PmiREN: Plant microRNA Encyclopedia

Ath-MIR162b

Basic info.

miRNA locus ID
Ath-MIR162b

miRNA locus accession
PmiREN000655

Organism
Arabidopsis thaliana

Genomic location
Ath-Chr5 7740590 7740715 -

Comments
A member of family MIR162

Confidence level

Secondary strurture and sequence

mature sequence star sequence

5'

3'

          AA    GA  T       G    C    C       A    ------C        TTTA
     GAGGA  GAGT  AG CGCTGGA GCAG GGTT ATCGATC ATTC       TGTGAATA    
     |||||  ||||  || ||||||| |||| |||| ||||||| ||||       ||||||||     
     CTTCT  TTCG  TC GCGACCT CGTC CCAA TAGCTAG TAAG       ACATTTGT    
CAGTA     CG    --  -       A    T    A       C    AACGAAA        TTTT

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-83	Aly-MIR162b	Aly-scaffold_6: 9808812-9808933 -	Arabidopsis thaliana	Ath-MIR162b	Ath-Chr5: 7740590-7740715 -
SY-464	Ath-MIR162a	Ath-Chr5: 2634916-2635038 -	Arabidopsis thaliana	Ath-MIR162b	Ath-Chr5: 7740590-7740715 -
SY-469	Ath-MIR162b	Ath-Chr5: 7740590-7740715 -	Brassica oleracea	Bol-MIR162	Bol-C07: 36847915-36848047 +
SY-470	Ath-MIR162b	Ath-Chr5: 7740590-7740715 -	Brassica rapa	Bra-MIR162a	Bra-A03: 22089695-22089829 +
SY-471	Ath-MIR162b	Ath-Chr5: 7740590-7740715 -	Eutrema salsugineum	Esa-MIR162b	Esa-scaffold_6: 2732097-2732235 -

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.
AT5G01420.1	NA	2	1 (1)
AT1G23490.1	NA	NA	2 (2)
AT3G50685.1	NA	NA	2 (1)
AT3G59800.1	NA	NA	2 (1)
AT5G59450.1	NA	NA	2 (2)
AT2G23180.1	2.0	NA	NA

Mature miRNA conservation

Link

Reference

>In Medicago truncatula, water deficit modulates the transcript accumulation of components of small RNA pathways. BMC Plant Biol, 2011

>Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts. Plant Physiol, 2006