PmiREN: Plant microRNA Encyclopedia

Bra-MIR169w

Basic info.

miRNA locus ID
Bra-MIR169w

miRNA locus accession
PmiREN002469

Organism
Brassica rapa

Genomic location
Bra-A08 1016926 1017048 -

Comments
A member of family MIR169

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  G     AT         T  T         A          ATTTTACTGAT G   CTAA
   GAAAA  AGAGAATGA AT GAGCCAAAG TGACTTGCCG           T AGT    
   |||||  ||||||||| || ||||||||| ||||||||||           | |||     
   CTTTT  TTTCTTACT TG CTCGGTTTT GTTGAACGGC           A TCA    
TAG     CT         T  T         A          -CGTTAGTTAT G   AAAA

Get mature sequence
Get star sequence
Get miRNA stem-loop seqence
Get miRNA stem-loop ± 20bp
Get dot-bracket miRNA secondary structure
Get miRNA stem-loop ± 500bp
Get miRNA Promoter

miRNA cluster info.

Cluster ID: 3274
Chromosome: Bra-A08
Cluster start: 1016926
Cluster end: 1019639

miRNA locus ID	miRNA locus accession	Chromosome	Strand	Start	End
Bra-MIR169u , Bra-MIR169v , Bra-MIR169w	PmiREN002467, PmiREN002468, PmiREN002469	Bra-A08	-	1016926	1019639

miRNA syntenic block

Syntenic block ID	miRNA locus 1	miRNA locus 1 position	Organism	miRNA locus 2	miRNA locus 2 position
SY-827	Bol-MIR169b	Bol-C03: 56791745-56791864 +	Brassica rapa	Bra-MIR169w	Bra-A08: 1016926-1017048 -
SY-831	Bol-MIR169e	Bol-C06: 21156226-21156337 -	Brassica rapa	Bra-MIR169w	Bra-A08: 1016926-1017048 -
SY-1036	Bra-MIR169r	Bra-A06: 678807-678928 -	Brassica rapa	Bra-MIR169w	Bra-A08: 1016926-1017048 -

Expression info.

Mature miRNA expression [+]

Reads per million (RPM)

star miRNA expression [+]

Reads per million (RPM)

Target gene info.[+]

Target gene ID	psRNAtarget	RNAhybrid	PARE-Seq? The first number (from 0-2) indicates the category of CleaveLand4 analysis result while the number in brackets displays the number of degradome libraries which verify the miRNA-target interaction. Click the number to download the selected figure of PARE-Seq reads distribution.
Brara.A03708.1	1.0	1	NA
Brara.C03118.1	1.0	NA	NA
Brara.J02572.1	1.0	1	NA

Mature miRNA conservation

Link

No link
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Reference

>Microsynteny and phylogenetic analysis of tandemly organised miRNA families across five members of Brassicaceae reveals complex retention and loss history. Plant Sci, 2016