PmiREN: Plant microRNA Encyclopedia

Ath-MIR397a

Basic info.

miRNA locus ID
Ath-MIR397a

miRNA locus accession
PmiREN000724

Organism
Arabidopsis thaliana

Genomic location
Ath-Chr4 2625940 2626068 +

Comments
A member of family MIR397

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

         --TTT   T      C                A     T   G     TTT      GT
 TTCCTGGG     GAA GAACAT ATTGAGTGCAGCGTTG TGTAA TTC TTTTG   TTCATT  
 ||||||||     ||| |||||| |||||||||||||||| ||||| ||| |||||   ||||||   
 AAGGACTT     CTT TTTGTA TAACTCGCGTTGCGAC ATATT AAG AAAAT   AGGTAA  
C        TTAAT   -      T                C     T   -     --T      GT

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-334	Aly-MIR397a	Aly-scaffold_6: 22804022-22804147 +	Arabidopsis thaliana	Ath-MIR397a	Ath-Chr4: 2625940-2626068 +
SY-683	Ath-MIR397a	Ath-Chr4: 2625940-2626068 +	Capsella rubella	Cru-MIR397a	Cru-scaffold_6: 14975608-14975750 +

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.
AT2G29130.1	0.5	NA	0 (3)
AT2G38080.1	0.5	NA	0 (3)
AT5G60020.1	1.0	NA	0 (3)
AT3G17880.1	2.5	2	2 (2)
AT1G66670.1	3.0	2	2 (3)
AT3G05350.1	3.5	NA	2 (1)
AT3G26650.1	4.0	NA	2 (4)
AT4G38430.1	4.0	NA	2 (2)
AT5G17520.1	4.0	NA	2 (3)
AT5G40160.1	4.5	NA	2 (3)
AT3G55630.3	5.0	NA	2 (3)
AT1G31300.1	NA	NA	2 (2)
AT2G38540.1	NA	NA	2 (3)
AT2G46560.1	NA	NA	2 (1)
AT3G15730.1	NA	NA	2 (3)
AT3G53580.1	NA	NA	2 (3)
AT5G57490.1	NA	NA	2 (2)
AT3G06470.1	2.0	2	4 (1)

Mature miRNA conservation

Link

Reference

>Uncovering miRNAs involved in crosstalk between nutrient deficiencies in Arabidopsis. Sci Rep, 2015

>MiR397b regulates both lignin content and seed number in Arabidopsis via modulating a laccase involved in lignin biosynthesis. Plant Biotechnol J, 2014

>SQUAMOSA Promoter Binding Protein-Like7 Is a Central Regulator for Copper Homeostasis in Arabidopsis. Plant Cell, 2009