Stem-loop sequence rno-mir-540

Accession

MI0003524 (change log)

Description

Rattus norvegicus miR-540 stem-loop

Gene family

MIPF0000212; mir-540

Literature search

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

Stem-loop

      ug   c      a      ac        u    -g     
5' ccc  ggg ugggcc aggguc  ccucugac cugu  gcca 
   |||  ||| |||||| ||||||  |||||||| ||||  ||| a
3' ggg  cuc auccgg uccuag  ggagacug gaca  uggg 
      gu   -      g      cu        -    ga     

Deep sequencing

28933 reads, 13.5 reads per million, 348 experiments

Confidence

Annotation confidence: high

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Genome context

• Coordinates (Rnor_6.0; GCA_000001895.4): chr6: 133706202-133706285 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from rno-mir-540

• rno-mir-493: chr6: 133699509-133699592 [+]
• rno-mir-337: chr6: 133705920-133706016 [+]
• rno-mir-3544: chr6: 133705932-133706019 [-]
• rno-mir-540: chr6: 133706202-133706285 [+]
• rno-mir-665: chr6: 133706457-133706550 [+]
• rno-mir-431: chr6: 133711425-133711538 [+]
• rno-mir-433: chr6: 133712334-133712426 [+]
• rno-mir-127: chr6: 133713430-133713526 [+]
• rno-mir-3543-1: chr6: 133715345-133715459 [-]
• rno-mir-434-1: chr6: 133715378-133715458 [+]

Database links

• EntrezGene:Mir540
• miRBase Tracker:MI0003524

Mature sequence rno-miR-540-5p

• Accession: MIMAT0017211
• Previous IDs: rno-miR-540*
• Sequence: 15 - caagggucacccucugacucugu - 37
• Deep sequencing: 5275 reads, 245 experiments
• Evidence: experimental; SOLiD [2]
• Predicted targets:
  • TargetScanVert:rno-miR-540-5p
  • miRDB:rno-miR-540-5p

Mature sequence rno-miR-540-3p

• Accession: MIMAT0003174
• Previous IDs: rno-miR-540
• Sequence: 52 - aggucagaggucgauccugggc - 73
• Deep sequencing: 23653 reads, 328 experiments
• Evidence: experimental; SOLiD [2]
• Predicted targets:
  • TargetScanVert:rno-miR-540-3p
  • miRDB:rno-miR-540-3p
  • microrna.org:rno-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: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).