Stem-loop rno-mir-542-1

Accession

MI0003528

Description

Rattus norvegicus rno-mir-542-1 precursor miRNA

Literature search

10 open access papers mention rno-mir-542-1
(30 sentences)

Sequence

52834 reads, 44 reads per million, 479 experiments

ucucagacguCUCGGGGAUCAUCAUGUCACGAgauaccacugcgcacuUGUGACAGAUUGAUAACUGAAAggucuggga
((((((((.(.((((..((((...(((((((((.............)))))))))...))))..)))).).))))))))

Structure

        g C    GG    UCA         auacc 
ucucagac u UCGG  AUCA   UGUCACGAg     a
|||||||| | ||||  ||||   |||||||||     c
agggucug A AGUC  UAGU   ACAGUGUuc     u
        g A    AA    UAG         acgcg 

Annotation confidence Medium

Comments

The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies [2]. The ends of the miRNA may be offset with respect to previous annotations.

Genome context

chrX: 158152146-158152224 [+]

Clustered miRNAs

6 other miRNAs are < 10 kb from rno-mir-542-1

Mature rno-miR-542-5p

• Accession: MIMAT0003178
• Description: Rattus norvegicus rno-miR-542-5p mature miRNA
• Sequence: 11 - CUCGGGGAUCAUCAUGUCACGA - 32
• Evidence: experimental ; cloned [1-2], SOLiD [3]

Mature rno-miR-542-3p

• Accession: MIMAT0003179
• Description: Rattus norvegicus rno-miR-542-3p mature miRNA
• Sequence: 49 - UGUGACAGAUUGAUAACUGAAA - 70
• Evidence: experimental ; cloned [2], SOLiD [3]

References

1. PubMed ID: 17604727
   A mammalian microRNA expression atlas based on small RNA library sequencing
   "Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M"
   "Cell (2007) 129:1401-1414


2. 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


3. 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