PmiREN: Plant microRNA Encyclopedia

Cru-MIR159a

Basic info.

miRNA locus ID
Cru-MIR159a

miRNA locus accession
PmiREN002746

Organism
Capsella rubella

Genomic location
Cru-scaffold_1 6244044 6244271 +

Comments
A member of family MIR159

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

AGA       -   -   G            GA       T       TT   -------A     T   -      G  A  C      TC      ---------  C     TAAT    AA
   AGATGGA AGA AGA GAAGAGCTCCTT  AGTTCAA GGAGGGT  AGC        GGGTG AGT AAAGCT CT AG TATGGA  CCATAA         GC TTATC    TCAA  
   ||||||| ||| ||| ||||||||||||  ||||||| |||||||  |||        ||||| ||| |||||| || || ||||||  ||||||         || |||||    ||||  C
   TCTGTCT TCT TCT CTTCTCGAGGGA  TTAGGTT CTTCTCA  TCG        CCCAC TCA TTTCGA GA TC ATACCT  GGTATT         TG AATAG    AGTT  
CCC       C   C   A            AG       T       CT   GTAACTTC     -   C      G  C  T      TA      TTTTATTTT  A     ---T    GA

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-64	Aly-MIR159a	Aly-scaffold_2: 15958622-15958842 -	Capsella rubella	Cru-MIR159a	Cru-scaffold_1: 6244044-6244271 +
SY-440	Ath-MIR159a	Ath-Chr1: 27713214-27713433 -	Capsella rubella	Cru-MIR159a	Cru-scaffold_1: 6244044-6244271 +
SY-445	Ath-MIR159b	Ath-Chr1: 6220630-6220853 +	Capsella rubella	Cru-MIR159a	Cru-scaffold_1: 6244044-6244271 +
SY-1208	Cru-MIR159a	Cru-scaffold_1: 6244044-6244271 +	Capsella rubella	Cru-MIR159b	Cru-scaffold_2: 11281838-11282056 -
SY-1209	Cru-MIR159a	Cru-scaffold_1: 6244044-6244271 +	Eutrema salsugineum	Esa-MIR159b	Esa-scaffold_9: 3074879-3075095 +

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.0005s2718.1	2.0	1	NA
Carub.0007s0248.1	2.0	2	NA
Carub.0007s1355.1	2.0	NA	NA

Mature miRNA conservation

Link

No link
No link

Reference

No reference

Cru-MIR159a

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