PmiREN: Plant microRNA Encyclopedia

Aly-MIR398a

Basic info.

miRNA locus ID
Aly-MIR398a

miRNA locus accession
PmiREN000516

Organism
Arabidopsis lyrata

Genomic location
Aly-scaffold_5 1852492 1852613 +

Comments
A member of family MIR398

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

           A  T  AATC       A   T A             C T        TTTACAT
      ACAGG GG GA    TCAAAGG GTG C TGAGAACACAGAT C ATGGTTTC       
      ||||| || ||    ||||||| ||| | ||||||||||||| | ||||||||        
      TGTCC CC CT    AGTTTCC CAC G ACTCTTGTGTTTG G TACCAAAG       
TTTCCT     -  T  ---A       C   T G             A T        TTACTTT

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-337	Aly-MIR398a	Aly-scaffold_5: 1852492-1852613 +	Arabidopsis thaliana	Ath-MIR398a	Ath-Chr2: 1040931-1041051 +
SY-338	Aly-MIR398a	Aly-scaffold_5: 1852492-1852613 +	Brassica rapa	Bra-MIR398d	Bra-A09: 15707792-15707915 +
SY-339	Aly-MIR398a	Aly-scaffold_5: 1852492-1852613 +	Capsella rubella	Cru-MIR398a	Cru-scaffold_5: 996451-996567 +
SY-340	Aly-MIR398a	Aly-scaffold_5: 1852492-1852613 +	Eutrema salsugineum	Esa-MIR398a	Esa-scaffold_6: 6956474-6956595 -

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.
AL6G25300.t2	0.0	0	NA

Mature miRNA conservation

Link

Reference

No reference

Aly-MIR398a

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