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BaseInfo

ncRNA ID	osa-miR5540
Species	Oryza sativa
Class	miRNA
Genome position	Chr1:35552728-35553070 [-]
Reference genome	MSU7
Source	miRBase
Length	21
Mature sequence(if miRNA)	11 - UUGUGCGAGAUCGACGGUAUA - 31
Stem-loop(if miRNA)	U       U      A                  UCGCACAACC                 U GA      A      A          CAUUGAAA  A         --ACC  -  - CG    ---   AUCA --    UAUUAUUAGCUAAUAGUUAAUUAUGUACUUGAUCACUAA  UUUGCGA AAUAUA CGUCGAUCUCGCACGAUC          GUUGCGCGAAAAUGACG G  UGUGAC UUGCAG CGGUAUUGCG        GU CGAGACCGC     GU GC A  AUAA   UUA    C  UAAU                                       U  ||||||| |||||| ||||||||||||||||||          ||||||||||||||||| |  |||||| |||||| ||||||||||        || |||||||||     || || |  ||||   |||    |  ||||                                       U  AAACGCU UUAUAU GCAGCUAGAGCGUGUUAG          UAACGCGCUUUUAUUGC U  GCACUG AGCGUC GCCAUAGCGC        CA GCUCUGGCG     GA UG U  UUAC   CUC    G  CCAG                                       A -       U      G                  ----------                 C AC      C      C          ACCCGAUA  C         CGCCA  A  C --    UUU   ---- CU    AACGACUUUGUCAGACGCUGUCAUAAUUGGCCGAGGUAA
Stem-loop sequence	UUUUGCGAUAAUAUAACGUCGAUCUCGCACGAUCUCGCACAACCGUUGCGCGAAAAUGACGUGGAUGUGACAUUGCAGACGGUAUUGCGCAUUGAAAGUACGAGACCGCACCGUGCACGAUAAUUAAUCACUAAUUAUUAUUAGCUAAUAGUUAAUUAUGUACUUGAUCACUAAUUAAAUGGAGCCGGUUAAUACUGUCGCAGACUGUUUCAGCAAGACCUCGCUCUUUCAUUUCGUAAGACCGCGCGGUCUCGCACAUAGCCCACGCGAUACCGCCUGCGACGUCACGCAUCCGUUAUUUUCGCGCAAUGAUUGUGCGAGAUCGACGGUAUAUUUUCGCAAA

Targets Info

Target Acc	Alignment	Exception	Target Description	Target Gene Name	Target Type	Method
HI404123.1	ncRNA:21   AUAUGGCAGCUAGAGCGUGUU   1   ||||||||||=|||||||||| targets:9   UAUACCGUCGGUCUCGCACAA   29 Target Full Sequence	1.5	Sequence 2248 from Patent EP2074227	NA	coding protein	psRNATarget
JB164584.1	ncRNA:21   AUAUGGCAGCUAGAGCGUGUU   1   ||||||||||=|||||||||| targets:9   UAUACCGUCGGUCUCGCACAA   29 Target Full Sequence	1.5	Sequence 2248 from Patent EP2559767	NA	coding protein	psRNATarget
LQ236253.1	ncRNA:21   AUAUGGCAGCUAGAGCGUGUU   1   ||||||||||=|||||||||| targets:9   UAUACCGUCGGUCUCGCACAA   29 Target Full Sequence	1.5	Sequence 2248 from Patent EP2985353	NA	coding protein	psRNATarget
AK289044.1	ncRNA:21   AUAUGGCAGCUAGAGCGUGUU   1   ||||||||||||||||||=|| targets:3240   UAUACCGUCGAUCUCGCAUAA   3260 Target Full Sequence	1.5	Oryza sativa Japonica Group cDNA, clone: J090092F18, full insert sequence	NA	coding protein	psRNATarget
AK109766.1	ncRNA:21   AUAUGGCAGCUAGAGCGUGUU   1   ||||=|||||||||||=|||| targets:1545   UAUAUCGUCGAUCUCGUACAA   1565 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA clone:002-146-H10, full insert sequence	NA	coding protein	psRNATarget
AK241210.1	ncRNA:21   AUAUGGCAGCUAGAGCGUGUU   1   ||*|||||||=|||||||||| targets:484   UAAACCGUCGGUCUCGCACAA   504 Target Full Sequence	2.5	Oryza sativa Japonica Group cDNA, clone: J065122M08, full insert sequence	NA	coding protein	psRNATarget
XM_015777198.1	ncRNA:21   AUAUGGCAGCUAGAGCGUGUU   1   ||*|||||||=|||||||||| targets:516   UAAACCGUCGGUCUCGCACAA   536 Target Full Sequence	2.5	PREDICTED: Oryza sativa Japonica Group transmembrane emp24 domain-containing protein p24delta9 (LOC9270833), transcript variant X2, mRNA	transmembrane emp24 domain-containing protein p24delta9(LOC9270833)	coding protein	psRNATarget
JB164647.1	ncRNA:19   AUGGCAGCUAGAGCGUGUU   1   |||=||||||||||||||| targets:1   UACUGUCGAUCUCGCACAA   19 Target Full Sequence	1.0	Sequence 2311 from Patent EP2559767	NA	coding protein	psRNATarget
HI404186.1	ncRNA:19   AUGGCAGCUAGAGCGUGUU   1   |||=||||||||||||||| targets:1   UACUGUCGAUCUCGCACAA   19 Target Full Sequence	1.0	Sequence 2311 from Patent EP2074227	NA	coding protein	psRNATarget
LQ236316.1	ncRNA:19   AUGGCAGCUAGAGCGUGUU   1   |||=||||||||||||||| targets:1   UACUGUCGAUCUCGCACAA   19 Target Full Sequence	1.0	Sequence 2311 from Patent EP2985353	NA	coding protein	psRNATarget

Reference

1	PMID:21679406 "Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa"; Wei LQ, Yan LF, Wang T; Genome Biol. 12:R53(2011).