PmiREN: Plant microRNA Encyclopedia

Cru-MIR169d

Basic info.

miRNA locus ID
Cru-MIR169d

miRNA locus accession
PmiREN002772

Organism
Capsella rubella

Genomic location
Cru-scaffold_3 4431202 4431418 -

Comments
A member of family MIR169

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

 TAT      -           C                      TAAAATGATC          --ATA     AC     GAAGAAAAC         AAATTCTTTAG       AAA
    GTGACG AAAGTAGTGTG AGCCAAGGATGACTTGCCGATT          TTTCTTTTTT     TATAT  TCTAT         TTTAGTTTC           TTCTTGA   
    |||||| ||||||||||| ||||||||||||||||||||||          ||||||||||     |||||  |||||         |||||||||           |||||||    
    CGCTGT TTTCATTGCAC TCGGTTCCTGTTGAACGGCTAG          AAAGAAGAAA     ATATA  AGGTA         AGATTAAAG           AAGGACT   
TACG      G           A                      -TACAATGAA          AACCG     AT     ---------         -----------       AGA

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-192	Aly-MIR169a	Aly-scaffold_3: 5439439-5439688 -	Capsella rubella	Cru-MIR169d	Cru-scaffold_3: 4431202-4431418 -
SY-557	Ath-MIR169a	Ath-Chr3: 4358990-4359222 -	Capsella rubella	Cru-MIR169d	Cru-scaffold_3: 4431202-4431418 -
SY-1018	Bra-MIR169h	Bra-A01: 27239224-27239432 +	Capsella rubella	Cru-MIR169d	Cru-scaffold_3: 4431202-4431418 -
SY-1023	Bra-MIR169j	Bra-A03: 17544406-17544602 -	Capsella rubella	Cru-MIR169d	Cru-scaffold_3: 4431202-4431418 -
SY-1026	Bra-MIR169l	Bra-A05: 24007347-24007484 +	Capsella rubella	Cru-MIR169d	Cru-scaffold_3: 4431202-4431418 -
SY-1233	Cru-MIR169d	Cru-scaffold_3: 4431202-4431418 -	Eutrema salsugineum	Esa-MIR169a	Esa-scaffold_13: 5033375-5033601 +

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	2.0	1	NA
Carub.0002s1967.1	2.0	2	NA
Carub.0003s1360.1	2.0	1	NA
Carub.0008s0723.1	2.0	NA	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