoenzyme 3 (LOC4335789), mRNA	beta-fructofuranosidase, insoluble isoenzyme 3(LOC4335789)	coding protein	psRNATarget
AK120779.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*||||||||||||||||||||| targets:1953   GUCCAACAUUUGACCGUUCGUCUU   1976 Target Full Sequence	0.0	Oryza sativa Japonica Group cDNA clone:J023009M11, full insert sequence	NA	coding protein	psRNATarget
XM_015768707.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*||||=|||||||||||||||| targets:1234   GUCCAACGUUUGACCGUUCGUCUU   1257 Target Full Sequence	1.0	PREDICTED: Oryza sativa Japonica Group cysteine-rich repeat secretory protein 15-like (LOC107279942), transcript variant X3, mRNA	cysteine-rich repeat secretory protein 15-like(LOC107279942)	coding protein	psRNATarget
XM_015768705.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*||||=|||||||||||||||| targets:1234   GUCCAACGUUUGACCGUUCGUCUU   1257 Target Full Sequence	1.0	PREDICTED: Oryza sativa Japonica Group cysteine-rich repeat secretory protein 15-like (LOC107279942), transcript variant X1, mRNA	cysteine-rich repeat secretory protein 15-like(LOC107279942)	coding protein	psRNATarget
XM_015768708.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*||||=|||||||||||||||| targets:1234   GUCCAACGUUUGACCGUUCGUCUU   1257 Target Full Sequence	1.0	PREDICTED: Oryza sativa Japonica Group cysteine-rich repeat secretory protein 15-like (LOC107279942), transcript variant X4, mRNA	cysteine-rich repeat secretory protein 15-like(LOC107279942)	coding protein	psRNATarget
XM_015768706.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*||||=|||||||||||||||| targets:1234   GUCCAACGUUUGACCGUUCGUCUU   1257 Target Full Sequence	1.0	PREDICTED: Oryza sativa Japonica Group cysteine-rich repeat secretory protein 15-like (LOC107279942), transcript variant X2, mRNA	cysteine-rich repeat secretory protein 15-like(LOC107279942)	coding protein	psRNATarget
AK103201.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   |||||||=|||||||*|||||||| targets:476   GUUCAACGUUUGACCAUUCGUCUU   499 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:J033122B04, full insert sequence	NA	coding protein	psRNATarget
AK064197.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*=|||=|||||||||||||||| targets:896   GUCUAACGUUUGACCGUUCGUCUU   919 Target Full Sequence	1.0	Oryza sativa Japonica Group cDNA clone:002-104-D06, full insert sequence	NA	coding protein	psRNATarget
AK109598.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*|=||=|||||||||||||||| targets:1660   GUCCGACGUUUGACCGUUCGUCUU   1683 Target Full Sequence	1.0	Oryza sativa Japonica Group cDNA clone:002-137-D09, full insert sequence	NA	coding protein	psRNATarget
AK120505.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   |||=|||=|||*|||||||||||| targets:920   GUUUAACGUUUCACCGUUCGUCUU   943 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:J013123A20, full insert sequence	NA	coding protein	psRNATarget
JB164349.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   |||=|||=|||||||||*|||||| targets:18   GUUUAACGUUUGACCGUCCGUCUU   41 Target Full Sequence	2.5	Sequence 2013 from Patent EP2559767	NA	coding protein	psRNATarget
HI403888.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   |||=|||=|||||||||*|||||| targets:18   GUUUAACGUUUGACCGUCCGUCUU   41 Target Full Sequence	2.5	Sequence 2013 from Patent EP2074227	NA	coding protein	psRNATarget
LQ236018.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   |||=|||=|||||||||*|||||| targets:18   GUUUAACGUUUGACCGUCCGUCUU   41 Target Full Sequence	2.5	Sequence 2013 from Patent EP2985353	NA	coding protein	psRNATarget
AK288661.1	ncRNA:24   CAAGUUGUA--AACUGGCAAGCAGAA   1   *||=|||||--||||||||||||||| targets:1357   UUUUAACAUAUUUGACCGUUCGUCUU   1382 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA, clone: J090057O08, full insert sequence	NA	coding protein	psRNATarget
XM_015757652.1	ncRNA:24   CAAGUUG---UAAACUGGCAAGCAGAA   1   *||=|||---||||||||||||||||| targets:1393   UUUUAACCAUAUUUGACCGUUCGUCUU   1419 Target Full Sequence	3.0	PREDICTED: Oryza sativa Japonica Group chlorophyllase-2, chloroplastic (LOC4348648), mRNA	chlorophyllase-2, chloroplastic(LOC4348648)	coding protein	psRNATarget
AK106724.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*||||||||||||||*|||||| targets:672   GUCCAACAUUUGACCGUCCGUCUU   695 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA clone:002-114-G11, full insert sequence	NA	coding protein	psRNATarget
CT827991.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*||||||||||||||*|||||| targets:659   GUCCAACAUUUGACCGUCCGUCUU   682 Target Full Sequence	1.5	Oryza sativa (indica cultivar-group) cDNA clone:OSIGCRA128H03, full insert sequence	NA	coding protein	psRNATarget
AK289044.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   **||||||||||||||*||||||| targets:456   UAUCAACAUUUGACCGCUCGUCUU   479 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA, clone: J090092F18, full insert sequence	NA	coding protein	psRNATarget
AK288458.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   *|*||||=|||||=|||||||||| targets:1165   AUCCAACGUUUGAUCGUUCGUCUU   1188 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA, clone: J090035E13, full insert sequence	NA	coding protein	psRNATarget
AK066541.1	ncRNA:24   CA--AGUUGUAAACUGGCAAGCAGAA   1   ||--|||||=|||||||||*|||||| targets:2913   GUGCUCAACGUUUGACCGUCCGUCUU   2938 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:J013070E20, full insert sequence	NA	coding protein	psRNATarget
XM_015775992.1	ncRNA:24   CA--AGUUGUAAACUGGCAAGCAGAA   1   ||--|||||=|||||||||*|||||| targets:2916   GUGCUCAACGUUUGACCGUCCGUCUU   2941 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group CBL-interacting protein kinase 10 (LOC4332786), transcript variant X1, mRNA	CBL-interacting protein kinase 10(LOC4332786)	coding protein	psRNATarget
XM_015775993.1	ncRNA:24   CA--AGUUGUAAACUGGCAAGCAGAA   1   ||--|||||=|||||||||*|||||| targets:1962   GUGCUCAACGUUUGACCGUCCGUCUU   1987 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group CBL-interacting protein kinase 10 (LOC4332786), transcript variant X2, mRNA	CBL-interacting protein kinase 10(LOC4332786)	coding protein	psRNATarget
CT828824.1	ncRNA:24   CA--AGUUGUAAACUGGCAAGCAGAA   1   ||--|||||=|||||||||*|||||| targets:1082   GUGCUCAACGUUUGACCGUCCGUCUU   1107 Target Full Sequence	2.5	Oryza sativa (indica cultivar-group) cDNA clone:OSIGCRA109D05, full insert sequence	NA	coding protein	psRNATarget
AK103228.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*||||=|||||||*|||||||| targets:2649   GUCCAACGUUUGACCAUUCGUCUU   2672 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:J033123C21, full insert sequence	NA	coding protein	psRNATarget
CT829159.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*||||=|||||||*|||||||| targets:888   GUCCAACGUUUGACCAUUCGUCUU   911 Target Full Sequence	2.5	Oryza sativa (indica cultivar-group) cDNA clone:OSIGCSN009P22, full insert sequence	NA	coding protein	psRNATarget
CT832631.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*||||=|||||||||*|||||| targets:345   GUCCAACGUUUGACCGUCCGUCUU   368 Target Full Sequence	2.5	Oryza sativa (indica cultivar-group) cDNA clone:OSIGCEA021A12, full insert sequence	NA	coding protein	psRNATarget
CT832630.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*||||=|||||||||*|||||| targets:345   GUCCAACGUUUGACCGUCCGUCUU   368 Target Full Sequence	2.5	Oryza sativa (indica cultivar-group) cDNA clone:OSIGCEA020B12, full insert sequence	NA	coding protein	psRNATarget
LQ236313.1	ncRNA:24   CAAG--UUGUA--AACUGGCAAGCAGAA   1   *|||--|||||--||||||||||||||| targets:22   UUUCUAAACAUGUUUGACCGUUCGUCUU   49 Target Full Sequence	2.5	Sequence 2308 from Patent EP2985353	NA	coding protein	psRNATarget
HI404183.1	ncRNA:24   CAAG--UUGUA--AACUGGCAAGCAGAA   1   *|||--|||||--||||||||||||||| targets:22   UUUCUAAACAUGUUUGACCGUUCGUCUU   49 Target Full Sequence	2.5	Sequence 2308 from Patent EP2074227	NA	coding protein	psRNATarget
JB164644.1	ncRNA:24   CAAG--UUGUA--AACUGGCAAGCAGAA   1   *|||--|||||--||||||||||||||| targets:22   UUUCUAAACAUGUUUGACCGUUCGUCUU   49 Target Full Sequence	2.5	Sequence 2308 from Patent EP2559767	NA	coding protein	psRNATarget
XM_015755113.1	ncRNA:24   CAAGUUGUA--AACUGGCAAGCAGAA   1   *||*|||||--||||||||||||||| targets:228   UUUAAACAUGUUUGACCGUUCGUCUU   253 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group zinc-finger homeodomain protein 9 (LOC4347054), mRNA	zinc-finger homeodomain protein 9(LOC4347054)	coding protein	psRNATarget
AK288428.1	ncRNA:24   CAAGUUGUA--AACUGGCAAGCAGAA   1   *||*|||||--||||||||||||||| targets:757   UUUAAACAUGUUUGACCGUUCGUCUU   782 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA, clone: J090032O10, full insert sequence	NA	coding protein	psRNATarget
AK065369.1	ncRNA:24   CAAGUUGUA--AACUGGCAAGCAGAA   1   *||*|||||--||||||||||||||| targets:1429   UUUAAACAUGUUUGACCGUUCGUCUU   1454 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:J013023A04, full insert sequence	NA	coding protein	psRNATarget
AK288987.1	ncRNA:24   CAAGUUGUA--AACUGGCAAGCAGAA   1   *||*|||||--||||||||||||||| targets:1744   UUUAAACAUGUUUGACCGUUCGUCUU   1769 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA, clone: J090086J09, full insert sequence	NA	coding protein	psRNATarget
AK289103.1	ncRNA:24   CAAGUUGUA--AACUGGCAAGCAGAA   1   *||*|||||--||||||||||||||| targets:234   UUUAAACAUGUUUGACCGUUCGUCUU   259 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA, clone: J090096G10, full insert sequence	NA	coding protein	psRNATarget
XM_015787231.1	ncRNA:24   CAAGUUGUA--AACUGGCAAGCAGAA   1   *||*|||||--||||||||||||||| targets:612   UUUAAACAUGUUUGACCGUUCGUCUU   637 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group uncharacterized LOC4339918 (LOC4339918), mRNA	uncharacterized LOC4339918(LOC4339918)	coding protein	psRNATarget
AK108096.1	ncRNA:24   CAAGUUGUA--AACUGGCAAGCAGAA   1   *||*|||||--||||||||||||||| targets:608   UUUAAACAUGUUUGACCGUUCGUCUU   633 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:002-139-A08, full insert sequence	NA	coding protein	psRNATarget
HI404491.1	ncRNA:24   CAAGUUGUA--AACUGGCAAGCAGAA   1   *||*|||||--||||||||||||||| targets:53   UUUAAACAUGUUUGACCGUUCGUCUU   78 Target Full Sequence	2.5	Sequence 2616 from Patent EP2074227	NA	coding protein	psRNATarget
JB164952.1	ncRNA:24   CAAGUUGUA--AACUGGCAAGCAGAA   1   *||*|||||--||||||||||||||| targets:53   UUUAAACAUGUUUGACCGUUCGUCUU   78 Target Full Sequence	2.5	Sequence 2616 from Patent EP2559767	NA	coding protein	psRNATarget
LQ236621.1	ncRNA:24   CAAGUUGUA--AACUGGCAAGCAGAA   1   *||*|||||--||||||||||||||| targets:53   UUUAAACAUGUUUGACCGUUCGUCUU   78 Target Full Sequence	2.5	Sequence 2616 from Patent EP2985353	NA	coding protein	psRNATarget
XM_015773784.1	ncRNA:24   CAA-GUUGUAAACUGGCAAGCAGAA   1   *||-||||=||||||||*||||||| targets:1931   AUUGCAACGUUUGACCGCUCGUCUU   1955 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group alanine aminotransferase 2 (LOC9266500), transcript variant X2, mRNA	alanine aminotransferase 2(LOC9266500)	coding protein	psRNATarget
XM_015773783.1	ncRNA:24   CAA-GUUGUAAACUGGCAAGCAGAA   1   *||-||||=||||||||*||||||| targets:1837   AUUGCAACGUUUGACCGCUCGUCUU   1861 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group alanine aminotransferase 2 (LOC9266500), transcript variant X1, mRNA	alanine aminotransferase 2(LOC9266500)	coding protein	psRNATarget
XM_015776704.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*=|||=|||||||||*|||||| targets:1603   GUCUAACGUUUGACCGUCCGUCUU   1626 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group glucan endo-1,3-beta-glucosidase 7 (LOC4332132), transcript variant X1, mRNA	glucan endo-1,3-beta-glucosidase 7(LOC4332132)	coding protein	psRNATarget
XM_015776705.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*=|||=|||||||||*|||||| targets:1597   GUCUAACGUUUGACCGUCCGUCUU   1620 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group glucan endo-1,3-beta-glucosidase 7 (LOC4332132), transcript variant X2, mRNA	glucan endo-1,3-beta-glucosidase 7(LOC4332132)	coding protein	psRNATarget
XM_015776706.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*=|||=|||||||||*|||||| targets:1591   GUCUAACGUUUGACCGUCCGUCUU   1614 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group glucan endo-1,3-beta-glucosidase 7 (LOC4332132), transcript variant X3, mRNA	glucan endo-1,3-beta-glucosidase 7(LOC4332132)	coding protein	psRNATarget
CT828091.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*=|||=|||||||||*|||||| targets:1576   GUCUAACGUUUGACCGUCCGUCUU   1599 Target Full Sequence	2.5	Oryza sativa (indica cultivar-group) cDNA clone:OSIGCRA128N06, full insert sequence	NA	coding protein	psRNATarget
AK242028.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   ||*=|||=|||||||||*|||||| targets:1480   GUCUAACGUUUGACCGUCCGUCUU   1503 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA, clone: J075115C11, full insert sequence	NA	coding protein	psRNATarget
HI404107.1	ncRNA:24   CAA--GUUGUAAACUGGCAAGCAGAA   1   *||--||||=|||||||*|||||||| targets:5   UUUGACAACGUUUGACCUUUCGUCUU   30 Target Full Sequence	2.5	Sequence 2232 from Patent EP2074227	NA	coding protein	psRNATarget
JB164568.1	ncRNA:24   CAA--GUUGUAAACUGGCAAGCAGAA   1   *||--||||=|||||||*|||||||| targets:5   UUUGACAACGUUUGACCUUUCGUCUU   30 Target Full Sequence	2.5	Sequence 2232 from Patent EP2559767	NA	coding protein	psRNATarget
LQ236237.1	ncRNA:24   CAA--GUUGUAAACUGGCAAGCAGAA   1   *||--||||=|||||||*|||||||| targets:5   UUUGACAACGUUUGACCUUUCGUCUU   30 Target Full Sequence	2.5	Sequence 2232 from Patent EP2985353	NA	coding protein	psRNATarget
AK108746.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   *|*||||=|||*|||||||||||| targets:1304   AUCCAACGUUUCACCGUUCGUCUU   1327 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:002-150-E12, full insert sequence	NA	coding protein	psRNATarget
AK108063.1	ncRNA:24   CAA--------GUUGUAAACUGGCAAGCAGAA   1   |||--------||||=|||||||||*|||||| targets:1344   GUUUUCGUGCCCAACGUUUGACCGUCCGUCUU   1375 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:002-138-B04, full insert sequence	NA	coding protein	psRNATarget
XM_015770137.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   |**||||=|||||||||*|||||| targets:3147   GCCCAACGUUUGACCGUCCGUCUU   3170 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group probable LRR receptor-like serine/threonine-protein kinase At4g36180 (LOC9268112), mRNA	probable LRR receptor-like serine/threonine-protein kinase At4g36180(LOC9268112)	coding protein	psRNATarget
AK289036.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   |**||||=|||||||||*|||||| targets:980   GCCCAACGUUUGACCGUCCGUCUU   1003 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA, clone: J090091J22, full insert sequence	NA	coding protein	psRNATarget
XM_015756907.1	ncRNA:24   CAAG-UUGUAAACUGGCAAGCAGAA   1   **||-|||=|||||||*|||||||| targets:1621   UAUCUAACGUUUGACCAUUCGUCUU   1645 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group probable inactive beta-glucosidase 33 (LOC4347547), mRNA	probable inactive beta-glucosidase 33(LOC4347547)	coding protein	psRNATarget
AK066336.1	ncRNA:24   CAAG-UUGUAAACUGGCAAGCAGAA   1   **||-|||=|||||||*|||||||| targets:1629   UAUCUAACGUUUGACCAUUCGUCUU   1653 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:J013063O11, full insert sequence	NA	coding protein	psRNATarget
AK288883.1	ncRNA:24   CAAGUUGUAAACUGGCAAGCAGAA   1   |*|*|||=|||||||*|||||||| targets:930   GAUAAACGUUUGACCUUUCGUCUU   953 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA, clone: J090079H22, full insert sequence	NA	coding protein	psRNATarget