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BaseInfo

ncRNA ID	novel_zma_miR4039
Species	Zea mays
Class	miRNA
Genome position	Chr4:205230498-205230553 [+]
Reference genome	RefGen_v4
Source	SRR2287159;SRR2287164;SRR5451006
Length	24
Mature sequence(if miRNA)	33 - ACUAGCGGACGACAAAUAUUCAAG - 56
Stem-loop(if miRNA)	--UUUU        -      C      A       UAUUUGUC UUCGUU AGUUCA A       |||||||| |||||| ||||||       AUAAACAG AGGCGA UCAAGU A GAACUU        C      -      A
Stem-loop sequence	UUUUUAUUUGUCUUCGUUCAGUUCAAAAAUGAACUAGCGGACGACAAAUAUUCAAG

Targets Info

Target Acc	Alignment	Exception	Target Description	Target Gene Name	Target Type	Method
EZ053859.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   =||||||||||||||||||||||| targets:66   UUUGAAUAUUUGUCGUCCGCUAGU   89 Target Full Sequence	0.0	TSA: Zea mays contig54981, mRNA sequence	NA	coding protein	psRNATarget
XM_008669376.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   *||||||||||||||||=|||||| targets:1133   AUUGAAUAUUUGUCGUCUGCUAGU   1156 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC100274235 (LOC100274235), transcript variant X1, mRNA	NA	coding protein	psRNATarget
BT042586.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   *||||||||||||||||=|||||| targets:1175   AUUGAAUAUUUGUCGUCUGCUAGU   1198 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFb0347D09 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001148605.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   *||||||||||||||||=|||||| targets:1175   AUUGAAUAUUUGUCGUCUGCUAGU   1198 Target Full Sequence	1.5	Zea mays uncharacterized LOC100274235 (LOC100274235), mRNA	NA	coding protein	psRNATarget
XM_008669377.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   *||||||||||||||||=|||||| targets:1236   AUUGAAUAUUUGUCGUCUGCUAGU   1259 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC100274235 (LOC100274235), transcript variant X2, mRNA	NA	coding protein	psRNATarget
EU957049.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   *||||||||||||||||=|||||| targets:2170   AUUGAAUAUUUGUCGUCUGCUAGU   2193 Target Full Sequence	1.5	Zea mays clone 1581267 mRNA sequence	NA	coding protein	psRNATarget
EZ071175.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   |||||||||||||||*|||||||| targets:106   CUUGAAUAUUUGUCGCCCGCUAGU   129 Target Full Sequence	1.5	TSA: Zea mays contig06812, mRNA sequence	NA	coding protein	psRNATarget
BT038580.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||||||||| targets:1344   CUCGAAUAUUUGUCGUCCGCUAGU   1367 Target Full Sequence	0.0	Zea mays full-length cDNA clone ZM_BFb0295B07 mRNA, complete cds	NA	coding protein	psRNATarget
EU965454.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||||||||| targets:1370   CUCGAAUAUUUGUCGUCCGCUAGU   1393 Target Full Sequence	0.0	Zea mays clone 286145 nucleic acid binding protein mRNA, complete cds	NA	coding protein	psRNATarget
NM_001156559.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||||||||| targets:1370   CUCGAAUAUUUGUCGUCCGCUAGU   1393 Target Full Sequence	0.0	Zea mays nucleic acid binding protein (LOC100283658), mRNA	NA	coding protein	psRNATarget
EU940941.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||||||||| targets:1740   CUCGAAUAUUUGUCGUCCGCUAGU   1763 Target Full Sequence	0.0	Zea mays clone 1218400 mRNA sequence	NA	coding protein	psRNATarget
EU954561.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||||||||| targets:2167   CUCGAAUAUUUGUCGUCCGCUAGU   2190 Target Full Sequence	0.0	Zea mays clone 1470172 regulatory subunit mRNA, complete cds	NA	coding protein	psRNATarget
NM_001153830.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||||||||| targets:2167   CUCGAAUAUUUGUCGUCCGCUAGU   2190 Target Full Sequence	0.0	Zea mays regulatory subunit (LOC100280910), mRNA	NA	coding protein	psRNATarget
XM_008645362.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||||||||| targets:2238   CUCGAAUAUUUGUCGUCCGCUAGU   2261 Target Full Sequence	0.0	PREDICTED: Zea mays regulatory subunit (LOC100280910), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_008645361.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||||||||| targets:2256   CUCGAAUAUUUGUCGUCCGCUAGU   2279 Target Full Sequence	0.0	PREDICTED: Zea mays regulatory subunit (LOC100280910), transcript variant X1, mRNA	NA	coding protein	psRNATarget
EU949554.1	ncRNA:24   GAA-CUUAUAAACAGCAGGCGAUCA   1   =||-||||||||||||||||||||| targets:410   UUUCGAAUAUUUGUCGUCCGCUAGU   434 Target Full Sequence	0.0	Zea mays clone 424261 mRNA sequence	NA	coding protein	psRNATarget
EZ113277.1	ncRNA:24   GAA-CUUAUAAACAGCAGGCGAUCA   1   =||-||||||||||||||||||||| targets:590   UUUCGAAUAUUUGUCGUCCGCUAGU   614 Target Full Sequence	0.0	TSA: Zea mays contig48938, mRNA sequence	NA	coding protein	psRNATarget
AY109049.2	ncRNA:24   GAA-CUUAUAAACAGCAGGCGAUCA   1   =||-||||||||||||||||||||| targets:463   UUUCGAAUAUUUGUCGUCCGCUAGU   487 Target Full Sequence	0.0	Zea mays PCO094720 mRNA sequence	NA	coding protein	psRNATarget
BT068579.1	ncRNA:24   GAA-CUUAUAAACAGCAGGCGAUCA   1   =||-||||||||||||||||||||| targets:1452   UUUCGAAUAUUUGUCGUCCGCUAGU   1476 Target Full Sequence	0.0	Zea mays full-length cDNA clone ZM_BFb0339J04 mRNA, complete cds	NA	coding protein	psRNATarget
BT034355.1	ncRNA:24   GAA-CUUAUAAACAGCAGGCGAUCA   1   =||-||||||||||||||||||||| targets:1549   UUUCGAAUAUUUGUCGUCCGCUAGU   1573 Target Full Sequence	0.0	Zea mays full-length cDNA clone ZM_BFc0007D11 mRNA, complete cds	NA	coding protein	psRNATarget
BT068416.1	ncRNA:24   GAA-CUUAUAAACAGCAGGCGAUCA   1   =||-||||||||||||||||||||| targets:1616   UUUCGAAUAUUUGUCGUCCGCUAGU   1640 Target Full Sequence	0.0	Zea mays full-length cDNA clone ZM_BFb0181F19 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001347903.1	ncRNA:24   GAA-CUUAUAAACAGCAGGCGAUCA   1   =||-||||||||||||||||||||| targets:1616   UUUCGAAUAUUUGUCGUCCGCUAGU   1640 Target Full Sequence	0.0	Zea mays Sulfoquinovosyl transferase SQD2 (pco094720a), mRNA	NA	coding protein	psRNATarget
XM_008652607.2	ncRNA:24   GAA-CUUAUAAACAGCAGGCGAUCA   1   =||-||||||||||||||||||||| targets:1660   UUUCGAAUAUUUGUCGUCCGCUAGU   1684 Target Full Sequence	0.0	PREDICTED: Zea mays Sulfoquinovosyl transferase SQD2 (pco094720a), transcript variant X1, mRNA	NA	coding protein	psRNATarget
BT061377.1	ncRNA:24   GAA-CUUAUAAACAGCAGGCGAUCA   1   =||-||||||||||||||||||||| targets:1703   UUUCGAAUAUUUGUCGUCCGCUAGU   1727 Target Full Sequence	0.0	Zea mays full-length cDNA clone ZM_BFb0140P11 mRNA, complete cds	NA	coding protein	psRNATarget
BT087620.1	ncRNA:24   GAA-CUUAUAAACAGCAGGCGAUCA   1   =||-||||||||||||||||||||| targets:1977   UUUCGAAUAUUUGUCGUCCGCUAGU   2001 Target Full Sequence	0.0	Zea mays full-length cDNA clone ZM_BFb0134K18 mRNA, complete cds	NA	coding protein	psRNATarget
EZ053711.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||||||=|| targets:112   CUCGAAUAUUUGUCGUCCGCUGGU   135 Target Full Sequence	1.5	TSA: Zea mays contig54833, mRNA sequence	NA	coding protein	psRNATarget
EZ062630.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*|=||||||||||||||||||| targets:55   CUCGGAUAUUUGUCGUCCGCUAGU   78 Target Full Sequence	0.0	TSA: Zea mays contig63752, mRNA sequence	NA	coding protein	psRNATarget
AY486125.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   |||*|||||||||||||=|||||| targets:1812   CUUAAAUAUUUGUCGUCUGCUAGU   1835 Target Full Sequence	1.5	Zea mays SNF1-related protein kinase mRNA, complete cds	NA	coding protein	psRNATarget
NM_001112203.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   |||*|||||||||||||=|||||| targets:1812   CUUAAAUAUUUGUCGUCUGCUAGU   1835 Target Full Sequence	1.5	Zea mays SNF1-related protein kinase (SnrK1), mRNA	NA	coding protein	psRNATarget
BT040546.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   |||*|||||||||||||=|||||| targets:1838   CUUAAAUAUUUGUCGUCUGCUAGU   1861 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFc0099N18 mRNA, complete cds	NA	coding protein	psRNATarget
AY107942.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   |||*|||||||||||||=|||||| targets:1845   CUUAAAUAUUUGUCGUCUGCUAGU   1868 Target Full Sequence	1.5	Zea mays PCO079657 mRNA sequence	NA	coding protein	psRNATarget
XM_008650732.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   |||*|||||||||||||=|||||| targets:1888   CUUAAAUAUUUGUCGUCUGCUAGU   1911 Target Full Sequence	1.5	PREDICTED: Zea mays SNF1-related protein kinase (SnrK1), transcript variant X1, mRNA	NA	coding protein	psRNATarget
BT060618.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   |||*|||||||||||||=|||||| targets:1838   CUUAAAUAUUUGUCGUCUGCUAGU   1861 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFb0024P20 mRNA, complete cds	NA	coding protein	psRNATarget
XM_008665300.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||||||=|| targets:2082   CUCGAAUAUUUGUCGUCCGCUGGU   2105 Target Full Sequence	1.5	PREDICTED: Zea mays trichohyalin-like (LOC103641991), transcript variant X3, mRNA	NA	coding protein	psRNATarget
XM_008665299.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||||||=|| targets:2094   CUCGAAUAUUUGUCGUCCGCUGGU   2117 Target Full Sequence	1.5	PREDICTED: Zea mays trichohyalin-like (LOC103641991), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008665301.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||||||=|| targets:2147   CUCGAAUAUUUGUCGUCCGCUGGU   2170 Target Full Sequence	1.5	PREDICTED: Zea mays trichohyalin-like (LOC103641991), transcript variant X2, mRNA	NA	coding protein	psRNATarget
XM_008669887.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||=|||||| targets:2511   CUCGAAUAUUUGUCGUCUGCUAGU   2534 Target Full Sequence	1.5	PREDICTED: Zea mays zeaxanthin epoxidase (LOC100285076), transcript variant X1, mRNA	NA	coding protein	psRNATarget
EZ049723.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||*|||||||| targets:60   CUCGAAUAUUUGUCGCCCGCUAGU   83 Target Full Sequence	1.5	TSA: Zea mays contig50841, mRNA sequence	NA	coding protein	psRNATarget
EZ051209.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||*|||||||||||| targets:3   CUCGAAUAUUUAUCGUCCGCUAGU   26 Target Full Sequence	1.5	TSA: Zea mays contig52329, mRNA sequence	NA	coding protein	psRNATarget
NM_001150789.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||--|||||||||||||||||||| targets:1060   CU--AAUAUUUGUCGUCCGCUAGU   1081 Target Full Sequence	0.0	Zea mays uncharacterized LOC100277135 (LOC100277135), mRNA	NA	coding protein	psRNATarget
EU966969.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||--|||||||||||||||||||| targets:1060   CU--AAUAUUUGUCGUCCGCUAGU   1081 Target Full Sequence	0.0	Zea mays clone 298544 hypothetical protein mRNA, complete cds	NA	coding protein	psRNATarget
BT083888.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||*|||||| targets:1117   CUCGAAUAUUUGUCGUCAGCUAGU   1140 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFb0051D08 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001177150.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||*|||||| targets:1268   CUCGAAUAUUUGUCGUCAGCUAGU   1291 Target Full Sequence	1.5	Zea mays hypothetical protein (umc1687), mRNA	NA	coding protein	psRNATarget
BT042757.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||*|||||| targets:1285   CUCGAAUAUUUGUCGUCAGCUAGU   1308 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFc0037D18 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001148677.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||||*|||||| targets:1285   CUCGAAUAUUUGUCGUCAGCUAGU   1308 Target Full Sequence	1.5	Zea mays hypothetical protein (umc1687), mRNA	NA	coding protein	psRNATarget
EU940900.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*|||||*||||||||||||||| targets:1248   CUCGAAUAAUUGUCGUCCGCUAGU   1271 Target Full Sequence	1.0	Zea mays clone 1168188 mRNA sequence	NA	coding protein	psRNATarget
BT042256.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||*|||||||| targets:858   CUCGAAUAUUUGUCGCCCGCUAGU   881 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFb0181G14 mRNA, complete cds	NA	coding protein	psRNATarget
AY104299.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||**|||||||||||||||||||| targets:1280   CUCAAAUAUUUGUCGUCCGCUAGU   1303 Target Full Sequence	0.0	Zea mays PCO075569 mRNA sequence	NA	coding protein	psRNATarget
NM_001157971.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||*|||||||| targets:2262   CUCGAAUAUUUGUCGCCCGCUAGU   2285 Target Full Sequence	1.5	Zea mays zeaxanthin epoxidase (LOC100285076), mRNA	NA	coding protein	psRNATarget
EU970775.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*||||||||||||*|||||||| targets:2262   CUCGAAUAUUUGUCGCCCGCUAGU   2285 Target Full Sequence	1.5	Zea mays clone 350572 zeaxanthin epoxidase mRNA, complete cds	NA	coding protein	psRNATarget
EZ059384.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   =||*||||||||||||||*||||| targets:13   UUUAAAUAUUUGUCGUCCACUAGU   36 Target Full Sequence	1.5	TSA: Zea mays contig60506, mRNA sequence	NA	coding protein	psRNATarget
BT038203.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*|||||*||||=|||||||||| targets:1614   CUCGAAUAGUUGUUGUCCGCUAGU   1637 Target Full Sequence	2.5	Zea mays full-length cDNA clone ZM_BFb0217A17 mRNA, complete cds	NA	coding protein	psRNATarget
NM_001165424.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*|||||*||||=|||||||||| targets:1614   CUCGAAUAGUUGUUGUCCGCUAGU   1637 Target Full Sequence	2.5	Zea mays uncharacterized LOC100303788 (LOC100303788), mRNA	NA	coding protein	psRNATarget
XM_008660527.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||*|||||*||||=|||||||||| targets:1673   CUCGAAUAGUUGUUGUCCGCUAGU   1696 Target Full Sequence	2.5	PREDICTED: Zea mays uncharacterized LOC100303788 (LOC100303788), transcript variant X1, mRNA	NA	coding protein	psRNATarget
XM_008675718.2	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   *|*|||||||||||*||||||||| targets:1139   AUCGAAUAUUUGUCAUCCGCUAGU   1162 Target Full Sequence	1.5	PREDICTED: Zea mays uncharacterized LOC103650050 (LOC103650050), mRNA	NA	coding protein	psRNATarget
EZ084539.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||**|||||||||||*|||||||| targets:30   CUCAAAUAUUUGUCGCCCGCUAGU   53 Target Full Sequence	1.5	TSA: Zea mays contig20183, mRNA sequence	NA	coding protein	psRNATarget
BT039911.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   ||**||||||||||||||||||*| targets:725   CUCAAAUAUUUGUCGUCCGCUAAU   748 Target Full Sequence	1.5	Zea mays full-length cDNA clone ZM_BFc0050M05 mRNA, complete cds	NA	coding protein	psRNATarget
EZ064379.1	ncRNA:24   GAACUUAUAAACAGCAGGCGAUCA   1   |||-||||||*|||||||*||||| targets:160   CUU-AAUAUUCGUCGUCCCCUAGU   182 Target Full Sequence	2.5	TSA: Zea mays contig00011, mRNA sequence	NA	coding protein	psRNATarget