PmiREN: Plant microRNA Encyclopedia

Bra-MIR169p

Basic info.

miRNA locus ID
Bra-MIR169p

miRNA locus accession
PmiREN002462

Organism
Brassica rapa

Genomic location
Bra-A09 1477043 1477232 -

Comments
A member of family MIR169

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  -C        T      -T            T    T     CTCTT   C    C  -T        TTTAAGTTG        -      A     ATTG
 G  GAAAAGAG CATGTT  AGTAGCCAAGGA GACT GCCTG     TTT ACCT CA  GATTCAAT         ATGGTTTT GGATTA TATGC    
 |  |||||||| ||||||  |||||||||||| |||| |||||     ||| |||| ||  ||||||||         |||||||| |||||| |||||    A
 C  CTTTTTTC GTACAG  TTATCGGTTCCT CTGA CGGAC     AGA TGGG GT  CTAAGTTA         TACTAAAA CTTAAT ATATG    
C TA        -      TT            -    -     --TTT   T    T  TT        ---------        A      A     AAGT

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: 3275
Chromosome: Bra-A09
Cluster start: 1475368
Cluster end: 1477232

miRNA locus ID	miRNA locus accession	Chromosome	Strand	Start	End
Bra-MIR169g , Bra-MIR169p , Bra-MIR5716	PmiREN002453, PmiREN002462, PmiREN002555	Bra-A09	-	1475368	1477232

miRNA syntenic block

Syntenic block ID	miRNA locus 1	miRNA locus 1 position	Organism	miRNA locus 2	miRNA locus 2 position
SY-578	Ath-MIR169j	Ath-Chr3: 9872336-9872523 -	Brassica rapa	Bra-MIR169p	Bra-A09: 1477043-1477232 -
SY-1013	Bra-MIR169e	Bra-A02: 27317508-27317695 -	Brassica rapa	Bra-MIR169p	Bra-A09: 1477043-1477232 -
SY-1028	Bra-MIR169m	Bra-A06: 25527117-25527308 +	Brassica rapa	Bra-MIR169p	Bra-A09: 1477043-1477232 -
SY-1033	Bra-MIR169p	Bra-A09: 1477043-1477232 -	Capsella rubella	Cru-MIR169e	Cru-scaffold_5: 1969964-1970154 -
SY-1034	Bra-MIR169p	Bra-A09: 1477043-1477232 -	Eutrema salsugineum	Esa-MIR169d	Esa-scaffold_6: 6265076-6265266 +

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	1.0	1	NA
Brara.B02046.1	1.0	NA	NA
Brara.E01518.1	1.0	1	NA
Brara.F00066.1	1.0	NA	NA
Brara.G03156.1	1.0	1	NA
Brara.H00096.1	1.0	1	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