PmiREN: Plant microRNA Encyclopedia

Cru-MIR399b

Basic info.

miRNA locus ID
Cru-MIR399b

miRNA locus accession
PmiREN002812

Organism
Capsella rubella

Genomic location
Cru-scaffold_1 9989761 9989903 +

Comments
A member of family MIR399

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  AAA      AAT C     A     A       A        A   -      --TTT  T TT      TC
     GGTGAA   G ATTAC GGGCA GATCTCT TTGGCAGG AAC CATTAC     GA C  TGCATG  
     ||||||   | ||||| ||||| ||||||| |||||||| ||| ||||||     || |  ||||||  T
     CCGCTT   C TAATG CCCGT TTAGAGG AACCGTCT TTG GTGATG     TT G  ACGTAT  
TATAA      CTT T     G     -       A        C   A      CATGT  C TT      TT

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: 3278
Chromosome: Cru-scaffold_1
Cluster start: 9989761
Cluster end: 9995062

miRNA locus ID	miRNA locus accession	Chromosome	Strand	Start	End
Cru-MIR399b , Cru-MIR399c	PmiREN002812, PmiREN002813	Cru-scaffold_1	+	9989761	9995062

miRNA syntenic block

Syntenic block ID	miRNA locus 1	miRNA locus 1 position	Organism	miRNA locus 2	miRNA locus 2 position
SY-359	Aly-MIR399d	Aly-scaffold_1: 12884715-12884820 +	Capsella rubella	Cru-MIR399b	Cru-scaffold_1: 9989761-9989903 +
SY-692	Ath-MIR399a	Ath-Chr1: 10227065-10227205 +	Capsella rubella	Cru-MIR399b	Cru-scaffold_1: 9989761-9989903 +
SY-702	Ath-MIR399f	Ath-Chr2: 14444989-14445124 +	Capsella rubella	Cru-MIR399b	Cru-scaffold_1: 9989761-9989903 +
SY-1178	Bra-MIR399e	Bra-A04: 17162059-17162193 +	Capsella rubella	Cru-MIR399b	Cru-scaffold_1: 9989761-9989903 +
SY-1181	Bra-MIR399f	Bra-A07: 9697003-9697138 -	Capsella rubella	Cru-MIR399b	Cru-scaffold_1: 9989761-9989903 +
SY-1182	Bra-MIR399g	Bra-A08: 18094144-18094280 -	Capsella rubella	Cru-MIR399b	Cru-scaffold_1: 9989761-9989903 +
SY-1259	Cru-MIR399b	Cru-scaffold_1: 9989761-9989903 +	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.
Carub.0004s1541.1	1.0	NA	NA
Carub.0001s1147.1	2.0	NA	NA

Mature miRNA conservation

Link

No link
No link

Reference

No reference

Cru-MIR399b

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