PmiREN: Plant microRNA Encyclopedia

Bra-MIR156q

Basic info.

miRNA locus ID
Bra-MIR156q

miRNA locus accession
PmiREN002398

Organism
Brassica rapa

Genomic location
Bra-A06 22782170 22782301 +

Comments
A member of family MIR156

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

GAGT  --    -   TT  ---T      A  -                    GGCT   T     ATTTGA
    GA  TAAG GAA  GA    GGTGAC GA AGAGAGTGAGCACACATGGT    TTC TGCAT      
    ||  |||| |||  ||    |||||| || ||||||||||||||||||||    ||| |||||      A
    CT  ATTC CTT  CT    CCACTG CT TCTCTCACTCGTGTGTATCG    AAG ACGTA      
      AC    T   TT  TGTT      C  A                    ----   T     ATTTGG

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: 3272
Chromosome: Bra-A06
Cluster start: 22782170
Cluster end: 22783068

miRNA locus ID	miRNA locus accession	Chromosome	Strand	Start	End
Bra-MIR156b , Bra-MIR156q	PmiREN002383, PmiREN002398	Bra-A06	+	22782170	22783068

miRNA syntenic block

Syntenic block ID	miRNA locus 1	miRNA locus 1 position	Organism	miRNA locus 2	miRNA locus 2 position
SY-28	Aly-MIR156f	Aly-scaffold_6: 11884619-11884750 +	Brassica rapa	Bra-MIR156q	Bra-A06: 22782170-22782301 +
SY-416	Ath-MIR156f	Ath-Chr5: 9136106-9136237 +	Brassica rapa	Bra-MIR156q	Bra-A06: 22782170-22782301 +
SY-907	Bra-MIR156q	Bra-A06: 22782170-22782301 +	Eutrema salsugineum	Esa-MIR156i	Esa-scaffold_6: 3821516-3821647 +

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