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BaseInfo

ncRNA ID	novel_zma_miR9253
Species	Zea mays
Class	miRNA
Genome position	Chr4:242637079-242637162 [+]
Reference genome	RefGen_v4
Source	SRR4237222;SRR4237223
Length	24
Mature sequence(if miRNA)	61 - AAUAUUCGAGAAUGGAGGUAGUAC - 84
Stem-loop(if miRNA)	--   C           UUU         CA U        A   ACU CCUCCGUUCUU   UAUUUGUCG  C UUAGUUCA A   ||| |||||||||||   |||||||||  | ||||||||   UGA GGAGGUAAGAG   AUAAACAGC  G GAUCAAGU A CA   U           CUU         AG C        A
Stem-loop sequence	ACUCCCUCCGUUCUUUUUUAUUUGUCGCACUUUAGUUCAAAAAUGAACUAGCGGACGACAAAUAUUCGAGAAUGGAGGUAGUAC

Targets Info

Target Acc	Alignment	Exception	Target Description	Target Gene Name	Target Type	Method
EZ082762.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:5   GUACUACCUCCGUUCUCGAAUAUU   28 Target Full Sequence	1.5	TSA: Zea mays contig18405, mRNA sequence	NA	coding protein	psRNATarget
HI409913.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:183   GUACUACCUCCGUUCUCGAAUAUU   206 Target Full Sequence	1.5	Sequence 8038 from Patent EP2074227	NA	coding protein	psRNATarget
LQ242043.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:183   GUACUACCUCCGUUCUCGAAUAUU   206 Target Full Sequence	1.5	Sequence 8038 from Patent EP2985353	NA	coding protein	psRNATarget
HI410075.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:183   GUACUACCUCCGUUCUCGAAUAUU   206 Target Full Sequence	1.5	Sequence 8200 from Patent EP2074227	NA	coding protein	psRNATarget
JB170374.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:183   GUACUACCUCCGUUCUCGAAUAUU   206 Target Full Sequence	1.5	Sequence 8038 from Patent EP2559767	NA	coding protein	psRNATarget
LQ242205.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:183   GUACUACCUCCGUUCUCGAAUAUU   206 Target Full Sequence	1.5	Sequence 8200 from Patent EP2985353	NA	coding protein	psRNATarget
JB170536.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:183   GUACUACCUCCGUUCUCGAAUAUU   206 Target Full Sequence	1.5	Sequence 8200 from Patent EP2559767	NA	coding protein	psRNATarget
EZ110367.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:420   GUACUACCUCCGUUCUCGAAUAUU   443 Target Full Sequence	1.5	TSA: Zea mays contig46027, mRNA sequence	NA	coding protein	psRNATarget
EU945472.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:428   GUACUACCUCCGUUCUCGAAUAUU   451 Target Full Sequence	1.5	Zea mays clone 274397 mRNA sequence	NA	coding protein	psRNATarget
XM_020537813.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:864   GUACUACCUCCGUUCUCGAAUAUU   887 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC103625705 (LOC103625705), transcript variant X4, mRNA	NA	coding protein	psRNATarget
XM_020537812.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:918   GUACUACCUCCGUUCUCGAAUAUU   941 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC103625705 (LOC103625705), transcript variant X3, mRNA	NA	coding protein	psRNATarget
XM_020537811.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:970   GUACUACCUCCGUUCUCGAAUAUU   993 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC103625705 (LOC103625705), transcript variant X2, mRNA	NA	coding protein	psRNATarget
EU962019.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:1018   GUACUACCUCCGUUCUCGAAUAUU   1041 Target Full Sequence	1.5	Zea mays clone 239644 mRNA sequence	NA	coding protein	psRNATarget
XM_020537810.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:1023   GUACUACCUCCGUUCUCGAAUAUU   1046 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC103625705 (LOC103625705), transcript variant X1, mRNA	NA	coding protein	psRNATarget
BT017193.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:951   GUACUACCUCCGUUCUCGAAUAUU   974 Target Full Sequence	1.5	Zea mays clone EL01N0371C09.c mRNA sequence	NA	coding protein	psRNATarget
EU965353.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:1019   GUACUACCUCCGUUCUCGAAUAUU   1042 Target Full Sequence	1.5	Zea mays clone 285514 CAPIP1 mRNA, complete cds	NA	coding protein	psRNATarget
BT040068.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:914   GUACUACCUCCGUUCUCGAAUAUU   937 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFc0063E17 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001147497.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:914   GUACUACCUCCGUUCUCGAAUAUU   937 Target Full Sequence	1.5	Zea mays CAPIP1 (LOC100273048), mRNA	NA	coding protein	psRNATarget
EU960779.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:1305   GUACUACCUCCGUUCUCGAAUAUU   1328 Target Full Sequence	1.5	Zea mays clone 228509 mRNA sequence	NA	coding protein	psRNATarget
XM_008658418.2	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||||=|||||||||||| targets:4921   GUACUACCUCCGUUCUCGAAUAUU   4944 Target Full Sequence	1.5	PREDICTED: Zea mays ABC transporter G family member 36 (LOC103636060), mRNA	NA	coding protein	psRNATarget
XM_020544837.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   ||||||||||||||||=||||||| targets:3669   GUACUACCUCCAUUCUUGAAUAUU   3692 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC103630305 (LOC103630305), mRNA	NA	coding protein	psRNATarget
BT083888.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||=|=|||||||||||| targets:1103   GUACUACCUUCGUUCUCGAAUAUU   1126 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0051D08 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001177150.2	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||=|=|||||||||||| targets:1254   GUACUACCUUCGUUCUCGAAUAUU   1277 Target Full Sequence	2.5	Zea mays hypothetical protein (umc1687), mRNA	NA	coding protein	psRNATarget
BT042757.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||=|=|||||||||||| targets:1271   GUACUACCUUCGUUCUCGAAUAUU   1294 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFc0037D18 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001148677.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||||=|=|||||||||||| targets:1271   GUACUACCUUCGUUCUCGAAUAUU   1294 Target Full Sequence	2.5	Zea mays hypothetical protein (umc1687), mRNA	NA	coding protein	psRNATarget
XM_008676081.2	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||=|||||||=|||||||||||| targets:2487   GUAUUACCUCCGUUCUCGAAUAUU   2510 Target Full Sequence	1.5	PREDICTED: Zea mays WPP domain-associated protein (LOC103650495), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008676082.2	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||=|||||||=|||||||||||| targets:2491   GUAUUACCUCCGUUCUCGAAUAUU   2514 Target Full Sequence	1.5	PREDICTED: Zea mays WPP domain-associated protein (LOC103650495), transcript variant X2, mRNA	NA	coding protein	psRNATarget
AY109416.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||=||=||||||||||||||||| targets:2445   GUAUUAUCUCCAUUCUCGAAUAUU   2468 Target Full Sequence	1.0	Zea mays CL694_1 mRNA sequence	NA	coding protein	psRNATarget
EZ104892.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||||||||=|||||||||||||| targets:47   CUACUACCUUCAUUCUCGAAUAUU   70 Target Full Sequence	1.0	TSA: Zea mays contig40549, mRNA sequence	NA	coding protein	psRNATarget
EU975574.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||||||||||=|||||||||||| targets:29   CUACUACCUCCGUUCUCGAAUAUU   52 Target Full Sequence	1.5	Zea mays clone 492870 hypothetical protein mRNA, complete cds	NA	coding protein	psRNATarget
XM_020545142.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||||||||||=|||||||||||| targets:381   AUACUACCUCCGUUCUCGAAUAUU   404 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC100382526 (LOC100382526), transcript variant X3, mRNA	NA	coding protein	psRNATarget
EZ091721.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   ||||||*||||||||||||||||| targets:54   GUACUAACUCCAUUCUCGAAUAUU   77 Target Full Sequence	1.0	TSA: Zea mays contig27370, mRNA sequence	NA	coding protein	psRNATarget
EZ053711.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||||||||=|=|||||||||||| targets:98   AUACUACCUUCGUUCUCGAAUAUU   121 Target Full Sequence	2.5	TSA: Zea mays contig54833, mRNA sequence	NA	coding protein	psRNATarget
EU950207.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *|||||=||||=|||||||||||| targets:31   CUACUAUCUCCGUUCUCGAAUAUU   54 Target Full Sequence	2.5	Zea mays clone 469419 mRNA sequence	NA	coding protein	psRNATarget
EU950983.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *|||||=|||=||||||||||||| targets:882   AUACUAUCUCUAUUCUCGAAUAUU   905 Target Full Sequence	2.0	Zea mays clone 677241 mRNA sequence	NA	coding protein	psRNATarget
BT061281.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||||=|||||=|||||||||||| targets:1370   AUACUGCCUCCGUUCUCGAAUAUU   1393 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0131A16 mRNA, complete cds	NA	coding protein	psRNATarget
XM_008658563.2	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *|||||=|||=||||||||||||| targets:2344   AUACUAUCUCUAUUCUCGAAUAUU   2367 Target Full Sequence	2.0	PREDICTED: Zea mays phosphatidylinositol/phosphatidylcholine transfer protein SFH6 (LOC103636210), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_008658562.2	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *|||||=|||=||||||||||||| targets:2386   AUACUAUCUCUAUUCUCGAAUAUU   2409 Target Full Sequence	2.0	PREDICTED: Zea mays phosphatidylinositol/phosphatidylcholine transfer protein SFH6 (LOC103636210), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008665300.2	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||||||||=|=|||||||||||| targets:2068   AUACUACCUUCGUUCUCGAAUAUU   2091 Target Full Sequence	2.5	PREDICTED: Zea mays trichohyalin-like (LOC103641991), transcript variant X3, mRNA	NA	coding protein	psRNATarget
XM_008665299.2	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||||||||=|=|||||||||||| targets:2080   AUACUACCUUCGUUCUCGAAUAUU   2103 Target Full Sequence	2.5	PREDICTED: Zea mays trichohyalin-like (LOC103641991), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008665301.2	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||||||||=|=|||||||||||| targets:2133   AUACUACCUUCGUUCUCGAAUAUU   2156 Target Full Sequence	2.5	PREDICTED: Zea mays trichohyalin-like (LOC103641991), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_020545884.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||||||=|||=|||||||||||| targets:3507   AUACUACUUCCGUUCUCGAAUAUU   3530 Target Full Sequence	2.5	PREDICTED: Zea mays E3 ubiquitin-protein ligase PUB23 (LOC103642284), mRNA	NA	coding protein	psRNATarget
EZ077311.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   ||||||||*||=|||||||||||| targets:110   GUACUACCCCCGUUCUCGAAUAUU   133 Target Full Sequence	2.5	TSA: Zea mays contig12948, mRNA sequence	NA	coding protein	psRNATarget
EU950930.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   ||||*||||||=|||||||||||| targets:340   GUACAACCUCCGUUCUCGAAUAUU   363 Target Full Sequence	1.5	Zea mays clone 660705 mRNA sequence	NA	coding protein	psRNATarget
EU965082.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||-|||||||||||||||||||| targets:1471   GUA-UACCUCCAUUCUCGAAUAUU   1493 Target Full Sequence	0.0	Zea mays clone 283672 mRNA sequence	NA	coding protein	psRNATarget
BT042256.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||||||*|||=|||||||||||| targets:844   GUACUACAUCCGUUCUCGAAUAUU   867 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0181G14 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001175535.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   ||||*||||||=|||||||||||| targets:1539   GUACAACCUCCGUUCUCGAAUAUU   1562 Target Full Sequence	1.5	Zea mays uncharacterized LOC100382838 (LOC100382838), mRNA	NA	coding protein	psRNATarget
BT065511.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   ||||*||||||=|||||||||||| targets:1539   GUACAACCUCCGUUCUCGAAUAUU   1562 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFb0202I04 mRNA, complete cds	NA	coding protein	psRNATarget
XM_020540634.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   ||||*||||||=|||||||||||| targets:1642   GUACAACCUCCGUUCUCGAAUAUU   1665 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC100382838 (LOC100382838), transcript variant X1, mRNA	NA	coding protein	psRNATarget
EU956971.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   |||-|||||||||||||||||||| targets:2273   GUA-UACCUCCAUUCUCGAAUAUU   2295 Target Full Sequence	0.0	Zea mays clone 1579127 mRNA sequence	NA	coding protein	psRNATarget
EU957483.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||||||||||||||||*|||||| targets:1944   UUACUACCUCCAUUCUCAAAUAUU   1967 Target Full Sequence	1.5	Zea mays clone 1594285 hypothetical protein mRNA, complete cds	NA	coding protein	psRNATarget
XM_008676285.2	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   ||*|||||||=|||=||||||||| targets:1009   GUUCUACCUCUAUUUUCGAAUAUU   1032 Target Full Sequence	2.5	PREDICTED: Zea mays transcription factor bHLH100-like (LOC103650720), transcript variant X1, mRNA	NA	coding protein	psRNATarget
EZ091447.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||*|||||||=|||||||||||| targets:62   AUAAUACCUCCGUUCUCGAAUAUU   85 Target Full Sequence	1.5	TSA: Zea mays contig27095, mRNA sequence	NA	coding protein	psRNATarget
NM_001151933.2	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||||||*|||=|||||||||||| targets:92   AUACUACAUCCGUUCUCGAAUAUU   115 Target Full Sequence	2.5	Zea mays uncharacterized LOC100278762 (LOC100278762), mRNA	NA	coding protein	psRNATarget
XM_008658000.2	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *|||||=*|||||||||||||||| targets:1017   AUACUAUAUCCAUUCUCGAAUAUU   1040 Target Full Sequence	2.0	PREDICTED: Zea mays uncharacterized LOC103635584 (LOC103635584), transcript variant X1, mRNA	NA	coding protein	psRNATarget
EU975204.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||||||*|||=|||||||||||| targets:92   AUACUACAUCCGUUCUCGAAUAUU   115 Target Full Sequence	2.5	Zea mays clone 484326 hypothetical protein mRNA, complete cds	NA	coding protein	psRNATarget
EZ059364.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *|||*|=||||||||||||||||| targets:134   AUACCAUCUCCAUUCUCGAAUAUU   157 Target Full Sequence	1.0	TSA: Zea mays contig60486, mRNA sequence	NA	coding protein	psRNATarget
XM_020546478.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *|||||||*||=|||||||||||| targets:2917   AUACUACCCCCGUUCUCGAAUAUU   2940 Target Full Sequence	2.5	PREDICTED: Zea mays uncharacterized LOC100194233 (LOC100194233), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_020546479.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *|||||||*||=|||||||||||| targets:2917   AUACUACCCCCGUUCUCGAAUAUU   2940 Target Full Sequence	2.5	PREDICTED: Zea mays uncharacterized LOC100194233 (LOC100194233), transcript variant X2, mRNA	NA	coding protein	psRNATarget
EU966414.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||=|||=|||*|||||||||||| targets:796   AUAUUACUUCCCUUCUCGAAUAUU   819 Target Full Sequence	2.5	Zea mays clone 294304 SWIb domain-containing protein mRNA, complete cds	NA	coding protein	psRNATarget
NM_001156819.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *||=|||=|||*|||||||||||| targets:796   AUAUUACUUCCCUUCUCGAAUAUU   819 Target Full Sequence	2.5	Zea mays SWIB/MDM2 domain superfamily protein (pco097858), mRNA	NA	coding protein	psRNATarget
AY105827.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *|=||||||=*||||||||||||| targets:852   UUGCUACCUUAAUUCUCGAAUAUU   875 Target Full Sequence	2.0	Zea mays PCO152724 mRNA sequence	NA	coding protein	psRNATarget
EU974031.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *|=||||||=*||||||||||||| targets:1409   UUGCUACCUUAAUUCUCGAAUAUU   1432 Target Full Sequence	2.0	Zea mays clone 438033 sel1-like repeat mRNA, complete cds	NA	coding protein	psRNATarget
XM_020545189.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *|=||||||=*||||||||||||| targets:2017   UUGCUACCUUAAUUCUCGAAUAUU   2040 Target Full Sequence	2.0	PREDICTED: Zea mays uncharacterized LOC100383612 (pco152724), transcript variant X8, mRNA	NA	coding protein	psRNATarget
EZ113291.1	ncRNA:24   CAUGAUGGAGGUAAGAGCUUAUAA   1   *|||*||||||*|||||||||||| targets:81   AUACAACCUCCCUUCUCGAAUAUU   104 Target Full Sequence	1.5	TSA: Zea mays contig48952, mRNA sequence	NA	coding protein	psRNATarget