PmiREN: Plant microRNA Encyclopedia

Aly-MIR393a

Basic info.

miRNA locus ID
Aly-MIR393a

miRNA locus accession
PmiREN000501

Organism
Arabidopsis lyrata

Genomic location
Aly-scaffold_4 19396116 19396270 +

Comments
A member of family MIR393

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  CAT   A   A     A              C    T     TAATAA         -ACCCCAATCT   -  TAAT
     AGC ACT GAGGA GGATCCAAAGGGAT GCAT GATCC      AGGTGAATT           TTT CT    
     ||| ||| ||||| |||||||||||||| |||| |||||      |||||||||           ||| ||     
     TCG TGG TTCCT CTTAGGTTTCTCTA CGTA CTAGG      TTCGTTTAA           AAA GA    
CTCCT   A   C     A              T    -     TTTTGG         AAAAACTAAAC   C  TTAA

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-290	Aly-MIR393a	Aly-scaffold_4: 19396116-19396270 +	Arabidopsis thaliana	Ath-MIR393a	Ath-Chr2: 16652091-16652245 +
SY-291	Aly-MIR393a	Aly-scaffold_4: 19396116-19396270 +	Brassica rapa	Bra-MIR393a	Bra-A04: 19205419-19205573 +
SY-292	Aly-MIR393a	Aly-scaffold_4: 19396116-19396270 +	Brassica rapa	Bra-MIR393b	Bra-A05: 3291935-3292095 -
SY-293	Aly-MIR393a	Aly-scaffold_4: 19396116-19396270 +	Brassica rapa	Bra-MIR393c	Bra-A09: 35133997-35134164 +
SY-294	Aly-MIR393a	Aly-scaffold_4: 19396116-19396270 +	Capsella rubella	Cru-MIR393a	Cru-scaffold_4: 11771167-11771330 +
SY-295	Aly-MIR393a	Aly-scaffold_4: 19396116-19396270 +	Eutrema salsugineum	Esa-MIR393a	Esa-scaffold_10: 10483751-10483910 +
SY-296	Aly-MIR393a	Aly-scaffold_4: 19396116-19396270 +	Eutrema salsugineum	Esa-MIR393b	Esa-scaffold_16: 74485-74658 -

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.
AL1G24460.t1	1.0	NA	NA
AL5G15690.t1	1.0	NA	NA
AL5G45760.t1	1.0	NA	NA
AL7G23690.t1	1.5	NA	NA
AL6G49750.t1	2.0	NA	NA

Mature miRNA conservation

Link

Reference

No reference

Aly-MIR393a

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