PmiREN: Plant microRNA Encyclopedia

Aly-MIR396a

Basic info.

miRNA locus ID
Aly-MIR396a

miRNA locus accession
PmiREN000512

Organism
Arabidopsis lyrata

Genomic location
Aly-scaffold_3 17432894 17433063 -

Comments
A member of family MIR396

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  ACGTGACCCTC        C            C            A -T  -TT    TT   -TTTTTTT    ----A     CT
             TCTGTATT TTCCACAGCTTT TTGAACTGCAAA C  TC   CAGA  TGT        ATAT     TATGT  
             |||||||| |||||||||||| |||||||||||| |  ||   ||||  |||        ||||     |||||  T
             AGGCATAG AGGGTGTCGAAA AACTTGGCGTTT G  AG   GTCT  ACA        TGTG     ATACG  
AAGAAACTGAGAC        A            T            A TT  CTC    CT   CTTGTTTT    ATAAA     CA

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-327	Aly-MIR396a	Aly-scaffold_3: 17432894-17433063 -	Arabidopsis thaliana	Ath-MIR396a	Ath-Chr2: 4142311-4142483 -
SY-328	Aly-MIR396a	Aly-scaffold_3: 17432894-17433063 -	Capsella rubella	Cru-MIR396a	Cru-scaffold_3: 10624783-10624945 -
SY-329	Aly-MIR396a	Aly-scaffold_3: 17432894-17433063 -	Eutrema salsugineum	Esa-MIR396a	Esa-scaffold_11: 11322331-11322501 +

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-MIR396a

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