PmiREN: Plant microRNA Encyclopedia

Aly-MIR399d

Basic info.

miRNA locus ID
Aly-MIR399d

miRNA locus accession
PmiREN000521

Organism
Arabidopsis lyrata

Genomic location
Aly-scaffold_1 12884715 12884820 +

Comments
A member of family MIR399

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

     A     A       A          AC      TT  C TT     CTC
ATTAC GGGCA GATCTCT TTGGCAGGAA  CATTAC  GA C  TGCAT   
||||| ||||| ||||||| ||||||||||  ||||||  || |  |||||    
TAATG CCCGT TTAGAGG AACCGTTCTT  GTGATG  TT G  ACGTA   
     G     -       A          GA      -T  C TT     TTT

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: 3156
Chromosome: Aly-scaffold_1
Cluster start: 12884715
Cluster end: 12891053

miRNA locus ID	miRNA locus accession	Chromosome	Strand	Start	End
Aly-MIR399a , Aly-MIR399d	PmiREN000520, PmiREN000521	Aly-scaffold_1	+	12884715	12891053

miRNA syntenic block

Syntenic block ID	miRNA locus 1	miRNA locus 1 position	Organism	miRNA locus 2	miRNA locus 2 position
SY-356	Aly-MIR399d	Aly-scaffold_1: 12884715-12884820 +	Arabidopsis thaliana	Ath-MIR399a	Ath-Chr1: 10227065-10227205 +
SY-357	Aly-MIR399d	Aly-scaffold_1: 12884715-12884820 +	Brassica rapa	Bra-MIR399f	Bra-A07: 9697003-9697138 -
SY-358	Aly-MIR399d	Aly-scaffold_1: 12884715-12884820 +	Brassica rapa	Bra-MIR399g	Bra-A08: 18094144-18094280 -
SY-359	Aly-MIR399d	Aly-scaffold_1: 12884715-12884820 +	Capsella rubella	Cru-MIR399b	Cru-scaffold_1: 9989761-9989903 +

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.
AL4G29460.t1	1.0	NA	NA
AL4G29470.t1	1.0	NA	NA

Mature miRNA conservation

Link

Reference

No reference

Aly-MIR399d

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