Stem-loop sequence mmu-mir-540

Accession

MI0003518 (change log)

Symbol

MGI:Mir540

Description

Mus musculus miR-540 stem-loop

Gene family

MIPF0000212; mir-540

Literature search

5 open access papers mention mmu-mir-540
(15 sentences)

Stem-loop

         a      ac        u    -g     
5' ugggcc aggguc  ccucugac cugu  gcca 
   |||||| ||||||  |||||||| ||||  ||| a
3' auccgg uccuag  ggagacug gaca  uggg 
         g      cu        -    ga     

Deep sequencing

29437 reads, 88.2 reads per million, 85 experiments

Confidence

Annotation confidence: high

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Genome context

• Coordinates (GRCm38; GCA_000001635.2): chr12: 109586080-109586146 [+]
• Overlapping transcripts:

  sense

  ENSMUST00000102167 ; Mir540-201; exon 1

Clustered miRNAs

< 10kb from mmu-mir-540

• mmu-mir-493: chr12: 109580233-109580315 [+]
• mmu-mir-337: chr12: 109585789-109585885 [+]
• mmu-mir-3544: chr12: 109585813-109585873 [-]
• mmu-mir-540: chr12: 109586080-109586146 [+]
• mmu-mir-665: chr12: 109586314-109586407 [+]
• mmu-mir-3070-1: chr12: 109587943-109588031 [+]
• mmu-mir-3070-2: chr12: 109588592-109588680 [+]
• mmu-mir-431: chr12: 109590447-109590537 [+]
• mmu-mir-433: chr12: 109591715-109591838 [+]
• mmu-mir-127: chr12: 109592846-109592915 [+]
• mmu-mir-434: chr12: 109594506-109594599 [+]
• mmu-mir-432: chr12: 109594956-109595030 [+]
• mmu-mir-3071: chr12: 109595318-109595397 [-]
• mmu-mir-136: chr12: 109595327-109595388 [+]

Database links

• EntrezGene:Mir540
• MGI:Mir540
• RNAcentral:URS0000759CB8_10090
• miRBase Tracker:MI0003518

Mature sequence mmu-miR-540-5p

• Accession: MIMAT0004786
• Sequence: 6 - caagggucacccucugacucugu - 28
• Deep sequencing: 3471 reads, 69 experiments
• Evidence: experimental; cloned [3], Illumina [4-5]
• Database links:
  • RNAcentral:URS000030F0C5_10090
• Predicted targets:
  • TargetScanVert:mmu-miR-540-5p
  • miRDB:mmu-miR-540-5p
  • microrna.org:mmu-miR-540-5p

Mature sequence mmu-miR-540-3p

• Accession: MIMAT0003167
• Previous IDs: mmu-miR-540
• Sequence: 43 - aggucagaggucgauccugg - 62
• Deep sequencing: 25961 reads, 80 experiments
• Evidence: experimental; cloned [1,3], miRAP-cloned [2], Illumina [4]
• Database links:
  • RNAcentral:URS00005B165A_10090
• Predicted targets:
  • TargetScanVert:mmu-miR-540-3p
  • miRDB:mmu-miR-540-3p
  • microrna.org:mmu-miR-540-3p

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: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).
3. 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).
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).