PmiREN: Plant microRNA Encyclopedia

Bra-MIR166c

Basic info.

miRNA locus ID
Bra-MIR166c

miRNA locus accession
PmiREN002432

Organism
Brassica rapa

Genomic location
Bra-A05 682813 682983 -

Comments
A member of family MIR166

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

     A     TTTCTCTT   A        TT      C    G   T    CT  AT    TCATGTTGGATCTTCTTCGATCTAATC
      GGGGT        TTG GGGGAATG  GTCTGG TCGA GAC CTGG  CT  CAAC                           
      |||||        ||| ||||||||  |||||| |||| ||| ||||  ||  ||||                            
      CCTCG        AAC CCCCTTAC  CGGACC GGCT CTG GATT  GG  ATTA                           
TAAGTC     ---TTATT   C        TT      A    G   T    TT  -A    GTCTAGAGTTTGTATCTCCAAACTAAG

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-121	Aly-MIR166b	Aly-scaffold_5: 20552771-20552919 +	Brassica rapa	Bra-MIR166c	Bra-A05: 682813-682983 -
SY-500	Ath-MIR166b	Ath-Chr3: 22922192-22922341 +	Brassica rapa	Bra-MIR166c	Bra-A05: 682813-682983 -
SY-777	Bol-MIR166a	Bol-C04: 3332597-3332767 +	Brassica rapa	Bra-MIR166c	Bra-A05: 682813-682983 -
SY-784	Bol-MIR166c	Bol-C08: 32995401-32995551 +	Brassica rapa	Bra-MIR166c	Bra-A05: 682813-682983 -
SY-790	Bol-MIR166d	Bol-C04: 40715614-40715778 +	Brassica rapa	Bra-MIR166c	Bra-A05: 682813-682983 -
SY-965	Bra-MIR166b	Bra-A04: 21244922-21245087 +	Brassica rapa	Bra-MIR166c	Bra-A05: 682813-682983 -
SY-970	Bra-MIR166c	Bra-A05: 682813-682983 -	Brassica rapa	Bra-MIR166f	Bra-A09: 37793849-37794001 +
SY-971	Bra-MIR166c	Bra-A05: 682813-682983 -	Capsella rubella	Cru-MIR166a	Cru-scaffold_4: 14490144-14490324 +
SY-972	Bra-MIR166c	Bra-A05: 682813-682983 -	Eutrema salsugineum	Esa-MIR166a	Esa-scaffold_22: 1329544-1329726 +
SY-973	Bra-MIR166c	Bra-A05: 682813-682983 -	Eutrema salsugineum	Esa-MIR166d	Esa-scaffold_19: 528598-528750 -

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.F00211.1	0.5	NA	NA
Brara.H00179.1	0.5	NA	NA
Brara.B01017.1	1.0	NA	NA
Brara.D02105.1	1.0	NA	NA
Brara.I02808.1	1.0	NA	NA
Brara.J01422.1	1.0	NA	NA
Brara.K00217.1	1.0	NA	NA
Brara.E00955.1	1.5	NA	NA
Brara.F01856.1	1.5	NA	NA

Mature miRNA conservation

Link

No link
No link

Reference

>Identification of cold stress responsive microRNAs in two winter turnip rape (Brassica rapa L.) by high throughput sequencing. BMC Plant Biol, 2018

>Association of microRNAs with Types of Leaf Curvature in Brassica rapa. Front Plant Sci, 2018