PmiREN: Plant microRNA Encyclopedia

Cru-MIR169a

Basic info.

miRNA locus ID
Cru-MIR169a

miRNA locus accession
PmiREN002769

Organism
Capsella rubella

Genomic location
Cru-scaffold_1 18887754 18887872 +

Comments
A member of family MIR169

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

  G     T       T    AT         AT          TT      ACG     TG
   GGAAA AAGAGAA GAGG  GAGCCAAGG  GACTTGCCGA  TTATCA   AATCT  
   ||||| ||||||| ||||  |||||||||  ||||||||||  ||||||   |||||   
   CTTTT TTCTCTT CTTT  CTCGGTTCC  TTGAACGGCT  GGTGGT   TTAGA  
TAG     C       C    GT         AG          -T      --A     CA

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-200	Aly-MIR169d	Aly-scaffold_1: 28725960-28726078 -	Capsella rubella	Cru-MIR169a	Cru-scaffold_1: 18887754-18887872 +
SY-562	Ath-MIR169d	Ath-Chr1: 20039479-20039596 -	Capsella rubella	Cru-MIR169a	Cru-scaffold_1: 18887754-18887872 +
SY-828	Bol-MIR169b	Bol-C03: 56791745-56791864 +	Capsella rubella	Cru-MIR169a	Cru-scaffold_1: 18887754-18887872 +
SY-832	Bol-MIR169e	Bol-C06: 21156226-21156337 -	Capsella rubella	Cru-MIR169a	Cru-scaffold_1: 18887754-18887872 +
SY-1035	Bra-MIR169q	Bra-A06: 679097-679215 -	Capsella rubella	Cru-MIR169a	Cru-scaffold_1: 18887754-18887872 +
SY-1039	Bra-MIR169u	Bra-A08: 1019521-1019639 -	Capsella rubella	Cru-MIR169a	Cru-scaffold_1: 18887754-18887872 +

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
No link

Reference

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