Stem-loop sequence mmu-mir-539

Accession

MI0003520 (change log)

Symbol

MGI:Mir539

Description

Mus musculus miR-539 stem-loop

Gene family

MIPF0000018; mir-154

Literature search

11 open access papers mention mmu-mir-539
(18 sentences)

Stem-loop

       ug                 g    -  g cu u 
5' uacu  aggagaaauuauccuug ugug uu g  c u
   ||||  ||||||||||||||||| |||| || |  |  
3' auga  uuuucuuuaauaggaac auac aa u  g u
       gu                 -    u  g ag u 

Deep sequencing

3585 reads, 26.9 reads per million, 52 experiments

Confidence

Annotation confidence: high

Feedback: Do you believe this miRNA is real?

Genome context

• Coordinates (GRCm38; GCA_000001635.2): chr12: 109728129-109728202 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from mmu-mir-539

• mmu-mir-495: chr12: 109718754-109718816 [+]
• mmu-mir-667: chr12: 109720006-109720097 [+]
• mmu-mir-376c: chr12: 109722718-109722803 [+]
• mmu-mir-654: chr12: 109723218-109723301 [+]
• mmu-mir-376b: chr12: 109723458-109723539 [+]
• mmu-mir-376a: chr12: 109723781-109723848 [+]
• mmu-mir-300: chr12: 109724313-109724391 [+]
• mmu-mir-381: chr12: 109726822-109726896 [+]
• mmu-mir-487b: chr12: 109727333-109727414 [+]
• mmu-mir-539: chr12: 109728129-109728202 [+]
• mmu-mir-544: chr12: 109729325-109729402 [+]
• mmu-mir-382: chr12: 109733771-109733846 [+]
• mmu-mir-134: chr12: 109734139-109734209 [+]
• mmu-mir-668: chr12: 109734732-109734797 [+]
• mmu-mir-485: chr12: 109734902-109734974 [+]
• mmu-mir-453: chr12: 109735619-109735700 [+]

Database links

• EntrezGene:Mir539
• MGI:Mir539
• RNAcentral:URS000075D463_10090
• miRBase Tracker:MI0003520

Mature sequence mmu-miR-539-5p

• Accession: MIMAT0003169
• Previous IDs: mmu-miR-539
• Sequence: 8 - ggagaaauuauccuuggugugu - 29
• Deep sequencing: 2962 reads, 50 experiments
• Evidence: experimental; MPSS [2], miRAP-cloned [3], Illumina [4-5]
• Database links:
  • RNAcentral:URS00003E59B7_10090
• Predicted targets:
  • TargetScanVert:mmu-miR-539-5p
  • miRDB:mmu-miR-539-5p
  • microrna.org:mmu-miR-539-5p

Mature sequence mmu-miR-539-3p

• Accession: MIMAT0017208
• Sequence: 48 - cauacaaggauaauuucuuuuu - 69
• Deep sequencing: 618 reads, 44 experiments
• Evidence: experimental; Illumina [5]
• Database links:
  • RNAcentral:URS000053F50A_10090
• Predicted targets:
  • TargetScanVert:mmu-miR-539-3p
  • miRDB:mmu-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:16582102 "The expression profile of microRNAs in mouse embryos" Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K, Mirochnitchenko O, Inouye M, Kato I Nucleic Acids Res. 34:1765-1771(2006).
3. PMID:16973894 "Mouse microRNA profiles determined with a new and sensitive cloning method" Takada S, Berezikov E, Yamashita Y, Lagos-Quintana M, Kloosterman WP, Enomoto M, Hatanaka H, Fujiwara S, Watanabe H, Soda M, Choi YL, Plasterk RH, Cuppen E, Mano H Nucleic Acids Res. 34:e115(2006).
4. PMID:20215419 "MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing" Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A, Marra MA, Rajkovic A Mol Hum Reprod. 16:463-471(2010).
5. PMID:20413612 "Mammalian microRNAs: experimental evaluation of novel and previously annotated genes" Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel DP Genes Dev. 24:992-1009(2010).