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BaseInfo

ncRNA ID	novel_zma_miR2440
Species	Zea mays
Class	miRNA
Genome position	Chr4:15650470-15650592 [-]
Reference genome	RefGen_v4
Source	SRR1583944
Length	24
Mature sequence(if miRNA)	100 - AGGGCUAGUUUGGAAACUUAAAUU - 123
Stem-loop(if miRNA)	--                         C                      G       UUAG   AGGGCUAGUUUGGAAACUUAAAUUC UUCCAGAAUUUCUGGGGAUUGA AGGGAAA    U   ||||||||||||||||||||||||| |||||||||||||||||||||| |||||||   UCCCGAUCAAACCUUUGAAUUUAGG GAGGUCUUGAGGGCCCUUAACU UCCCUUU    U AU                         A                      -       UAAU
Stem-loop sequence	AGGGCUAGUUUGGAAACUUAAAUUCCUUCCAGAAUUUCUGGGGAUUGAGAGGGAAAUUAGUUUAAUUUUCCCUUCAAUUCCCGGGAGUUCUGGAGAGGAUUUAAGUUUCCAAACUAGCCCUUA

Targets Info

Target Acc	Alignment	Exception	Target Description	Target Gene Name	Target Type	Method
XM_008676159.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||||||||||||||||||||||| targets:2664   GAUUUAAGUUUCCAAACUAGCCCU   2687 Target Full Sequence	0.0	PREDICTED: Zea mays VIN3-like protein 1 (LOC103650592), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_020550313.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||||||||||||||||||||||| targets:2344   GAUUUAAGUUUCCAAACUAGCCCU   2367 Target Full Sequence	0.0	PREDICTED: Zea mays VIN3-like protein 1 (LOC103650592), transcript variant X2, mRNA	NA	coding protein	psRNATarget
EZ071161.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||||||||||||||||||||||=| targets:118   AAUUUAAGUUUCCAAACUAGCCUU   141 Target Full Sequence	1.5	TSA: Zea mays contig06798, mRNA sequence	NA	coding protein	psRNATarget
XM_020550081.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   |||||=|||||||||||||||=|| targets:2430   AAUUUGAGUUUCCAAACUAGCUCU   2453 Target Full Sequence	2.5	PREDICTED: Zea mays uncharacterized LOC109944788 (LOC109944788), mRNA	NA	coding protein	psRNATarget
XM_008679616.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||||=|||||||||||||||||| targets:1220   GAUUUGAGUUUCCAAACUAGCCCU   1243 Target Full Sequence	1.0	PREDICTED: Zea mays uncharacterized LOC103652675 (LOC103652675), mRNA	NA	coding protein	psRNATarget
EZ069159.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||||=|||||||||||||||||| targets:88   GAUUUGAGUUUCCAAACUAGCCCU   111 Target Full Sequence	1.0	TSA: Zea mays contig04794, mRNA sequence	NA	coding protein	psRNATarget
XM_008676335.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||||=|||||||||||||||=|| targets:4404   GAUUUGAGUUUCCAAACUAGCUCU   4427 Target Full Sequence	2.5	PREDICTED: Zea mays Serine/arginine repetitive matrix protein 2 isoform 4 (LOC103650763), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_008676333.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||||=|||||||||||||||=|| targets:4391   GAUUUGAGUUUCCAAACUAGCUCU   4414 Target Full Sequence	2.5	PREDICTED: Zea mays Serine/arginine repetitive matrix protein 2 isoform 4 (LOC103650763), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008676336.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||||=|||||||||||||||=|| targets:4377   GAUUUGAGUUUCCAAACUAGCUCU   4400 Target Full Sequence	2.5	PREDICTED: Zea mays Serine/arginine repetitive matrix protein 2 isoform 4 (LOC103650763), transcript variant X3, mRNA	NA	coding protein	psRNATarget
XM_008671736.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||||=|||||=|||||||||||| targets:2517   GAUUUGAGUUUUCAAACUAGCCCU   2540 Target Full Sequence	2.5	PREDICTED: Zea mays probable serine/threonine-protein kinase PBL28 (LOC103647166), mRNA	NA	coding protein	psRNATarget
XM_008659899.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||||=|||||||=|||||||||| targets:2352   GAUUUGAGUUUCCGAACUAGCCCU   2375 Target Full Sequence	2.5	PREDICTED: Zea mays carotene epsilon-monooxygenase, chloroplastic (LOC103637620), mRNA	NA	coding protein	psRNATarget
NM_001175825.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||||||||||=|||||||||||* targets:2095   GAUUUAAGUUUUCAAACUAGCCCA   2118 Target Full Sequence	2.5	Zea mays putative DEAD-box ATP-dependent RNA helicase family protein (LOC100383160), mRNA	NA	coding protein	psRNATarget
BT066418.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||||||||||=|||||||||||* targets:2095   GAUUUAAGUUUUCAAACUAGCCCA   2118 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFc0124A04 mRNA, complete cds	NA	coding protein	psRNATarget
XM_008655231.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =|||||||||||||||||||*||| targets:2857   GAUUUAAGUUUCCAAACUAGACCU   2880 Target Full Sequence	1.5	PREDICTED: Zea mays probable indole-3-acetic acid-amido synthetase GH3.11 (LOC103633549), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_020541149.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =|||||||||||||||||||*||| targets:2772   GAUUUAAGUUUCCAAACUAGACCU   2795 Target Full Sequence	1.5	PREDICTED: Zea mays probable indole-3-acetic acid-amido synthetase GH3.11 (LOC103633549), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_020541150.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =|||||||||||||||||||*||| targets:2756   GAUUUAAGUUUCCAAACUAGACCU   2779 Target Full Sequence	1.5	PREDICTED: Zea mays probable indole-3-acetic acid-amido synthetase GH3.11 (LOC103633549), transcript variant X3, mRNA	NA	coding protein	psRNATarget
XM_020541151.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =|||||||||||||||||||*||| targets:2716   GAUUUAAGUUUCCAAACUAGACCU   2739 Target Full Sequence	1.5	PREDICTED: Zea mays probable indole-3-acetic acid-amido synthetase GH3.11 (LOC103633549), transcript variant X4, mRNA	NA	coding protein	psRNATarget
XM_020541153.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =|||||||||||||||||||*||| targets:2637   GAUUUAAGUUUCCAAACUAGACCU   2660 Target Full Sequence	1.5	PREDICTED: Zea mays probable indole-3-acetic acid-amido synthetase GH3.11 (LOC103633549), transcript variant X6, mRNA	NA	coding protein	psRNATarget
XM_020541152.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =|||||||||||||||||||*||| targets:2631   GAUUUAAGUUUCCAAACUAGACCU   2654 Target Full Sequence	1.5	PREDICTED: Zea mays probable indole-3-acetic acid-amido synthetase GH3.11 (LOC103633549), transcript variant X5, mRNA	NA	coding protein	psRNATarget
JB167567.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||*|||||||||||||||||||| targets:93   GAUGUAAGUUUCCAAACUAGCCCU   116 Target Full Sequence	0.0	Sequence 5231 from Patent EP2559767	NA	coding protein	psRNATarget
HI407106.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||*|||||||||||||||||||| targets:93   GAUGUAAGUUUCCAAACUAGCCCU   116 Target Full Sequence	0.0	Sequence 5231 from Patent EP2074227	NA	coding protein	psRNATarget
LQ239236.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||*|||||||||||||||||||| targets:93   GAUGUAAGUUUCCAAACUAGCCCU   116 Target Full Sequence	0.0	Sequence 5231 from Patent EP2985353	NA	coding protein	psRNATarget
XM_008660198.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   |||||==|*||||||||||||||| targets:1003   AAUUUGGGGUUCCAAACUAGCCCU   1026 Target Full Sequence	3.0	PREDICTED: Zea mays ER membrane protein complex subunit 7-like protein (LOC100277198), transcript variant X1, mRNA	NA	coding protein	psRNATarget
BT017648.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   =||||=||||||||||||||||*| targets:309   GAUUUGAGUUUCCAAACUAGCCAU   332 Target Full Sequence	2.5	Zea mays clone EL01N0439D04.c mRNA sequence	NA	coding protein	psRNATarget
EZ069250.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   |||||==|*||||||||||||||| targets:156   AAUUUGGGGUUCCAAACUAGCCCU   179 Target Full Sequence	3.0	TSA: Zea mays contig04885, mRNA sequence	NA	coding protein	psRNATarget
EU955577.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   *||*|=|||||||||||||||||| targets:2116   UAUAUGAGUUUCCAAACUAGCCCU   2139 Target Full Sequence	1.0	Zea mays clone 1537616 kelch motif family protein mRNA, complete cds	NA	coding protein	psRNATarget
EU955577.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   **|*|=|||||||||||||||||| targets:2157   UCUAUGAGUUUCCAAACUAGCCCU   2180 Target Full Sequence	1.0	Zea mays clone 1537616 kelch motif family protein mRNA, complete cds	NA	coding protein	psRNATarget
NM_001154017.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   *||*|=|||||||||||||||||| targets:2115   UAUAUGAGUUUCCAAACUAGCCCU   2138 Target Full Sequence	1.0	Zea mays kelch motif family protein (LOC100281098), mRNA	NA	coding protein	psRNATarget
NM_001154017.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   **|*|=|||||||||||||||||| targets:2156   UCUAUGAGUUUCCAAACUAGCCCU   2179 Target Full Sequence	1.0	Zea mays kelch motif family protein (LOC100281098), mRNA	NA	coding protein	psRNATarget
XM_020547541.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*==|||*||||||||||||| targets:1964   AAAUGGGGUUCCCAAACUAGCCCU   1987 Target Full Sequence	3.0	PREDICTED: Zea mays uncharacterized LOC100273682 (LOC100273682), transcript variant X1, mRNA	NA	coding protein	psRNATarget
EZ111591.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   *||||=||||||||||||||||*| targets:104   CAUUUGAGUUUCCAAACUAGCCAU   127 Target Full Sequence	2.5	TSA: Zea mays contig47252, mRNA sequence	NA	coding protein	psRNATarget
XM_008654469.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*||=||*||||||||||||||| targets:3570   AAAUUGAGCUUCCAAACUAGCCCU   3593 Target Full Sequence	2.0	PREDICTED: Zea mays U-box domain-containing protein 35 (LOC103632728), mRNA	NA	coding protein	psRNATarget
NM_001150806.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*||=||||*||||||||||||| targets:1055   AAAUUGAGUUCCCAAACUAGCCCU   1078 Target Full Sequence	2.0	Zea mays Tyrosine specific protein phosphatase-like (LOC100277156), mRNA	NA	coding protein	psRNATarget
EU967093.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*||=||||*||||||||||||| targets:1005   AAAUUGAGUUCCCAAACUAGCCCU   1028 Target Full Sequence	2.0	Zea mays clone 299427 hypothetical protein mRNA, complete cds	NA	coding protein	psRNATarget
BT084259.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*||=||||*||||||||||||| targets:1009   AAAUUGAGUUCCCAAACUAGCCCU   1032 Target Full Sequence	2.0	Zea mays full-length cDNA clone ZM_BFb0094M03 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001154870.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ***||=|||||=|||||||||||| targets:912   CCGUUGAGUUUUCAAACUAGCCCU   935 Target Full Sequence	2.5	Zea mays 60S ribosomal protein L23 (LOC100281952), mRNA	NA	coding protein	psRNATarget
EU958754.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ***||=|||||=|||||||||||| targets:912   CCGUUGAGUUUUCAAACUAGCCCU   935 Target Full Sequence	2.5	Zea mays clone 207771 60S ribosomal protein L23 mRNA, complete cds	NA	coding protein	psRNATarget
BT069551.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||||*|=|||*||||||||||||| targets:321   AAUUGAGGUUCCCAAACUAGCCCU   344 Target Full Sequence	2.0	Zea mays full-length cDNA clone ZM_BFb0167A20 mRNA, complete cds	NA	coding protein	psRNATarget
XM_008666283.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ==**|=|||||||||||||||||| targets:3391   GGGAUGAGUUUCCAAACUAGCCCU   3414 Target Full Sequence	1.0	PREDICTED: Zea mays protein indeterminate-domain 16 (LOC103643131), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008666284.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ==**|=|||||||||||||||||| targets:3308   GGGAUGAGUUUCCAAACUAGCCCU   3331 Target Full Sequence	1.0	PREDICTED: Zea mays protein indeterminate-domain 16 (LOC103643131), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_020544094.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*==||||||||||||||||| targets:1306   AAAUAGGGUUUCCAAACUAGCCCU   1329 Target Full Sequence	2.0	PREDICTED: Zea mays 3-ketoacyl-CoA synthase 6 (LOC103638222), mRNA	NA	coding protein	psRNATarget
EU967323.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*||==|*||||||||||||||| targets:970   AAAUUGGGGUUCCAAACUAGCCCU   993 Target Full Sequence	3.0	Zea mays clone 301481 hypothetical protein mRNA, complete cds	NA	coding protein	psRNATarget
NM_001150835.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*||==|*||||||||||||||| targets:970   AAAUUGGGGUUCCAAACUAGCCCU   993 Target Full Sequence	3.0	Zea mays ER membrane protein complex subunit 7-like protein (LOC100277198), mRNA	NA	coding protein	psRNATarget
EU951374.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*==||||||||||||||||| targets:414   AAAUGGGGUUUCCAAACUAGCCCU   437 Target Full Sequence	2.0	Zea mays clone 697858 mRNA sequence	NA	coding protein	psRNATarget
EZ080886.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*|=|||||||||=||||||| targets:122   AAAUGAGGUUUCCAAAUUAGCCCU   145 Target Full Sequence	2.5	TSA: Zea mays contig16525, mRNA sequence	NA	coding protein	psRNATarget
XM_008652587.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*|=||||||||||||||||* targets:1077   AAAUGAGGUUUCCAAACUAGCCCC   1100 Target Full Sequence	2.0	PREDICTED: Zea mays Chaperone DnaJ-domain superfamily protein (LOC100191793), transcript variant X1, mRNA	NA	coding protein	psRNATarget
BT034002.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*|=||||||||||||||||* targets:1017   AAAUGAGGUUUCCAAACUAGCCCC   1040 Target Full Sequence	2.0	Zea mays full-length cDNA clone ZM_BFc0044B05 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001137218.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*|=||||||||||||||||* targets:1017   AAAUGAGGUUUCCAAACUAGCCCC   1040 Target Full Sequence	2.0	Zea mays Chaperone DnaJ-domain superfamily protein (LOC100191793), mRNA	NA	coding protein	psRNATarget
XM_008652589.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*|=||||||||||||||||* targets:999   AAAUGAGGUUUCCAAACUAGCCCC   1022 Target Full Sequence	2.0	PREDICTED: Zea mays Chaperone DnaJ-domain superfamily protein (LOC100191793), transcript variant X3, mRNA	NA	coding protein	psRNATarget
XM_008652590.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*|=||||||||||||||||* targets:972   AAAUGAGGUUUCCAAACUAGCCCC   995 Target Full Sequence	2.0	PREDICTED: Zea mays Chaperone DnaJ-domain superfamily protein (LOC100191793), transcript variant X4, mRNA	NA	coding protein	psRNATarget
NM_001350117.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   |||*-|=|||||=||||||||||| targets:3269   AAUG-AGGUUUCUAAACUAGCCCU   3291 Target Full Sequence	2.5	Zea mays uncharacterized LOC100283404 (pco107270a), mRNA	NA	coding protein	psRNATarget
NM_001350811.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*=||||*||||||||||||| targets:2559   AAAUGGAGUUCCCAAACUAGCCCU   2582 Target Full Sequence	2.0	Zea mays uncharacterized LOC100278071 (LOC100278071), mRNA	NA	coding protein	psRNATarget
XM_020552563.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*=||||*||||||||||||| targets:455   AAAUGGAGUUCCCAAACUAGCCCU   478 Target Full Sequence	2.0	PREDICTED: Zea mays probable alpha,alpha-trehalose-phosphate synthase [UDP-forming] 10 (LOC103653427), transcript variant X2, mRNA	NA	coding protein	psRNATarget
NM_001152323.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*=|||*|||||||||||||| targets:1177   AAAUGGAGUCUCCAAACUAGCCCU   1200 Target Full Sequence	2.0	Zea mays uncharacterized LOC100279302 (LOC100279302), mRNA	NA	coding protein	psRNATarget
BT053999.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*=|||*|||||||||||||| targets:1177   AAAUGGAGUCUCCAAACUAGCCCU   1200 Target Full Sequence	2.0	Zea mays full-length cDNA clone ZM_BFc0109O10 mRNA, complete cds	NA	coding protein	psRNATarget
XM_008669712.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*=||||||||||||||*||| targets:2199   AAAUAGAGUUUCCAAACUAGGCCU   2222 Target Full Sequence	2.5	PREDICTED: Zea mays DHHC zinc finger domain containing protein (LOC100281605), transcript variant X2, mRNA	NA	coding protein	psRNATarget
EU957224.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*=||||||||||||||*||| targets:1970   AAAUAGAGUUUCCAAACUAGGCCU   1993 Target Full Sequence	2.5	Zea mays clone 1586117 DHHC zinc finger domain containing protein mRNA, complete cds	NA	coding protein	psRNATarget
NM_001154524.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*=||||||||||||||*||| targets:1970   AAAUAGAGUUUCCAAACUAGGCCU   1993 Target Full Sequence	2.5	Zea mays DHHC zinc finger domain containing protein (LOC100281605), mRNA	NA	coding protein	psRNATarget
BT065747.2	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*=|||*|||||||||||||| targets:7   AAAUGGAGUCUCCAAACUAGCCCU   30 Target Full Sequence	2.0	Zea mays full-length cDNA clone ZM_BFc0062G24 mRNA, complete cds	NA	coding protein	psRNATarget
JB167282.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*|=|||*||||||||||||| targets:107   AAAUGAGGUUCCCAAACUAGCCCU   130 Target Full Sequence	2.0	Sequence 4946 from Patent EP2559767	NA	coding protein	psRNATarget
LQ238951.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*|=|||*||||||||||||| targets:107   AAAUGAGGUUCCCAAACUAGCCCU   130 Target Full Sequence	2.0	Sequence 4946 from Patent EP2985353	NA	coding protein	psRNATarget
HI406821.1	ncRNA:24   UUAAAUUCAAAGGUUUGAUCGGGA   1   ||*|*|=|||*||||||||||||| targets:107   AAAUGAGGUUCCCAAACUAGCCCU   130 Target Full Sequence	2.0	Sequence 4946 from Patent EP2074227	NA	coding protein	psRNATarget