PmiREN: Plant microRNA Encyclopedia

Bra-MIR398a

Basic info.

miRNA locus ID
Bra-MIR398a

miRNA locus accession
PmiREN002532

Organism
Brassica rapa

Genomic location
Bra-A03 2903551 2903686 +

Comments
A member of family MIR398

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  TTTGAGGGTGGAC    A     TC   A             TAATCAA   C    -------      C
               CTCG CAGGG  GAC TGAGAACACATGG       AGG TGTA       ATGACG 
               |||| |||||  ||| |||||||||||||       ||| ||||       |||||| C
               GAGT GTCCC  CTG ACTCTTGTGTACT       TCT ACAT       TACTGC 
TGCCGTCTCTTTCTC    C     CA   G             -TTTCTC   -    ACAATGT      A

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-342	Aly-MIR398b	Aly-scaffold_6: 5876508-5876628 +	Brassica rapa	Bra-MIR398a	Bra-A03: 2903551-2903686 +
SY-686	Ath-MIR398b	Ath-Chr5: 4691014-4691147 +	Brassica rapa	Bra-MIR398a	Bra-A03: 2903551-2903686 +
SY-1163	Bra-MIR398a	Bra-A03: 2903551-2903686 +	Brassica rapa	Bra-MIR398b	Bra-A10: 15810197-15810331 -
SY-1164	Bra-MIR398a	Bra-A03: 2903551-2903686 +	Capsella rubella	Cru-MIR398b	Cru-scaffold_6: 4729354-4729490 +
SY-1165	Bra-MIR398a	Bra-A03: 2903551-2903686 +	Eutrema salsugineum	Esa-MIR398b	Esa-scaffold_2: 4759541-4759674 +

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.J02011.1	0.0	NA	NA

Mature miRNA conservation

Link

Reference

No reference

Bra-MIR398a

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