Stem-loop rno-mir-540

Accession

MI0003524

Description

Rattus norvegicus rno-mir-540 precursor miRNA

Gene family

MIPF0000212; mir-540

Literature search

3 open access papers mention rno-mir-540
(3 sentences)

Sequence

24468 reads, 48 reads per million, 331 experiments

cccuggggcugggcCAAGGGUCACCCUCUGACUCUGUggccaaggguagacAGGUCAGAGGUCGAUCCUGGGCcuacucugggg
((((((((.((((((.((((((..((((((((.((((.(((...)))..))))))))))))..)))))).))))))))))))))

Structure

        c      A      AC        U    -g   a 
cccugggg ugggcC AGGGUC  CCUCUGAC CUGU  gcc  
|||||||| |||||| ||||||  |||||||| ||||  ||| a
ggggucuc aucCGG UCCUAG  GGAGACUG GAca  ugg  
        -      G      CU        -    ga   g 

Annotation confidence High

Genome context

chr6: 133706202-133706285 [+]

Clustered miRNAs

9 other miRNAs are < 10 kb from rno-mir-540

Mature rno-miR-540-5p

• Accession: MIMAT0017211
• Description: Rattus norvegicus rno-miR-540-5p mature miRNA
• Sequence: 15 - CAAGGGUCACCCUCUGACUCUGU - 37
• Evidence: experimental ; SOLiD [2]

Mature rno-miR-540-3p

• Accession: MIMAT0003174
• Description: Rattus norvegicus rno-miR-540-3p mature miRNA
• Sequence: 52 - AGGUCAGAGGUCGAUCCUGGGC - 73
• Evidence: experimental ; SOLiD [2]

References

1. PubMed ID: 20403161
   Small RNA expression and strain specificity in the rat
   Linsen SE, de Wit E, de Bruijn E, Cuppen E
   BMC Genomics (2010) 11:249


2. PubMed ID: 16274478
   Identification of clustered microRNAs using an ab initio prediction method
   Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T, van Nimwegen E, Zavolan M
   BMC Bioinformatics (2005) 6:267