PmiREN: Plant microRNA Encyclopedia

Bra-MIR156j

Basic info.

miRNA locus ID
Bra-MIR156j

miRNA locus accession
PmiREN002391

Organism
Brassica rapa

Genomic location
Bra-A01 2925936 2926060 +

Comments
A member of family MIR156

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

GTTTTAGAAAAACGCAAA  AA        -    -         A   ---     CTT     GT
                  GA  CTGACAGA AGAG AGTGAGCAC CAA   AGGCA   TGCAT  
                  ||  |||||||| |||| ||||||||| |||   |||||   |||||  T
                  CT  GACTGTCT TCTC TCACTCGTG GTT   TTCGT   ACGTA  
    TTCTTAGCCACGGC  TG        A    G         C   CTC     -TT     GC

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-4	Aly-MIR156a	Aly-scaffold_4: 3693798-3693921 -	Brassica rapa	Bra-MIR156j	Bra-A01: 2925936-2926060 +
SY-390	Ath-MIR156a	Ath-Chr2: 10676450-10676573 -	Brassica rapa	Bra-MIR156j	Bra-A01: 2925936-2926060 +
SY-403	Ath-MIR156c	Ath-Chr4: 15415406-15415530 -	Brassica rapa	Bra-MIR156j	Bra-A01: 2925936-2926060 +
SY-891	Bra-MIR156j	Bra-A01: 2925936-2926060 +	Brassica rapa	Bra-MIR156c	Bra-Scaffold16715: 106195-106319 +
SY-892	Bra-MIR156j	Bra-A01: 2925936-2926060 +	Brassica rapa	Bra-MIR156f	Bra-A09: 38656170-38656292 +
SY-893	Bra-MIR156j	Bra-A01: 2925936-2926060 +	Capsella rubella	Cru-MIR156a	Cru-scaffold_4: 2142098-2142223 -
SY-894	Bra-MIR156j	Bra-A01: 2925936-2926060 +	Capsella rubella	Cru-MIR156d	Cru-scaffold_7: 3310268-3310392 +
SY-895	Bra-MIR156j	Bra-A01: 2925936-2926060 +	Eutrema salsugineum	Esa-MIR156f	Esa-scaffold_1: 3452779-3452903 +

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

No link
No 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