PmiREN: Plant microRNA Encyclopedia

Bra-MIR156e

Basic info.

miRNA locus ID
Bra-MIR156e

miRNA locus accession
PmiREN002386

Organism
Brassica rapa

Genomic location
Bra-A08 14748884 14749006 -

Comments
A member of family MIR156

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

     T  AACA     -------           -     -       T    AG   CT     GTG
AGAAA GC    GAGAA       AACTGACAGAA GAGAG TGAGCAC TGCA  GCA  GTTAT   
||||| ||    |||||       ||||||||||| ||||| ||||||| ||||  |||  |||||    
TCTTT CG    CTCTT       TTGACTGTCTT CTCTC ACTCGTG GTGT  CGT  CAATA   
     -  ----     CAGTCCG           T     C       C    -G   TT     ACT

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-12	Aly-MIR156b	Aly-scaffold_7: 4534112-4534233 -	Brassica rapa	Bra-MIR156e	Bra-A08: 14748884-14749006 -
SY-397	Ath-MIR156b	Ath-Chr4: 15074925-15075046 +	Brassica rapa	Bra-MIR156e	Bra-A08: 14748884-14749006 -
SY-715	Bol-MIR156	Bol-C03: 54389745-54389867 -	Brassica rapa	Bra-MIR156e	Bra-A08: 14748884-14749006 -
SY-883	Bra-MIR156e	Bra-A08: 14748884-14749006 -	Brassica rapa	Bra-MIR156t	Bra-Scaffold19799: 61328-61449 -
SY-884	Bra-MIR156e	Bra-A08: 14748884-14749006 -	Eutrema salsugineum	Esa-MIR156e	Esa-scaffold_1: 3805364-3805485 -
SY-896	Bra-MIR156k	Bra-A01: 3266796-3266917 -	Brassica rapa	Bra-MIR156e	Bra-A08: 14748884-14749006 -

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.B01839.1	1.0	1	NA
Brara.C01719.1	1.0	1	NA
Brara.D00262.1	1.0	1	NA
Brara.D02060.1	1.0	1	NA
Brara.D02564.1	1.0	1	NA
Brara.E00270.1	1.0	1	NA
Brara.E01026.1	1.0	1	NA
Brara.F03810.1	1.0	NA	NA
Brara.G00852.1	1.0	1	NA
Brara.G00853.1	1.0	1	NA
Brara.G01764.1	1.0	1	NA
Brara.G02852.1	1.0	0	NA
Brara.H02059.1	1.0	NA	NA
Brara.I01777.1	1.0	NA	NA
Brara.I03020.1	1.0	1	NA
Brara.I03021.1	1.5	1	NA
Brara.A03153.1	2.0	1	NA
Brara.C01519.1	2.0	1	NA
Brara.E02615.1	2.0	1	NA

Mature miRNA conservation

Link

Reference

>Genome-wide analysis of the SBP-box gene family in Chinese cabbage (Brassica rapa subsp. pekinensis). Genome, 2015

>BrpSPL9 (Brassica rapa ssp. pekinensis SPL9) controls the earliness of heading time in Chinese cabbage. Plant Biotechnol J, 2014