PmiREN: Plant microRNA Encyclopedia

Cru-MIR398b

Basic info.

miRNA locus ID
Cru-MIR398b

miRNA locus accession
PmiREN002809

Organism
Capsella rubella

Genomic location
Cru-scaffold_6 4729354 4729490 +

Comments
A member of family MIR398

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

TGAA     ---T   T    A     T    A           ---     ATCAACGGCTGTAATGACGA
    GGTGG    GGA CTCG CAGGG TGAT TGAGAACACAT   TTGCA                    
    |||||    ||| |||| ||||| |||| |||||||||||   |||||                     
    CCATC    TCT GAGT GTCCC ACTG ACTCTTGTGTA   TTGCT                    
 TTG     TCTT   C    C     C    G           CTT     CTCTACATTGTTAATGTACT

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: 3283
Chromosome: Cru-scaffold_6
Cluster start: 4729354
Cluster end: 4733696

miRNA locus ID	miRNA locus accession	Chromosome	Strand	Start	End
Cru-MIR398b , Cru-MIR398c	PmiREN002809, PmiREN002810	Cru-scaffold_6	+	4729354	4733696

miRNA syntenic block

Syntenic block ID	miRNA locus 1	miRNA locus 1 position	Organism	miRNA locus 2	miRNA locus 2 position
SY-344	Aly-MIR398b	Aly-scaffold_6: 5876508-5876628 +	Capsella rubella	Cru-MIR398b	Cru-scaffold_6: 4729354-4729490 +
SY-688	Ath-MIR398b	Ath-Chr5: 4691014-4691147 +	Capsella rubella	Cru-MIR398b	Cru-scaffold_6: 4729354-4729490 +
SY-1164	Bra-MIR398a	Bra-A03: 2903551-2903686 +	Capsella rubella	Cru-MIR398b	Cru-scaffold_6: 4729354-4729490 +
SY-1166	Bra-MIR398b	Bra-A10: 15810197-15810331 -	Capsella rubella	Cru-MIR398b	Cru-scaffold_6: 4729354-4729490 +
SY-1258	Cru-MIR398b	Cru-scaffold_6: 4729354-4729490 +	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.
Carub.0006s1273.1	0.0	0	NA

Mature miRNA conservation

Link

No link
No link

Reference

No reference

Cru-MIR398b

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