PmiREN: Plant microRNA Encyclopedia

Bra-MIR169q

Basic info.

miRNA locus ID
Bra-MIR169q

miRNA locus accession
PmiREN002463

Organism
Brassica rapa

Genomic location
Bra-A06 679097 679215 -

Comments
A member of family MIR169

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  G     AT      T  T  T         A          ATTTTA    ---   ACCT
   GAAAA  AGAGAA GA AT GAGCCAAAG TGACTTGCCG      CCAA   CAA    
   |||||  |||||| || || ||||||||| ||||||||||      ||||   |||     
   CTTTT  TCTCTT CT TG CTCGGTTTT GCTGAACGGC      GGTT   GTT    
TAG     CT      C  T  T         A          --CATC    ATA   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: 3271
Chromosome: Bra-A06
Cluster start: 678807
Cluster end: 679215

miRNA locus ID	miRNA locus accession	Chromosome	Strand	Start	End
Bra-MIR169q , Bra-MIR169r	PmiREN002463, PmiREN002464	Bra-A06	-	678807	679215

miRNA syntenic block

Syntenic block ID	miRNA locus 1	miRNA locus 1 position	Organism	miRNA locus 2	miRNA locus 2 position
SY-198	Aly-MIR169d	Aly-scaffold_1: 28725960-28726078 -	Brassica rapa	Bra-MIR169q	Bra-A06: 679097-679215 -
SY-826	Bol-MIR169b	Bol-C03: 56791745-56791864 +	Brassica rapa	Bra-MIR169q	Bra-A06: 679097-679215 -
SY-1035	Bra-MIR169q	Bra-A06: 679097-679215 -	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