PmiREN: Plant microRNA Encyclopedia

Aly-MIR398b

Basic info.

miRNA locus ID
Aly-MIR398b

miRNA locus accession
PmiREN000517

Organism
Arabidopsis lyrata

Genomic location
Aly-scaffold_6 5876508 5876628 +

Comments
A member of family MIR398

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

GAA     ---T   T    A     T    A              TAATCAACGGCTG        C
   GGTAG    GGA CTCG CAGGG TGAT TGAGGACACATGTG             TAATGACG 
   |||||    ||| |||| ||||| |||| ||||||||||||||             |||||||| C
   CCATC    TCT GAGT GTCCC ACTG ACTCTTGTGTACAT             GTTACTGC 
 AG     TCTT   C    C     C    G              ------------T        A

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-341	Aly-MIR398b	Aly-scaffold_6: 5876508-5876628 +	Arabidopsis thaliana	Ath-MIR398b	Ath-Chr5: 4691014-4691147 +
SY-342	Aly-MIR398b	Aly-scaffold_6: 5876508-5876628 +	Brassica rapa	Bra-MIR398a	Bra-A03: 2903551-2903686 +
SY-343	Aly-MIR398b	Aly-scaffold_6: 5876508-5876628 +	Brassica rapa	Bra-MIR398b	Bra-A10: 15810197-15810331 -
SY-344	Aly-MIR398b	Aly-scaffold_6: 5876508-5876628 +	Capsella rubella	Cru-MIR398b	Cru-scaffold_6: 4729354-4729490 +
SY-345	Aly-MIR398b	Aly-scaffold_6: 5876508-5876628 +	Eutrema salsugineum	Esa-MIR398b	Esa-scaffold_2: 4759541-4759674 +

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-MIR398b

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