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BaseInfo

ncRNA ID	novel_zma_miR3997
Species	Zea mays
Class	miRNA
Genome position	Chr2:43330892-43331027 [-]
Reference genome	RefGen_v4
Source	SRR2287159
Length	24
Mature sequence(if miRNA)	113 - ACACCGGACUGUCUGGUGCCCACA - 136
Stem-loop(if miRNA)	--         U     GU    A          U        ------- A  A   AA    AGCCC   G   ACACCGGAC GUCUG  GCCC CACGCCGGAC GUCCGGUG       C CC GGG  CCAC     AAC A   ||||||||| |||||  |||| |||||||||| ||||||||       | || |||  ||||     ||| C   UGUGGCCUG CAGGC  UGGG GUGUGGCCUG CAGGCCAC       G GG CCC  GGUG     UUG U GG         U     --    A          U        CAGAAGA A  -   AC    -GACC   A
Stem-loop sequence	ACACCGGACUGUCUGGUGCCCACACGCCGGACUGUCCGGUGCACCAGGGAACCACAGCCCAACGACUAGUUCCAGGUGGCACCCGGAGAGAAGACCACCGGACUGUCCGGUGUGAGGGUCGGACUGUCCGGUGUGG

Targets Info

Target Acc	Alignment	Exception	Target Description	Target Gene Name	Target Type	Method
LQ242135.1	ncRNA:24   ACACC-CGUGGUCUGUCAGGCCACA   1   *||||-||||||||||||||||||* targets:4   AGUGGCGCACCAGACAGUCCGGUGC   28 Target Full Sequence	3.0	Sequence 8130 from Patent EP2985353	NA	coding protein	psRNATarget
HI410005.1	ncRNA:24   ACACC-CGUGGUCUGUCAGGCCACA   1   *||||-||||||||||||||||||* targets:4   AGUGGCGCACCAGACAGUCCGGUGC   28 Target Full Sequence	3.0	Sequence 8130 from Patent EP2074227	NA	coding protein	psRNATarget
JB170466.1	ncRNA:24   ACACC-CGUGGUCUGUCAGGCCACA   1   *||||-||||||||||||||||||* targets:4   AGUGGCGCACCAGACAGUCCGGUGC   28 Target Full Sequence	3.0	Sequence 8130 from Patent EP2559767	NA	coding protein	psRNATarget
BT066461.2	ncRNA:24   ACACC-CGUGGUCUGUCAGGCCACA   1   *||||-||||||||||||||||||* targets:484   GGUGGCGCACCAGACAGUCCGGUGC   508 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0008E18 mRNA, complete cds	NA	coding protein	psRNATarget
BT066461.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ******|||||||||||||||||* targets:727   GUGCACCACCAGACAGUCCGGUGA   750 Target Full Sequence	2.0	Zea mays full-length cDNA clone ZM_BFb0008E18 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001175715.1	ncRNA:24   ACACC-CGUGGUCUGUCAGGCCACA   1   **|||-|||||=||||||||||||| targets:779   CCUGGCGCACCGGACAGUCCGGUGU   803 Target Full Sequence	3.0	Zea mays uncharacterized LOC100383038 (LOC100383038), mRNA	NA	coding protein	psRNATarget
BT066013.2	ncRNA:24   ACACC-CGUGGUCUGUCAGGCCACA   1   **|||-|||||=||||||||||||| targets:779   CCUGGCGCACCGGACAGUCCGGUGU   803 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0155M15 mRNA, complete cds	NA	coding protein	psRNATarget
BT086229.2	ncRNA:24   ACACC-CGUGGUCUGUCAGGCCACA   1   **|||-|||||=||||||||||||| targets:829   CCUGGUGCACCGGACAGUCCGGUGU   853 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFc0134M03 mRNA, complete cds	NA	coding protein	psRNATarget
BT086229.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**|||==||||||||||||| targets:534   GGUGCACACUGGACAGUCCGGUGU   557 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFc0134M03 mRNA, complete cds	NA	coding protein	psRNATarget
EU940831.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:296   GGUGCACACCGGACAGUCCGGUGC   319 Target Full Sequence	3.0	Zea mays clone 1157596 mRNA sequence	NA	coding protein	psRNATarget
EU940831.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:410   GGUGCACACCGGACAGUCCGGUGA   433 Target Full Sequence	3.0	Zea mays clone 1157596 mRNA sequence	NA	coding protein	psRNATarget
EU947920.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ||*|||||||=|||*||||||||| targets:395   UGGGGGCACCGGACUGUCCGGUGU   418 Target Full Sequence	2.5	Zea mays clone 366338 mRNA sequence	NA	coding protein	psRNATarget
BT069634.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ||*|||||||=|||*||||||||| targets:471   UGGGGGCACCGGACUGUCCGGUGU   494 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0193J19 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001176828.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ||*|||||||=|||*||||||||| targets:471   UGGGGGCACCGGACUGUCCGGUGU   494 Target Full Sequence	2.5	Zea mays uncharacterized LOC100384263 (LOC100384263), mRNA	NA	coding protein	psRNATarget
EU950973.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||*|||||=||||||||||||* targets:183   GGUGUGCACCGGACAGUCCGGUGC   206 Target Full Sequence	2.0	Zea mays clone 677173 mRNA sequence	NA	coding protein	psRNATarget
HI409994.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ||*|||||||||||*||||||||* targets:5   UGGGGGCACCAGACUGUCCGGUGC   28 Target Full Sequence	2.5	Sequence 8119 from Patent EP2074227	NA	coding protein	psRNATarget
LQ242124.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ||*|||||||||||*||||||||* targets:5   UGGGGGCACCAGACUGUCCGGUGC   28 Target Full Sequence	2.5	Sequence 8119 from Patent EP2985353	NA	coding protein	psRNATarget
JB170455.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ||*|||||||||||*||||||||* targets:5   UGGGGGCACCAGACUGUCCGGUGC   28 Target Full Sequence	2.5	Sequence 8119 from Patent EP2559767	NA	coding protein	psRNATarget
BT068112.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:471   GGUGCACACCGGACAGUCCGGUGC   494 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0045K13 mRNA, complete cds	NA	coding protein	psRNATarget
BT068112.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:601   GGUGCACACCGGACAGUCCGGUGA   624 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0045K13 mRNA, complete cds	NA	coding protein	psRNATarget
XM_008663618.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ***|||||||=|||*||||||||| targets:617   GAGGGGCACCGGACUGUCCGGUGU   640 Target Full Sequence	2.5	PREDICTED: Zea mays uncharacterized LOC103640564 (LOC103640564), mRNA	NA	coding protein	psRNATarget
NM_001175661.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ||-|||||||=|||*||||||||| targets:1176   UG-GGGCACCGGACUGUCCGGUGU   1198 Target Full Sequence	2.5	Zea mays uncharacterized LOC100382977 (LOC100382977), mRNA	NA	coding protein	psRNATarget
BT065862.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ||-|||||||=|||*||||||||| targets:1176   UG-GGGCACCGGACUGUCCGGUGU   1198 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFc0155J05 mRNA, complete cds	NA	coding protein	psRNATarget
BT066811.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:600   GGUGCACACCGGACAGUCCGGUGC   623 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0073A15 mRNA, complete cds	NA	coding protein	psRNATarget
BT066811.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:698   GGUGCACACCGGACAGUCCGGUGA   721 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0073A15 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001175949.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:600   GGUGCACACCGGACAGUCCGGUGC   623 Target Full Sequence	3.0	Zea mays uncharacterized LOC100383289 (LOC100383289), mRNA	NA	coding protein	psRNATarget
NM_001175949.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:698   GGUGCACACCGGACAGUCCGGUGA   721 Target Full Sequence	3.0	Zea mays uncharacterized LOC100383289 (LOC100383289), mRNA	NA	coding protein	psRNATarget
BT065921.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:715   GGUGCACACCGGACAGUCCGGUGA   738 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFc0044K19 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001175687.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:715   GGUGCACACCGGACAGUCCGGUGA   738 Target Full Sequence	3.0	Zea mays uncharacterized LOC100383005 (LOC100383005), mRNA	NA	coding protein	psRNATarget
LQ241754.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ***|||||||=|||*||||||||| targets:8   AAGGGGCACCGGACUGUCCGGUGU   31 Target Full Sequence	2.5	Sequence 7749 from Patent EP2985353	NA	coding protein	psRNATarget
HI409624.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ***|||||||=|||*||||||||| targets:8   AAGGGGCACCGGACUGUCCGGUGU   31 Target Full Sequence	2.5	Sequence 7749 from Patent EP2074227	NA	coding protein	psRNATarget
JB170085.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ***|||||||=|||*||||||||| targets:8   AAGGGGCACCGGACUGUCCGGUGU   31 Target Full Sequence	2.5	Sequence 7749 from Patent EP2559767	NA	coding protein	psRNATarget
JB170393.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ***|**||||=||||||||||||* targets:31   GUGGCCCACCGGACAGUCCGGUGC   54 Target Full Sequence	3.0	Sequence 8057 from Patent EP2559767	NA	coding protein	psRNATarget
LQ242062.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ***|**||||=||||||||||||* targets:31   GUGGCCCACCGGACAGUCCGGUGC   54 Target Full Sequence	3.0	Sequence 8057 from Patent EP2985353	NA	coding protein	psRNATarget
HI409932.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   ***|**||||=||||||||||||* targets:31   GUGGCCCACCGGACAGUCCGGUGC   54 Target Full Sequence	3.0	Sequence 8057 from Patent EP2074227	NA	coding protein	psRNATarget
EU964336.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|*|||||||=|||*||||||||| targets:456   AGGGGGCACCGGACUGUCCGGUGU   479 Target Full Sequence	2.5	Zea mays clone 278065 mRNA sequence	NA	coding protein	psRNATarget
EU948808.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|*|||||||=|||*||||||||| targets:750   AGGGGGCACCGGACUGUCCGGUGU   773 Target Full Sequence	2.5	Zea mays clone 385792 mRNA sequence	NA	coding protein	psRNATarget
BT065201.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:743   GGUGCACACCGGACAGUCCGGUGC   766 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0032D05 mRNA, complete cds	NA	coding protein	psRNATarget
BT065201.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   |*****||||=||||||||||||* targets:815   UUGUCCCACCGGACAGUCCGGUGC   838 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0032D05 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001165868.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||| targets:623   GGUGCACACCGGACAGUCCGGUGU   646 Target Full Sequence	2.0	Zea mays uncharacterized LOC100304434 (LOC100304434), mRNA	NA	coding protein	psRNATarget
NM_001165868.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:840   GGUGCACACCGGACAGUCCGGUGC   863 Target Full Sequence	3.0	Zea mays uncharacterized LOC100304434 (LOC100304434), mRNA	NA	coding protein	psRNATarget
NM_001165868.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:737   GGUGCACACCGGACAGUCCGGUGA   760 Target Full Sequence	3.0	Zea mays uncharacterized LOC100304434 (LOC100304434), mRNA	NA	coding protein	psRNATarget
BT061141.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||| targets:623   GGUGCACACCGGACAGUCCGGUGU   646 Target Full Sequence	2.0	Zea mays full-length cDNA clone ZM_BFb0115B09 mRNA, complete cds	NA	coding protein	psRNATarget
BT061141.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:840   GGUGCACACCGGACAGUCCGGUGC   863 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0115B09 mRNA, complete cds	NA	coding protein	psRNATarget
BT061141.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:737   GGUGCACACCGGACAGUCCGGUGA   760 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0115B09 mRNA, complete cds	NA	coding protein	psRNATarget
BT019242.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|*|||||||=|||*||||||||| targets:836   AGGGGGCACCGGACUGUCCGGUGU   859 Target Full Sequence	2.5	Zea mays clone Contig915.F mRNA sequence	NA	coding protein	psRNATarget
EU960150.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|*|||||||=|||*||||||||| targets:1418   AGGGGGCACCGGACUGUCCGGUGU   1441 Target Full Sequence	2.5	Zea mays clone 222169 hypothetical protein mRNA, complete cds	NA	coding protein	psRNATarget
BT061123.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:284   GGUGCACACCGGACAGUCCGGUGC   307 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0108I22 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001176839.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|*|||||||=|||*||||||||| targets:1736   AGGGGGCACCGGACUGUCCGGUGU   1759 Target Full Sequence	2.5	Zea mays uncharacterized LOC100384275 (LOC100384275), mRNA	NA	coding protein	psRNATarget
BT069667.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|*|||||||=|||*||||||||| targets:1736   AGGGGGCACCGGACUGUCCGGUGU   1759 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0206D24 mRNA, complete cds	NA	coding protein	psRNATarget
BT060603.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||*|||||=|||*||||||||| targets:1301   GGUGAGCACCGGACUGUCCGGUGU   1324 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0021N16 mRNA, complete cds	NA	coding protein	psRNATarget
BT064005.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|*|||||||=|||*||||||||| targets:1507   AGGGGGCACCGGACUGUCCGGUGU   1530 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFc0130B19 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001175099.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|*|||||||=|||*||||||||| targets:1507   AGGGGGCACCGGACUGUCCGGUGU   1530 Target Full Sequence	2.5	Zea mays uncharacterized LOC100382353 (LOC100382353), mRNA	NA	coding protein	psRNATarget
XM_020546123.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:4495   GGUGCACACCGGACAGUCCGGUGC   4518 Target Full Sequence	3.0	PREDICTED: Zea mays protein NUCLEAR FUSION DEFECTIVE 4-like (LOC103641819), mRNA	NA	coding protein	psRNATarget
XM_020546123.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:4610   GGUGCACACCGGACAGUCCGGUGA   4633 Target Full Sequence	3.0	PREDICTED: Zea mays protein NUCLEAR FUSION DEFECTIVE 4-like (LOC103641819), mRNA	NA	coding protein	psRNATarget
BT038885.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|**|||=||=||||||||||||* targets:861   GGGAGGCGCCGGACAGUCCGGUGC   884 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0337O17 mRNA, complete cds	NA	coding protein	psRNATarget
EU968231.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|**|||=||=||||||||||||* targets:1232   GGGAGGCGCCGGACAGUCCGGUGC   1255 Target Full Sequence	3.0	Zea mays clone 317172 hypothetical protein mRNA, complete cds	NA	coding protein	psRNATarget
BT061124.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:448   GGUGCACACCGGACAGUCCGGUGC   471 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0108N24 mRNA, complete cds	NA	coding protein	psRNATarget
BT061124.2	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:562   GGUGCACACCGGACAGUCCGGUGA   585 Target Full Sequence	3.0	Zea mays full-length cDNA clone ZM_BFb0108N24 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001165861.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:448   GGUGCACACCGGACAGUCCGGUGC   471 Target Full Sequence	3.0	Zea mays uncharacterized LOC100304427 (LOC100304427), mRNA	NA	coding protein	psRNATarget
NM_001165861.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:562   GGUGCACACCGGACAGUCCGGUGA   585 Target Full Sequence	3.0	Zea mays uncharacterized LOC100304427 (LOC100304427), mRNA	NA	coding protein	psRNATarget
EU940845.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:1400   GGUGCACACCGGACAGUCCGGUGC   1423 Target Full Sequence	3.0	Zea mays clone 1163633 mRNA sequence	NA	coding protein	psRNATarget
HI409351.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:31   GGUGUACACCGGACAGUCCGGUGC   54 Target Full Sequence	3.0	Sequence 7476 from Patent EP2074227	NA	coding protein	psRNATarget
JB169812.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:31   GGUGUACACCGGACAGUCCGGUGC   54 Target Full Sequence	3.0	Sequence 7476 from Patent EP2559767	NA	coding protein	psRNATarget
LQ241481.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|||**||||=||||||||||||* targets:31   GGUGUACACCGGACAGUCCGGUGC   54 Target Full Sequence	3.0	Sequence 7476 from Patent EP2985353	NA	coding protein	psRNATarget
EZ078101.1	ncRNA:24   ACACCCGUGGUCUGUCAGGCCACA   1   *|**||||=|||||*||||||||| targets:66   AGAAGGCAUCAGACUGUCCGGUGU   89 Target Full Sequence	2.5	TSA: Zea mays contig13740, mRNA sequence	NA	coding protein	psRNATarget