PmiREN: Plant microRNA Encyclopedia

Bra-MIR160e

Basic info.

miRNA locus ID
Bra-MIR160e

miRNA locus accession
PmiREN002414

Organism
Brassica rapa

Genomic location
Bra-A09 14418668 14418789 -

Comments
A member of family MIR160

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

GATG      CA   -----   --AT   C       C          G     GTA        GT
    TGTCAT  TGC     CTG    TGC TGGCTCC TGTATGCCAC AGTGG   TCGATTTT  
    ||||||  |||     |||    ||| ||||||| |||||||||| |||||   ||||||||  T
    ATAGTA  ACG     GAC    ACG ACCGAGG GCATGCGGTG TCGTC   GGTTAAAA  
          -A   AAGAA   CAGT   A       A          G     ---        AG

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-77	Aly-MIR160c	Aly-scaffold_8: 677270-677391 +	Brassica rapa	Bra-MIR160e	Bra-A09: 14418668-14418789 -
SY-460	Ath-MIR160c	Ath-Chr5: 19009076-19009198 -	Brassica rapa	Bra-MIR160e	Bra-A09: 14418668-14418789 -
SY-936	Bra-MIR160e	Bra-A09: 14418668-14418789 -	Capsella rubella	Cru-MIR160c	Cru-scaffold_8: 399218-399340 +
SY-937	Bra-MIR160e	Bra-A09: 14418668-14418789 -	Eutrema salsugineum	Esa-MIR160c	Esa-scaffold_20: 2068305-2068426 -

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.G02126.1	0.5	NA	NA
Brara.G03536.1	0.5	NA	NA
Brara.G01369.1	1.0	NA	NA
Brara.A00733.1	1.5	NA	NA
Brara.K00855.1	1.5	NA	NA

Mature miRNA conservation

Link

No link
No link

Reference

>Systematic identification of long non-coding RNAs during pollen development and fertilization in Brassica rapa. Plant J, 2018