PmiREN: Plant microRNA Encyclopedia

Bra-MIR169u

Basic info.

miRNA locus ID
Bra-MIR169u

miRNA locus accession
PmiREN002467

Organism
Brassica rapa

Genomic location
Bra-A08 1019521 1019639 -

Comments
A member of family MIR169

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  G     AT      T  TAAT         A          ATT      AAGAATTTA
   GGAAA  AGAGAA GA    GAGCCAAAG TGACTTGCCG   TTACCA         
   |||||  |||||| ||    ||||||||| ||||||||||   ||||||         A
   CTTTT  TCTCTT CT    CTCGGTTTC GCTGAACGGT   AGTGGT         
TAG     CT      C  TTGT         A          --C      AATAGTCAA

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-199	Aly-MIR169d	Aly-scaffold_1: 28725960-28726078 -	Brassica rapa	Bra-MIR169u	Bra-A08: 1019521-1019639 -
SY-829	Bol-MIR169c	Bol-C06: 21189916-21190035 -	Brassica rapa	Bra-MIR169u	Bra-A08: 1019521-1019639 -
SY-1039	Bra-MIR169u	Bra-A08: 1019521-1019639 -	Capsella rubella	Cru-MIR169a	Cru-scaffold_1: 18887754-18887872 +

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