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BaseInfo

ncRNA ID	novel_zma_miR3840
Species	Zea mays
Class	miRNA
Genome position	Chr5:121267792-121267927 [-]
Reference genome	RefGen_v4
Source	SRR2287159;SRR2287160;SRR1997865;SRR1997866;SRR2089707;SRR2089708
Length	24
Mature sequence(if miRNA)	113 - AGGGCUGAUUUGGUGAUUACGGAU - 136
Stem-loop(if miRNA)	---    C          A   C                          A     CU    CA     A    AGGG UGAUUUGGUG UUA GGAUCCCUAGGGGAUCUAUGGGGGAG AAUCC  UUUG  AUUCA U    |||| |||||||||| ||| |||||||||||||||||||||||||| |||||  ||||  |||||    UCCC ACUAAACCAC AGU CCUAGGGAUUCCCUAGGUACCUCUUC UUAGG  GAAC  UAAGU U GAU    A          C   C                          A     -C    AA     U
Stem-loop sequence	AGGGCUGAUUUGGUGAUUACGGAUCCCUAGGGGAUCUAUGGGGGAGAAAUCCCUUUUGCAAUUCAAUUUUGAAUAACAAGCGGAUUACUUCUCCAUGGAUCCCUUAGGGAUCCCUGACCACCAAAUCAACCCUUAG

Targets Info

Target Acc	Alignment	Exception	Target Description	Target Gene Name	Target Type	Method
EU941266.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*||||||=|||||||||||| targets:686   AUCCCUAAUCAUCAAAUCAGCCCU   709 Target Full Sequence	1.5	Zea mays clone 1435213 mRNA sequence	NA	coding protein	psRNATarget
BT068562.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*||||||||||||=|||||| targets:1077   AUCCCUAAUCACCAAAUUAGCCCU   1100 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFb0331B04 mRNA, complete cds	NA	coding protein	psRNATarget
XM_008681394.2	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|||||||||||||||=||| targets:4510   AUCCCUAAUCACCAAAUCAGUCCU   4533 Target Full Sequence	1.5	PREDICTED: Zea mays disease resistance protein RPM1-like (LOC103654547), transcript variant X3, mRNA	NA	coding protein	psRNATarget
XM_008681392.2	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|||||||||||||||=||| targets:4684   AUCCCUAAUCACCAAAUCAGUCCU   4707 Target Full Sequence	1.5	PREDICTED: Zea mays disease resistance protein RPM1-like (LOC103654547), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_020552825.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|||||||||||||||=||| targets:4775   AUCCCUAAUCACCAAAUCAGUCCU   4798 Target Full Sequence	1.5	PREDICTED: Zea mays disease resistance protein RPM1-like (LOC103654547), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_020545246.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*||||||||||||||||||* targets:152   AUCCCUAAUCACCAAAUCAGCCCG   175 Target Full Sequence	1.0	PREDICTED: Zea mays methyl binding domain113 (cl26423_1), transcript variant X7, mRNA	NA	coding protein	psRNATarget
JB163906.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|==|||||||||||||||| targets:61   AUCCCUGGUCACCAAAUCAGCCCU   84 Target Full Sequence	2.0	Sequence 1570 from Patent EP2559767	NA	coding protein	psRNATarget
HI403445.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|==|||||||||||||||| targets:61   AUCCCUGGUCACCAAAUCAGCCCU   84 Target Full Sequence	2.0	Sequence 1570 from Patent EP2074227	NA	coding protein	psRNATarget
LQ235575.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|==|||||||||||||||| targets:61   AUCCCUGGUCACCAAAUCAGCCCU   84 Target Full Sequence	2.0	Sequence 1570 from Patent EP2985353	NA	coding protein	psRNATarget
JB163762.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|==|||||||||||||||| targets:96   AUCCCUGGUCACCAAAUCAGCCCU   119 Target Full Sequence	2.0	Sequence 1426 from Patent EP2559767	NA	coding protein	psRNATarget
HI403301.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|==|||||||||||||||| targets:96   AUCCCUGGUCACCAAAUCAGCCCU   119 Target Full Sequence	2.0	Sequence 1426 from Patent EP2074227	NA	coding protein	psRNATarget
LQ235431.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|==|||||||||||||||| targets:96   AUCCCUGGUCACCAAAUCAGCCCU   119 Target Full Sequence	2.0	Sequence 1426 from Patent EP2985353	NA	coding protein	psRNATarget
HI402947.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|||||||||||||||||*| targets:114   AUCCCUAAUCACCAAAUCAGCCAU   137 Target Full Sequence	1.5	Sequence 1072 from Patent EP2074227	NA	coding protein	psRNATarget
LQ235077.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|||||||||||||||||*| targets:114   AUCCCUAAUCACCAAAUCAGCCAU   137 Target Full Sequence	1.5	Sequence 1072 from Patent EP2985353	NA	coding protein	psRNATarget
JB163408.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|||||||||||||||||*| targets:114   AUCCCUAAUCACCAAAUCAGCCAU   137 Target Full Sequence	1.5	Sequence 1072 from Patent EP2559767	NA	coding protein	psRNATarget
BT066676.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|||*||||||||||||||| targets:1339   AUCCCUAACCACCAAAUCAGCCCU   1362 Target Full Sequence	1.0	Zea mays full-length cDNA clone ZM_BFb0044C22 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001175907.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|||*||||||||||||||| targets:1339   AUCCCUAACCACCAAAUCAGCCCU   1362 Target Full Sequence	1.0	Zea mays CCAAT-HAP2 transcription factor (CA2P12), mRNA	NA	coding protein	psRNATarget
XM_008675221.2	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|==|||||||||||||||* targets:180   AUCCCUGGUCACCAAAUCAGCCCG   203 Target Full Sequence	3.0	PREDICTED: Zea mays gibberellin responsive 1 (gar1), transcript variant X2, mRNA	NA	coding protein	psRNATarget
JB170445.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|=||||||||||||||*|| targets:113   AUCCCUGAUCACCAAAUCAGCACU   136 Target Full Sequence	2.5	Sequence 8109 from Patent EP2559767	NA	coding protein	psRNATarget
LQ242114.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|=||||||||||||||*|| targets:113   AUCCCUGAUCACCAAAUCAGCACU   136 Target Full Sequence	2.5	Sequence 8109 from Patent EP2985353	NA	coding protein	psRNATarget
HI409984.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*|=||||||||||||||*|| targets:113   AUCCCUGAUCACCAAAUCAGCACU   136 Target Full Sequence	2.5	Sequence 8109 from Patent EP2074227	NA	coding protein	psRNATarget
AY108273.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||*||*||||||||||||=||| targets:454   AUCCCUAUUCACCAAAUCAGUCCU   477 Target Full Sequence	2.5	Zea mays PCO108913 mRNA sequence	NA	coding protein	psRNATarget
BT088155.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||**|||||||||||||||=|| targets:1493   AUCCCGAAUCACCAAAUCAGCUCU   1516 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFc0038D09 mRNA, complete cds	NA	coding protein	psRNATarget
XM_008649119.2	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||*|*||||||||||||||||=|| targets:35   AUACCUAAUCACCAAAUCAGCUCU   58 Target Full Sequence	1.5	PREDICTED: Zea mays PHD transcription factor (PHD35), transcript variant X1, mRNA	NA	coding protein	psRNATarget
BT018533.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   *||=*|=||||=|||||||||||| targets:1918   UUCUCUGAUCAUCAAAUCAGCCCU   1941 Target Full Sequence	2.5	Zea mays clone EL01N0434E06.d mRNA sequence	NA	coding protein	psRNATarget
EU950017.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||**==|||||||||||||||| targets:512   AUCCCGGGUCACCAAAUCAGCCCU   535 Target Full Sequence	3.0	Zea mays clone 457681 mRNA sequence	NA	coding protein	psRNATarget
XM_020540504.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||**==|||||||||||||||| targets:1877   AUCCCGGGUCACCAAAUCAGCCCU   1900 Target Full Sequence	3.0	PREDICTED: Zea mays nucleolar RNA helicase 2 (LOC100281387), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_020540503.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||**==|||||||||||||||| targets:2315   AUCCCGGGUCACCAAAUCAGCCCU   2338 Target Full Sequence	3.0	PREDICTED: Zea mays nucleolar RNA helicase 2 (LOC100281387), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_020538171.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   =|||*|=|||||||||||||*||| targets:1   GUCCCUGAUCACCAAAUCAGACCU   24 Target Full Sequence	2.5	PREDICTED: Zea mays uncharacterized LOC109939824 (LOC109939824), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008671854.2	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   ||||**==|||||||||||||||| targets:70   AUCCCCGGUCACCAAAUCAGCCCU   93 Target Full Sequence	3.0	PREDICTED: Zea mays alpha-glucosidase 2 (LOC103647311), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_008680925.2	ncRNA:24   UAG-GCAUUAGUGGUUUAGUCGGGA   1   ||=-|*|==|||||||||||||||| targets:1825   AUUGCAUGGUCACCAAAUCAGCCCU   1849 Target Full Sequence	2.0	PREDICTED: Zea mays 4-coumarate--CoA ligase-like 3 (LOC103654103), mRNA	NA	coding protein	psRNATarget
AF244696.1	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   |||*-||=|||||||||||||=|| targets:864   AUCA-UAGUCACCAAAUCAGCUCU   886 Target Full Sequence	2.5	Zea mays glutathione S-transferase GST 31 mRNA, complete cds	NA	coding protein	psRNATarget
BT054307.1	ncRNA:24   UAG-GCAUUAGUGGUUUAGUCGGGA   1   |||-|*|*||||=|||||||||||| targets:1091   AUCUCCUUAUCAUCAAAUCAGCCCU   1115 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0234I14 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001152477.1	ncRNA:24   UAG-GCAUUAGUGGUUUAGUCGGGA   1   |||-|*|*||||=|||||||||||| targets:1091   AUCUCCUUAUCAUCAAAUCAGCCCU   1115 Target Full Sequence	2.5	Zea mays Putative SAC3/GANP family protein (LOC100279473), mRNA	NA	coding protein	psRNATarget
XM_020538905.1	ncRNA:24   UAG-GCAUUAGUGGUUUAGUCGGGA   1   |||-|*|*||||=|||||||||||| targets:3860   AUCUCCUUAUCAUCAAAUCAGCCCU   3884 Target Full Sequence	2.5	PREDICTED: Zea mays Putative SAC3/GANP family protein (LOC100279473), transcript variant X4, mRNA	NA	coding protein	psRNATarget
XM_020538904.1	ncRNA:24   UAG-GCAUUAGUGGUUUAGUCGGGA   1   |||-|*|*||||=|||||||||||| targets:3863   AUCUCCUUAUCAUCAAAUCAGCCCU   3887 Target Full Sequence	2.5	PREDICTED: Zea mays Putative SAC3/GANP family protein (LOC100279473), transcript variant X3, mRNA	NA	coding protein	psRNATarget
XM_008649499.2	ncRNA:24   UAG-GCAUUAGUGGUUUAGUCGGGA   1   |||-|*|*||||=|||||||||||| targets:3952   AUCUCCUUAUCAUCAAAUCAGCCCU   3976 Target Full Sequence	2.5	PREDICTED: Zea mays Putative SAC3/GANP family protein (LOC100279473), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008649500.2	ncRNA:24   UAG-GCAUUAGUGGUUUAGUCGGGA   1   |||-|*|*||||=|||||||||||| targets:3952   AUCUCCUUAUCAUCAAAUCAGCCCU   3976 Target Full Sequence	2.5	PREDICTED: Zea mays Putative SAC3/GANP family protein (LOC100279473), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_008663725.2	ncRNA:24   UAGGCAUUAGUGGUUUAGUCGGGA   1   =||*|*|*|||||||||||||||| targets:153   GUCAGAAUUCACCAAAUCAGCCCU   176 Target Full Sequence	2.0	PREDICTED: Zea mays scramblase family protein (LOC100282688), transcript variant X1, mRNA	NA	coding protein	psRNATarget