PmiREN: Plant microRNA Encyclopedia

Cru-MIR169c

Basic info.

miRNA locus ID
Cru-MIR169c

miRNA locus accession
PmiREN002771

Organism
Capsella rubella

Genomic location
Cru-scaffold_7 7418995 7419123 +

Comments
A member of family MIR169

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  G     AT      T    TT         AT         ATTCTT      -  -A    TTG
   GAAGA  AGAGAA GAGG  GAGCCAAGG  GACTTGCCG      ACCAAA CG  AATC   
   |||||  |||||| ||||  |||||||||  |||||||||      |||||| ||  ||||   A
   CTTTT  TCTCTT CTTT  CTCGGTTCC  TTGAACGGC      TGGTTT GT  TTAG   
TAG     CT      C    GT         AG         --CTGT      T  AG    TCA

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-208	Aly-MIR169g	Aly-scaffold_7: 9193033-9193153 +	Capsella rubella	Cru-MIR169c	Cru-scaffold_7: 7418995-7419123 +
SY-824	Bol-MIR169a	Bol-C03: 50192527-50192643 +	Capsella rubella	Cru-MIR169c	Cru-scaffold_7: 7418995-7419123 +
SY-1010	Bra-MIR169d	Bra-A01: 6326029-6326149 -	Capsella rubella	Cru-MIR169c	Cru-scaffold_7: 7418995-7419123 +
SY-1038	Bra-MIR169s	Bra-A08: 12392918-12393036 +	Capsella rubella	Cru-MIR169c	Cru-scaffold_7: 7418995-7419123 +
SY-1232	Cru-MIR169c	Cru-scaffold_7: 7418995-7419123 +	Eutrema salsugineum	Esa-MIR169c	Esa-scaffold_1: 7989367-7989491 +

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.0003s0503.1	1.5	NA	NA
Carub.0007s3046.1	2.0	NA	NA
Carub.0008s1615.1	2.0	NA	NA

Mature miRNA conservation

Link

No link
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Reference

>Microsynteny and phylogenetic analysis of tandemly organised miRNA families across five members of Brassicaceae reveals complex retention and loss history. Plant Sci, 2016