PmiREN: Plant microRNA Encyclopedia

Bra-MIR393a

Basic info.

miRNA locus ID
Bra-MIR393a

miRNA locus accession
PmiREN002510

Organism
Brassica rapa

Genomic location
Bra-A04 19205419 19205573 +

Comments
A member of family MIR393

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

TTCAT   A   A     A     C        C    T     T            TTCTCCTTAATATTTTCTTAAT      CAAA
     AGC ACT GAGGA GGATC AAAGGGAT GCAT GATCC AAGTCGAGTGAA                      TATTGG    
     ||| ||| ||||| ||||| |||||||| |||| ||||| ||||||||||||                      ||||||    A
     TCG TGG TTCCT CTTAG TTTCCCTA CGTA CTAGG TTTGGTTCGTTT                      ATAACC    
  ACT   A   C     A     C        T    -     T            ---------------------T      CTAA

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-291	Aly-MIR393a	Aly-scaffold_4: 19396116-19396270 +	Brassica rapa	Bra-MIR393a	Bra-A04: 19205419-19205573 +
SY-642	Ath-MIR393a	Ath-Chr2: 16652091-16652245 +	Brassica rapa	Bra-MIR393a	Bra-A04: 19205419-19205573 +
SY-1121	Bra-MIR393a	Bra-A04: 19205419-19205573 +	Brassica rapa	Bra-MIR393b	Bra-A05: 3291935-3292095 -
SY-1122	Bra-MIR393a	Bra-A04: 19205419-19205573 +	Brassica rapa	Bra-MIR393c	Bra-A09: 35133997-35134164 +
SY-1123	Bra-MIR393a	Bra-A04: 19205419-19205573 +	Capsella rubella	Cru-MIR393a	Cru-scaffold_4: 11771167-11771330 +
SY-1124	Bra-MIR393a	Bra-A04: 19205419-19205573 +	Capsella rubella	Cru-MIR393b	Cru-scaffold_5: 10912783-10912975 +
SY-1125	Bra-MIR393a	Bra-A04: 19205419-19205573 +	Eutrema salsugineum	Esa-MIR393a	Esa-scaffold_10: 10483751-10483910 +
SY-1126	Bra-MIR393a	Bra-A04: 19205419-19205573 +	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.
Brara.D00378.1	0.0	0	NA
Brara.B03253.1	1.0	NA	NA
Brara.H02636.1	1.0	NA	NA
Brara.I05093.1	1.0	NA	NA
Brara.D00040.1	1.5	NA	NA
Brara.G01991.1	1.5	NA	NA
Brara.I04357.1	1.5	NA	NA
Brara.I00210.1	2.0	NA	NA

Mature miRNA conservation

Link

No link
No link

Reference

No reference

Bra-MIR393a

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