PmiREN: Plant microRNA Encyclopedia

Bra-MIR169s

Basic info.

miRNA locus ID
Bra-MIR169s

miRNA locus accession
PmiREN002465

Organism
Brassica rapa

Genomic location
Bra-A08 12392918 12393036 +

Comments
A member of family MIR169

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  G     AT      T    TT         AT          TTTTTT   AC     TAT
   GAAGA  AGAGAA GAAG  GAGCCAAGG  GACTTGCCGA      CCA  GAATC   
   |||||  |||||| ||||  |||||||||  ||||||||||      |||  |||||    
   CTTTT  TCTCTT CTTT  CTCGGTTTC  TTGAACGGTT      GGT  TTTAG   
TAG     CT      C    GT         AG          ---TGT   --     TCA

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:
Chromosome:
Cluster start:
Cluster end:

No miRNA locus in ± 10k bp interval.

miRNA syntenic block

Syntenic block ID	miRNA locus 1	miRNA locus 1 position	Organism	miRNA locus 2	miRNA locus 2 position
SY-207	Aly-MIR169g	Aly-scaffold_7: 9193033-9193153 +	Brassica rapa	Bra-MIR169s	Bra-A08: 12392918-12393036 +
SY-823	Bol-MIR169a	Bol-C03: 50192527-50192643 +	Brassica rapa	Bra-MIR169s	Bra-A08: 12392918-12393036 +
SY-1038	Bra-MIR169s	Bra-A08: 12392918-12393036 +	Capsella rubella	Cru-MIR169c	Cru-scaffold_7: 7418995-7419123 +

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	1.5	2	NA
Brara.C03118.1	1.5	NA	NA
Brara.J02572.1	1.5	2	NA

Mature miRNA conservation

Link

No link
No link

Reference

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