PmiREN: Plant microRNA Encyclopedia

Cru-MIR393a

Basic info.

miRNA locus ID
Cru-MIR393a

miRNA locus accession
PmiREN002790

Organism
Capsella rubella

Genomic location
Cru-scaffold_4 11771167 11771330 +

Comments
A member of family MIR393

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  CATAGCA   A     A              C    T     T        -------------A      TTCTCCACTCATTTGTT
         ACT GAGGA GGATCCAAAGGGAT GCAT GATCC AAACTAAG              GGTGGA                 
         ||| ||||| |||||||||||||| |||| ||||| ||||||||              ||||||                  
         TGG TTCCT CTTAGGTTTCTCTA CGTA CTAGG TTTGGTTC              TAAACA                 
TTACTTCGA   G     A              C    -     T        GTTAAAAAAAACAC      AACGATTAATAATTCTT

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-294	Aly-MIR393a	Aly-scaffold_4: 19396116-19396270 +	Capsella rubella	Cru-MIR393a	Cru-scaffold_4: 11771167-11771330 +
SY-644	Ath-MIR393a	Ath-Chr2: 16652091-16652245 +	Capsella rubella	Cru-MIR393a	Cru-scaffold_4: 11771167-11771330 +
SY-651	Ath-MIR393b	Ath-Chr3: 20691637-20691818 +	Capsella rubella	Cru-MIR393a	Cru-scaffold_4: 11771167-11771330 +
SY-1123	Bra-MIR393a	Bra-A04: 19205419-19205573 +	Capsella rubella	Cru-MIR393a	Cru-scaffold_4: 11771167-11771330 +
SY-1127	Bra-MIR393b	Bra-A05: 3291935-3292095 -	Capsella rubella	Cru-MIR393a	Cru-scaffold_4: 11771167-11771330 +
SY-1245	Cru-MIR393a	Cru-scaffold_4: 11771167-11771330 +	Capsella rubella	Cru-MIR393b	Cru-scaffold_5: 10912783-10912975 +
SY-1246	Cru-MIR393a	Cru-scaffold_4: 11771167-11771330 +	Eutrema salsugineum	Esa-MIR393a	Esa-scaffold_10: 10483751-10483910 +
SY-1247	Cru-MIR393a	Cru-scaffold_4: 11771167-11771330 +	Eutrema salsugineum	Esa-MIR393b	Esa-scaffold_16: 74485-74658 -

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.0001s1256.1	1.0	NA	NA
Carub.0005s0486.1	1.0	NA	NA
Carub.0005s2963.1	1.0	NA	NA
Carub.0006s3387.1	2.0	NA	NA

Mature miRNA conservation

Link

No link
No link

Reference

No reference

Cru-MIR393a

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