Stem-loop sequence rno-mir-539

Accession

MI0003526 (change log)

Description

Rattus norvegicus miR-539 stem-loop

Gene family

MIPF0000018; mir-154

Literature search

5 open access papers mention rno-mir-539
(23 sentences)

Stem-loop

                           g    -    cu u 
5' auacuugaggagaaauuauccuug ugug uuug  c u
   |||||||||||||||||||||||| |||| ||||  |  
3' uaugagcuuuucuuuaaugggaac auac aagu  g u
                           -    u    ag u 

Deep sequencing

16501 reads, 0.342 reads per million, 292 experiments

Confidence

Annotation confidence: high

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Genome context

• Coordinates (Rnor_6.0; GCA_000001895.4): chr6: 133877832-133877907 [+]
• Overlapping transcripts:

  antisense

  ENSRNOT00000054596 ; Mir3576-201; exon 1

Clustered miRNAs

< 10kb from rno-mir-539

• rno-mir-495: chr6: 133868288-133868367 [+]
• rno-mir-667: chr6: 133869570-133869661 [+]
• rno-mir-376c: chr6: 133872439-133872522 [+]
• rno-mir-376b: chr6: 133873095-133873180 [+]
• rno-mir-3595: chr6: 133873587-133873706 [-]
• rno-mir-376a: chr6: 133873605-133873686 [+]
• rno-mir-300: chr6: 133874152-133874230 [+]
• rno-mir-381: chr6: 133876615-133876675 [+]
• rno-mir-487b: chr6: 133877124-133877205 [+]
• rno-mir-3576: chr6: 133877812-133877926 [-]
• rno-mir-539: chr6: 133877832-133877907 [+]
• rno-mir-6331: chr6: 133878578-133878700 [+]
• rno-mir-544: chr6: 133879169-133879246 [+]
• rno-mir-3592: chr6: 133884161-133884276 [-]
• rno-mir-382: chr6: 133884178-133884257 [+]
• rno-mir-134: chr6: 133884547-133884619 [+]
• rno-mir-668: chr6: 133885141-133885208 [+]
• rno-mir-485: chr6: 133885299-133885377 [+]

Database links

• EntrezGene:Mir539
• miRBase Tracker:MI0003526

Mature sequence rno-miR-539-5p

• Accession: MIMAT0003176
• Previous IDs: rno-miR-539
• Sequence: 9 - ggagaaauuauccuuggugugu - 30
• Deep sequencing: 11374 reads, 260 experiments
• Evidence: experimental; cloned [2], SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-539-5p
  • miRDB:rno-miR-539-5p
  • microrna.org:rno-miR-539-5p

Mature sequence rno-miR-539-3p

• Accession: MIMAT0017212
• Previous IDs: rno-miR-539*
• Sequence: 49 - cauacaaggguaauuucuuuuc - 70
• Deep sequencing: 5124 reads, 230 experiments
• Evidence: experimental; SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-539-3p
  • miRDB:rno-miR-539-3p

References

1. PMID: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. 6:267(2005).
2. PMID: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. 129:1401-1414(2007).
3. PMID:20403161 "Small RNA expression and strain specificity in the rat" Linsen SE, de Wit E, de Bruijn E, Cuppen E BMC Genomics. 11:249(2010).