PmiREN: Plant microRNA Encyclopedia

Aly-MIR396b

Basic info.

miRNA locus ID
Aly-MIR396b

miRNA locus accession
PmiREN000513

Organism
Arabidopsis lyrata

Genomic location
Aly-scaffold_7 18203546 18203709 +

Comments
A member of family MIR396

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

AGAAG      ----     A                    A   T      CA      --T   -------------          CTAA
     ATCCTG    GTCAT TTTTTCCACAGCTTTCTTGA CTT CTTTTT  TTTCCA   TGT             TTTTTTTTTT    
     ||||||    ||||| |||||||||||||||||||| ||| ||||||  ||||||   |||             ||||||||||     
     TGGGAC    CAGTA AAAAGGGTGTCGAAAGAACT GAA GAAGAA  AAAGGT   ACG             AGAAAAAAAA    
  TTT      TTAA     C                    C   -      AC      TTT   ATTTAAAATCTCT          ACCA

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-330	Aly-MIR396b	Aly-scaffold_7: 18203546-18203709 +	Arabidopsis thaliana	Ath-MIR396b	Ath-Chr5: 13611788-13611944 +
SY-331	Aly-MIR396b	Aly-scaffold_7: 18203546-18203709 +	Brassica rapa	Bra-MIR396a	Bra-A08: 8513338-8513490 +
SY-332	Aly-MIR396b	Aly-scaffold_7: 18203546-18203709 +	Capsella rubella	Cru-MIR396b	Cru-scaffold_7: 13784082-13784252 +
SY-333	Aly-MIR396b	Aly-scaffold_7: 18203546-18203709 +	Eutrema salsugineum	Esa-MIR396b	Esa-scaffold_18: 2696056-2696216 +

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.
AL1G50040.t1	2.0	2	NA
AL8G17690.t1	2.0	1	NA

Mature miRNA conservation

Link

Reference

No reference

Aly-MIR396b

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