PmiREN: Plant microRNA Encyclopedia

Bra-MIR399e

Basic info.

miRNA locus ID
Bra-MIR399e

miRNA locus accession
PmiREN002540

Organism
Brassica rapa

Genomic location
Bra-A04 17162059 17162193 +

Comments
A member of family MIR399

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  AAA     A  T C     A     A               -  AACTA   CT    TCTT     TGC
     GGTGC AA G ATTAC GGGCA GATCTCCTTTGGCAG GA     TTA  CCAT    GCATA   
     ||||| || | ||||| ||||| ||||||||||||||| ||     |||  ||||    |||||    
     CCGTG TT C TAATG CCCGT TTAGAGGAAACCGTC CT     AAT  GGTG    TGTAT   
TATGA     C  T T     G     -               T  ---CA   AT    --TT     TTA

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-700	Ath-MIR399f	Ath-Chr2: 14444989-14445124 +	Brassica rapa	Bra-MIR399e	Bra-A04: 17162059-17162193 +
SY-1177	Bra-MIR399e	Bra-A04: 17162059-17162193 +	Brassica rapa	Bra-MIR399g	Bra-A08: 18094144-18094280 -
SY-1178	Bra-MIR399e	Bra-A04: 17162059-17162193 +	Capsella rubella	Cru-MIR399b	Cru-scaffold_1: 9989761-9989903 +
SY-1179	Bra-MIR399e	Bra-A04: 17162059-17162193 +	Capsella rubella	Cru-MIR399d	Cru-scaffold_4: 9363165-9363304 +

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.D01377.1	2.0	NA	NA
Brara.D02054.1	2.0	NA	NA

Mature miRNA conservation

Link

No link
No link

Reference

No reference

Bra-MIR399e

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