PmiREN: Plant microRNA Encyclopedia

Bra-MIR169i

Basic info.

miRNA locus ID
Bra-MIR169i

miRNA locus accession
PmiREN002455

Organism
Brassica rapa

Genomic location
Bra-A02 27317149 27317322 -

Comments
A member of family MIR169

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  GAAT       T     TT  -          T    T     -TT  --    AG                GTGTCATGTTTAAAAGTT
      AGAAGAA CATAT  GG TAGCCAAGGA GACT GCCTA   TC  TTTG  AAGTAAAATGGGCATG                  
      ||||||| |||||  || |||||||||| |||| |||||   ||  ||||  ||||||||||||||||                   
      TCTTCTT GTATA  CC ATCGGTTCCT CTGA CGGAT   AG  AAAC  TTCGTTTTACCAGTTT                  
ACTCTC       -     TT  T          -    -     TAT  TA    -A                TAACTTTGATGGATGTCA

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: 3269
Chromosome: Bra-A02
Cluster start: 27317149
Cluster end: 27317695

miRNA locus ID	miRNA locus accession	Chromosome	Strand	Start	End
Bra-MIR169e , Bra-MIR169i	PmiREN002451, PmiREN002455	Bra-A02	-	27317149	27317695

miRNA syntenic block

Syntenic block ID	miRNA locus 1	miRNA locus 1 position	Organism	miRNA locus 2	miRNA locus 2 position
SY-216	Aly-MIR169i	Aly-scaffold_5: 3130593-3130764 -	Brassica rapa	Bra-MIR169i	Bra-A02: 27317149-27317322 -
SY-574	Ath-MIR169i	Ath-Chr3: 9871979-9872146 -	Brassica rapa	Bra-MIR169i	Bra-A02: 27317149-27317322 -
SY-1020	Bra-MIR169i	Bra-A02: 27317149-27317322 -	Brassica rapa	Bra-MIR169g	Bra-A09: 1476069-1476241 -
SY-1021	Bra-MIR169i	Bra-A02: 27317149-27317322 -	Brassica rapa	Bra-MIR169k	Bra-A06: 25527480-25527663 +

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.B02046.1	1.0	NA	NA
Brara.G03156.1	1.0	0	NA
Brara.A03216.1	1.5	1	NA
Brara.E01518.1	1.5	1	NA
Brara.F00066.1	1.5	NA	NA
Brara.H00096.1	1.5	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