PmiREN: Plant microRNA Encyclopedia

Bra-MIR164a

Basic info.

miRNA locus ID
Bra-MIR164a

miRNA locus accession
PmiREN002420

Organism
Brassica rapa

Genomic location
Bra-A05 199663 199779 -

Comments
A member of family MIR164

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  GCGGATGAGAACCTCCAC       A  CA             CCAACAA   C    TC
                    GTTGGAG AG  GGGCACGTGCAAA       ACA GAGA  
                    ||||||| ||  |||||||||||||       ||| ||||   
                    CAACCTC TC  CTCGTGCACGTTT       TGT CTCT  
CAGTTACCACTCCTCGAGTA       C  CC             -----AA   A    AT

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-88	Aly-MIR164a	Aly-scaffold_4: 23120157-23120273 +	Brassica rapa	Bra-MIR164a	Bra-A05: 199663-199779 -
SY-472	Ath-MIR164a	Ath-Chr2: 19520750-19520869 +	Brassica rapa	Bra-MIR164a	Bra-A05: 199663-199779 -
SY-945	Bra-MIR164a	Bra-A05: 199663-199779 -	Capsella rubella	Cru-MIR164a	Cru-scaffold_4: 14858719-14858835 +
SY-946	Bra-MIR164a	Bra-A05: 199663-199779 -	Eutrema salsugineum	Esa-MIR164b	Esa-scaffold_22: 1698371-1698492 +
SY-953	Bra-MIR164e	Bra-A04: 21524409-21524525 +	Brassica rapa	Bra-MIR164a	Bra-A05: 199663-199779 -

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.B00259.1	0.5	1	NA
Brara.B03769.1	0.5	1	NA
Brara.C04256.1	0.5	1	NA
Brara.J02533.1	0.5	1	NA
Brara.A03159.1	1.0	1	NA
Brara.B01408.1	1.0	1	NA
Brara.C03443.1	1.0	1	NA
Brara.C03560.1	1.0	1	NA
Brara.H00015.1	1.0	NA	NA
Brara.J00883.1	1.0	1	NA
Brara.E02808.1	1.5	1	NA
Brara.D00978.1	2.0	2	NA
Brara.G01456.1	2.0	2	NA

Mature miRNA conservation

Link

Reference

>Sequence and functional characterization of MIRNA164 promoters from Brassica shows copy number dependent regulatory diversification among homeologs. Funct Integr Genomics, 2018