PmiREN: Plant microRNA Encyclopedia

Bra-MIR164c

Basic info.

miRNA locus ID
Bra-MIR164c

miRNA locus accession
PmiREN002422

Organism
Brassica rapa

Genomic location
Bra-A09 2590117 2590236 -

Comments
A member of family MIR164

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  AAT   T   TA    T  C     A  C              CTA    GA   CTGT
     GGG GAG  ACAC TG TGGAG AG AGGGCACGTGCGAA   ATGA  GAT    
     ||| |||  |||| || ||||| || ||||||||||||||   ||||  |||     
     CCC CTC  TGTG AC ACCTC TC TCTTGTGCACGTTT   TACT  TTG    
CTTCC   T   TG    C  A     A  A              TTA    AG   TACA

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-481	Ath-MIR164c	Ath-Chr5: 9852664-9852787 +	Brassica rapa	Bra-MIR164c	Bra-A09: 2590117-2590236 -
SY-756	Bol-MIR164a	Bol-C02: 42582788-42582909 +	Brassica rapa	Bra-MIR164c	Bra-A09: 2590117-2590236 -
SY-763	Bol-MIR164c	Bol-C09: 3215110-3215229 +	Brassica rapa	Bra-MIR164c	Bra-A09: 2590117-2590236 -
SY-947	Bra-MIR164b	Bra-A02: 29559939-29560062 +	Brassica rapa	Bra-MIR164c	Bra-A09: 2590117-2590236 -
SY-950	Bra-MIR164c	Bra-A09: 2590117-2590236 -	Eutrema salsugineum	Esa-MIR164a	Esa-scaffold_6: 4116889-4117012 -
SY-951	Bra-MIR164d	Bra-A06: 23205955-23206076 -	Brassica rapa	Bra-MIR164c	Bra-A09: 2590117-2590236 -

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