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BaseInfo

ncRNA ID	novel_zma_miR3649
Species	Zea mays
Class	miRNA
Genome position	Chr10:121060436-121060520 [-]
Reference genome	RefGen_v4
Source	SRR2287031;SRR2287159;SRR2287162;SRR2287163
Length	24
Mature sequence(if miRNA)	62 - AUGUAGAUUGAGUGAGAUUGGAUG - 85
Stem-loop(if miRNA)	--AUGUA     AG  A  -     UGUAU    AUCCUAAUC        GAUUG  UG GA UUGGA     UUAA         A        |||||  || || |||||     ||||         A        CUAAC  AC CU AACCU     AAUU         A UGUGUAA     CU  -  C     UUUUU    CUUCAAACU
Stem-loop sequence	AUGUAGAUUGAGUGAGAUUGGAUGUAUUUAAAUCCUAAUCAAAUCAAACUUCUUAAUUUUUUCCAACUCCAUCCAAUCAAUGUGU

Targets Info

Target Acc	Alignment	Exception	Target Description	Target Gene Name	Target Type	Method
AY112141.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   ||||=||||||||||||||||||| targets:228   CAUCUAAUCUCACUCAAUCUACAU   251 Target Full Sequence	0.0	Zea mays CL24213_1 mRNA sequence	NA	coding protein	psRNATarget
XM_020549703.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:2348   CAUCCAAUCUCACUCAAUCCACAU   2371 Target Full Sequence	1.5	PREDICTED: Zea mays protein kinase domain containing protein (LOC100281444), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_020549704.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:2288   CAUCCAAUCUCACUCAAUCCACAU   2311 Target Full Sequence	1.5	PREDICTED: Zea mays protein kinase domain containing protein (LOC100281444), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_008674604.2	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:2281   CAUCCAAUCUCACUCAAUCCACAU   2304 Target Full Sequence	1.5	PREDICTED: Zea mays protein kinase domain containing protein (LOC100281444), transcript variant X3, mRNA	NA	coding protein	psRNATarget
EU956718.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:2153   CAUCCAAUCUCACUCAAUCCACAU   2176 Target Full Sequence	1.5	Zea mays clone 1571610 protein kinase domain containing protein mRNA, complete cds	NA	coding protein	psRNATarget
NM_001154362.2	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:2152   CAUCCAAUCUCACUCAAUCCACAU   2175 Target Full Sequence	1.5	Zea mays protein kinase domain containing protein (LOC100281444), mRNA	NA	coding protein	psRNATarget
BT063416.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:2080   CAUCCAAUCUCACUCAAUCCACAU   2103 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFc0061L20 mRNA, complete cds	NA	coding protein	psRNATarget
BT062183.2	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:246   CAUCCAAUCUCACUCAAUCCACAU   269 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFb0224O15 mRNA, complete cds	NA	coding protein	psRNATarget
BT086633.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:455   CAUCCAAUCUCACUCAAUCCACAU   478 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFa0068P14 mRNA, complete cds	NA	coding protein	psRNATarget
JB166338.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:87   CAUCCAAUCUCACUCAAUCCACAU   110 Target Full Sequence	1.5	Sequence 4002 from Patent EP2559767	NA	coding protein	psRNATarget
HI405877.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:87   CAUCCAAUCUCACUCAAUCCACAU   110 Target Full Sequence	1.5	Sequence 4002 from Patent EP2074227	NA	coding protein	psRNATarget
LQ238007.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:87   CAUCCAAUCUCACUCAAUCCACAU   110 Target Full Sequence	1.5	Sequence 4002 from Patent EP2985353	NA	coding protein	psRNATarget
LQ238023.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:79   CAUCCAAUCUCACUCAAUCCACAU   102 Target Full Sequence	1.5	Sequence 4018 from Patent EP2985353	NA	coding protein	psRNATarget
JB166354.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:79   CAUCCAAUCUCACUCAAUCCACAU   102 Target Full Sequence	1.5	Sequence 4018 from Patent EP2559767	NA	coding protein	psRNATarget
HI405893.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:79   CAUCCAAUCUCACUCAAUCCACAU   102 Target Full Sequence	1.5	Sequence 4018 from Patent EP2074227	NA	coding protein	psRNATarget
EZ092645.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||||||||||||*|||| targets:16   CAUCCAAUCUCACUCAAUCCACAU   39 Target Full Sequence	1.5	TSA: Zea mays contig28294, mRNA sequence	NA	coding protein	psRNATarget
XM_008674375.2	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   ||||=||||||||||||||*|||| targets:3438   CAUCUAAUCUCACUCAAUCCACAU   3461 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC100276614 (LOC100276614), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008674376.2	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   ||||=||||||||||||||*|||| targets:3407   CAUCUAAUCUCACUCAAUCCACAU   3430 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC100276614 (LOC100276614), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_008674377.2	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   ||||=||||||||||||||*|||| targets:3394   CAUCUAAUCUCACUCAAUCCACAU   3417 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC100276614 (LOC100276614), transcript variant X3, mRNA	NA	coding protein	psRNATarget
JB166339.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   =||||||||||||||||||*|||| targets:91   UAUCCAAUCUCACUCAAUCCACAU   114 Target Full Sequence	1.5	Sequence 4003 from Patent EP2559767	NA	coding protein	psRNATarget
HI405878.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   =||||||||||||||||||*|||| targets:91   UAUCCAAUCUCACUCAAUCCACAU   114 Target Full Sequence	1.5	Sequence 4003 from Patent EP2074227	NA	coding protein	psRNATarget
LQ238008.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   =||||||||||||||||||*|||| targets:91   UAUCCAAUCUCACUCAAUCCACAU   114 Target Full Sequence	1.5	Sequence 4003 from Patent EP2985353	NA	coding protein	psRNATarget
XM_020545430.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:5804   CAUCCAAUCCCACUCAAUCCACAU   5827 Target Full Sequence	2.5	PREDICTED: Zea mays uncharacterized LOC109942872 (LOC109942872), mRNA	NA	coding protein	psRNATarget
XM_008658241.2	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:1229   CAUCCAAUCCCACUCAAUCCACAU   1252 Target Full Sequence	2.5	PREDICTED: Zea mays probable peptidyl-tRNA hydrolase 2 (LOC103635865), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_020549842.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:1199   CAUCCAAUCCCACUCAAUCCACAU   1222 Target Full Sequence	2.5	PREDICTED: Zea mays uncharacterized LOC100381972 (LOC100381972), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_020549841.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:1199   CAUCCAAUCCCACUCAAUCCACAU   1222 Target Full Sequence	2.5	PREDICTED: Zea mays uncharacterized LOC100381972 (LOC100381972), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_020549843.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:1081   CAUCCAAUCCCACUCAAUCCACAU   1104 Target Full Sequence	2.5	PREDICTED: Zea mays uncharacterized LOC100381972 (LOC100381972), transcript variant X3, mRNA	NA	coding protein	psRNATarget
NM_001175969.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:1958   CAUCCAAUCCCACUCAAUCCACAU   1981 Target Full Sequence	2.5	Zea mays uncharacterized LOC100383311 (LOC100383311), mRNA	NA	coding protein	psRNATarget
BT066874.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:1958   CAUCCAAUCCCACUCAAUCCACAU   1981 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0081D21 mRNA, complete cds	NA	coding protein	psRNATarget
XM_008679547.2	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:2500   CAUCCAAUCCCACUCAAUCCACAU   2523 Target Full Sequence	2.5	PREDICTED: Zea mays putative methyltransferase PMT15 (LOC101027245), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008661718.2	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:2211   CAUCCAAUCCCACUCAAUCCACAU   2234 Target Full Sequence	2.5	PREDICTED: Zea mays serine/arginine repetitive matrix protein 1 (LOC103638926), mRNA	NA	coding protein	psRNATarget
EU955633.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:1815   CAUCCAAUCCCACUCAAUCCACAU   1838 Target Full Sequence	2.5	Zea mays clone 1540038 transposon protein mRNA, complete cds	NA	coding protein	psRNATarget
NM_001154031.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:1815   CAUCCAAUCCCACUCAAUCCACAU   1838 Target Full Sequence	2.5	Zea mays uncharacterized LOC100281112 (LOC100281112), mRNA	NA	coding protein	psRNATarget
BT088232.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:1530   CAUCCAAUCCCACUCAAUCCACAU   1553 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFc0086F14 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001279968.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:1530   CAUCCAAUCCCACUCAAUCCACAU   1553 Target Full Sequence	2.5	Zea mays putative methyltransferase PMT15 (LOC101027245), mRNA	NA	coding protein	psRNATarget
BT069115.2	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:528   CAUCCAAUCCCACUCAAUCCACAU   551 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0186N21 mRNA, complete cds	NA	coding protein	psRNATarget
BT085319.2	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:176   CAUCCAAUCCCACUCAAUCCACAU   199 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0375P22 mRNA, complete cds	NA	coding protein	psRNATarget
XM_020552889.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:874   CAUCCAAUCCCACUCAAUCCACAU   897 Target Full Sequence	2.5	PREDICTED: Zea mays pre-mRNA-splicing factor CWC21-like (LOC103654764), transcript variant X5, mRNA	NA	coding protein	psRNATarget
EU951448.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:745   CAUCCAAUCCCACUCAAUCCACAU   768 Target Full Sequence	2.5	Zea mays clone 701961 mRNA sequence	NA	coding protein	psRNATarget
EZ064016.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:120   CAUCCAAUCCCACUCAAUCCACAU   143 Target Full Sequence	2.5	TSA: Zea mays contig65139, mRNA sequence	NA	coding protein	psRNATarget
HI403094.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:98   CAUCCAAUCCCACUCAAUCCACAU   121 Target Full Sequence	2.5	Sequence 1219 from Patent EP2074227	NA	coding protein	psRNATarget
JB163555.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:98   CAUCCAAUCCCACUCAAUCCACAU   121 Target Full Sequence	2.5	Sequence 1219 from Patent EP2559767	NA	coding protein	psRNATarget
LQ235224.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:98   CAUCCAAUCCCACUCAAUCCACAU   121 Target Full Sequence	2.5	Sequence 1219 from Patent EP2985353	NA	coding protein	psRNATarget
JB166302.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:89   CAUCCAAUCCCACUCAAUCCACAU   112 Target Full Sequence	2.5	Sequence 3966 from Patent EP2559767	NA	coding protein	psRNATarget
LQ237971.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:89   CAUCCAAUCCCACUCAAUCCACAU   112 Target Full Sequence	2.5	Sequence 3966 from Patent EP2985353	NA	coding protein	psRNATarget
HI405841.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:89   CAUCCAAUCCCACUCAAUCCACAU   112 Target Full Sequence	2.5	Sequence 3966 from Patent EP2074227	NA	coding protein	psRNATarget
LQ238032.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:80   CAUCCAAUCCCACUCAAUCCACAU   103 Target Full Sequence	2.5	Sequence 4027 from Patent EP2985353	NA	coding protein	psRNATarget
HI405902.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:80   CAUCCAAUCCCACUCAAUCCACAU   103 Target Full Sequence	2.5	Sequence 4027 from Patent EP2074227	NA	coding protein	psRNATarget
JB166363.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:80   CAUCCAAUCCCACUCAAUCCACAU   103 Target Full Sequence	2.5	Sequence 4027 from Patent EP2559767	NA	coding protein	psRNATarget
JB166350.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:79   CAUCCAAUCCCACUCAAUCCACAU   102 Target Full Sequence	2.5	Sequence 4014 from Patent EP2559767	NA	coding protein	psRNATarget
HI405889.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:79   CAUCCAAUCCCACUCAAUCCACAU   102 Target Full Sequence	2.5	Sequence 4014 from Patent EP2074227	NA	coding protein	psRNATarget
LQ238019.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||||||||*|||||||||*|||| targets:79   CAUCCAAUCCCACUCAAUCCACAU   102 Target Full Sequence	2.5	Sequence 4014 from Patent EP2985353	NA	coding protein	psRNATarget
XM_020546136.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   ||*|||||=*|||||||||||||| targets:3279   CACCCAAUUCCACUCAAUCUACAU   3302 Target Full Sequence	2.0	PREDICTED: Zea mays protein FAR1-RELATED SEQUENCE 6 (LOC103642139), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_020546135.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   ||*|||||=*|||||||||||||| targets:3132   CACCCAAUUCCACUCAAUCUACAU   3155 Target Full Sequence	2.0	PREDICTED: Zea mays protein FAR1-RELATED SEQUENCE 6 (LOC103642139), transcript variant X1, mRNA	NA	coding protein	psRNATarget
BT066987.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||=|||||*|||||||||*|||| targets:1415   CAUUCAAUCCCACUCAAUCCACAU   1438 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0138F03 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001174368.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   ||*=|||||||||||||||*|||| targets:1443   CACUCAAUCUCACUCAAUCCACAU   1466 Target Full Sequence	1.5	Zea mays hypothetical protein (LOC100381539), mRNA	NA	coding protein	psRNATarget
BT061560.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   ||*=|||||||||||||||*|||| targets:1443   CACUCAAUCUCACUCAAUCCACAU   1466 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFb0158C09 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001147844.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||=|||||*|||||||||*|||| targets:1124   CAUUCAAUCCCACUCAAUCCACAU   1147 Target Full Sequence	2.5	Zea mays Phytanoyl-CoA dioxygenase (LOC100273407), mRNA	NA	coding protein	psRNATarget
BT041052.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||=|||||*|||||||||*|||| targets:1124   CAUUCAAUCCCACUCAAUCCACAU   1147 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFc0169K03 mRNA, complete cds	NA	coding protein	psRNATarget
EU948930.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   ||*|||||=*|||||||||||||| targets:420   CACCCAAUUCCACUCAAUCUACAU   443 Target Full Sequence	2.0	Zea mays clone 390579 mRNA sequence	NA	coding protein	psRNATarget
EU942673.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||=|||||*|||||||||*|||| targets:91   CAUUCAAUCCCACUCAAUCCACAU   114 Target Full Sequence	2.5	Zea mays clone 1529344 mRNA sequence	NA	coding protein	psRNATarget
HI403020.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||=|||||*|||||||||*|||| targets:98   CAUUCAAUCCCACUCAAUCCACAU   121 Target Full Sequence	2.5	Sequence 1145 from Patent EP2074227	NA	coding protein	psRNATarget
LQ235150.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||=|||||*|||||||||*|||| targets:98   CAUUCAAUCCCACUCAAUCCACAU   121 Target Full Sequence	2.5	Sequence 1145 from Patent EP2985353	NA	coding protein	psRNATarget
JB163481.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   |||=|||||*|||||||||*|||| targets:98   CAUUCAAUCCCACUCAAUCCACAU   121 Target Full Sequence	2.5	Sequence 1145 from Patent EP2559767	NA	coding protein	psRNATarget
LQ235220.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   *||||||||*|||||||||*|||| targets:98   AAUCCAAUCCCACUCAAUCCACAU   121 Target Full Sequence	2.5	Sequence 1215 from Patent EP2985353	NA	coding protein	psRNATarget
JB163551.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   *||||||||*|||||||||*|||| targets:98   AAUCCAAUCCCACUCAAUCCACAU   121 Target Full Sequence	2.5	Sequence 1215 from Patent EP2559767	NA	coding protein	psRNATarget
HI403090.1	ncRNA:24   GUAGGUUAGAGUGAGUUAGAUGUA   1   *||||||||*|||||||||*|||| targets:98   AAUCCAAUCCCACUCAAUCCACAU   121 Target Full Sequence	2.5	Sequence 1215 from Patent EP2074227	NA	coding protein	psRNATarget