PmiREN: Plant microRNA Encyclopedia

Bra-MIR169l

Basic info.

miRNA locus ID
Bra-MIR169l

miRNA locus accession
PmiREN002458

Organism
Brassica rapa

Genomic location
Bra-A05 24007347 24007484 +

Comments
A member of family MIR169

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

 TAA     -     T      C                      ---------------        CT     GT
    GTGAC CAAAG AGTGTG AGCCAAGGATGACTTGCCGATT               TAAAATAT  GATAA  
    ||||| ||||| |||||| ||||||||||||||||||||||               ||||||||  |||||  A
    CGCTG GTTTC TTGCAT TCGGTTCCTGTTGAACGGCTAG               ATTTTATG  TTGTT  
TACG     T     T      A                      TACTAAAAAAAAGAA        CT     TT

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-191	Aly-MIR169a	Aly-scaffold_3: 5439439-5439688 -	Brassica rapa	Bra-MIR169l	Bra-A05: 24007347-24007484 +
SY-556	Ath-MIR169a	Ath-Chr3: 4358990-4359222 -	Brassica rapa	Bra-MIR169l	Bra-A05: 24007347-24007484 +
SY-1017	Bra-MIR169h	Bra-A01: 27239224-27239432 +	Brassica rapa	Bra-MIR169l	Bra-A05: 24007347-24007484 +
SY-1022	Bra-MIR169j	Bra-A03: 17544406-17544602 -	Brassica rapa	Bra-MIR169l	Bra-A05: 24007347-24007484 +
SY-1026	Bra-MIR169l	Bra-A05: 24007347-24007484 +	Capsella rubella	Cru-MIR169d	Cru-scaffold_3: 4431202-4431418 -
SY-1027	Bra-MIR169l	Bra-A05: 24007347-24007484 +	Eutrema salsugineum	Esa-MIR169a	Esa-scaffold_13: 5033375-5033601 +

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.A03216.1	2.0	1	NA
Brara.B02046.1	2.0	NA	NA
Brara.E01518.1	2.0	2	NA
Brara.F00066.1	2.0	NA	NA
Brara.G03156.1	2.0	2	NA
Brara.H00096.1	2.0	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