PmiREN: Plant microRNA Encyclopedia

Bra-MIR396a

Basic info.

miRNA locus ID
Bra-MIR396a

miRNA locus accession
PmiREN002529

Organism
Brassica rapa

Genomic location
Bra-A08 8513338 8513490 +

Comments
A member of family MIR396

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

TGAAGA     ----     A                    A    -C      -ATTTCCCTTAT      CCAAAATA
      TCCTG    GTTAT TTTTTCCACAGCTTTCTTGA CTTT  TTTTTC            TTAGAG        
      |||||    ||||| |||||||||||||||||||| ||||  ||||||            ||||||        A
      GGGAC    CAGTA AAAAGGGTGTCGAAAGAACT GAAA  AAAAAG            AATCTC        
  TTTT     TTAA     C                    C    AA      ATCACAATTTAC      TAAAAATC

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-331	Aly-MIR396b	Aly-scaffold_7: 18203546-18203709 +	Brassica rapa	Bra-MIR396a	Bra-A08: 8513338-8513490 +
SY-680	Ath-MIR396b	Ath-Chr5: 13611788-13611944 +	Brassica rapa	Bra-MIR396a	Bra-A08: 8513338-8513490 +
SY-1159	Bra-MIR396a	Bra-A08: 8513338-8513490 +	Capsella rubella	Cru-MIR396b	Cru-scaffold_7: 13784082-13784252 +
SY-1160	Bra-MIR396a	Bra-A08: 8513338-8513490 +	Eutrema salsugineum	Esa-MIR396b	Esa-scaffold_18: 2696056-2696216 +

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.C03329.1	2.0	NA	NA
Brara.G02611.1	2.0	NA	NA

Mature miRNA conservation

Link

Reference

No reference

Bra-MIR396a

>