PmiREN: Plant microRNA Encyclopedia

Cru-MIR169e

Basic info.

miRNA locus ID
Cru-MIR169e

miRNA locus accession
PmiREN002773

Organism
Capsella rubella

Genomic location
Cru-scaffold_5 1969964 1970154 -

Comments
A member of family MIR169

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

 GCAGAAAGAGT      T  -          T    T       T   TTTT A    C         TTTTATGTT         TC           AATT
            CATGTT AG TAGCCAAGGA GACT GCCTAAA CTT    C CCAC AAGATTCAA         CATGGTTTT  GATTATTATGC    
            |||||| || |||||||||| |||| ||||||| |||    | |||| |||||||||         |||||||||  |||||||||||    T
            GTACAG TC ATCGGTTCCT CTGA CGGATTT GGA    G GGTG TTCTAAGTT         GTACTAAAG  TTAATAATATG    
CTTACTTTTTTC      T  T          -    -       T   --TT -    -         ---------         -T           GGAA

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-219	Aly-MIR169j	Aly-scaffold_5: 3130948-3131137 -	Capsella rubella	Cru-MIR169e	Cru-scaffold_5: 1969964-1970154 -
SY-579	Ath-MIR169j	Ath-Chr3: 9872336-9872523 -	Capsella rubella	Cru-MIR169e	Cru-scaffold_5: 1969964-1970154 -
SY-1014	Bra-MIR169e	Bra-A02: 27317508-27317695 -	Capsella rubella	Cru-MIR169e	Cru-scaffold_5: 1969964-1970154 -
SY-1029	Bra-MIR169m	Bra-A06: 25527117-25527308 +	Capsella rubella	Cru-MIR169e	Cru-scaffold_5: 1969964-1970154 -
SY-1033	Bra-MIR169p	Bra-A09: 1477043-1477232 -	Capsella rubella	Cru-MIR169e	Cru-scaffold_5: 1969964-1970154 -
SY-1234	Cru-MIR169e	Cru-scaffold_5: 1969964-1970154 -	Eutrema salsugineum	Esa-MIR169d	Esa-scaffold_6: 6265076-6265266 +

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.
Carub.0001s4340.1	1.0	1	NA
Carub.0002s1967.1	1.0	1	NA
Carub.0003s1360.1	1.0	1	NA

Mature miRNA conservation

Link

No link
No link

Reference

>Microsynteny and phylogenetic analysis of tandemly organised miRNA families across five members of Brassicaceae reveals complex retention and loss history. Plant Sci, 2016