Stem-loop sequence rno-mir-880

Accession

MI0006122 (change log)

Description

Rattus norvegicus miR-880 stem-loop

Gene family

MIPF0000433; mir-880

Literature search

4 open access papers mention rno-mir-880
(8 sentences)

Stem-loop

   --   ac   aa        u   uau    c  uuccu 
5'   ugc  ugc  uacucaga ugg   gagu ac     a
     |||  |||  |||||||| |||   |||| ||      
3'   acg  acg  augagucu acu   cuca ug     a
   ac   ga   ag        u   uac    u  uacaa 

Deep sequencing

996 reads, 71.9 reads per million, 32 experiments

Confidence

Annotation confidence: not enough data

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Genome context

• Coordinates (Rnor_6.0; GCA_000001895.4): chrX: 151281988-151282065 [-]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from rno-mir-880

• rno-mir-871: chrX: 151287787-151287863 [-]
• rno-mir-881: chrX: 151283910-151283986 [-]
• rno-mir-878: chrX: 151283461-151283537 [-]
• rno-mir-880: chrX: 151281988-151282065 [-]
• rno-mir-463: chrX: 151276029-151276106 [-]
• rno-mir-741: chrX: 151274356-151274451 [-]
• rno-mir-3551: chrX: 151272824-151272905 [-]
• rno-mir-471: chrX: 151272104-151272181 [-]

Database links

• EntrezGene:Mir880
• miRBase Tracker:MI0006122

Mature sequence rno-miR-880-5p

• Accession: MIMAT0017292
• Previous IDs: rno-miR-880*
• Sequence: 11 - uacucagauugguaugaguca - 31
• Deep sequencing: 5 reads, 5 experiments
• Evidence: experimental; SOLiD [2]
• Predicted targets:
  • TargetScanVert:rno-miR-880-5p
  • miRDB:rno-miR-880-5p

Mature sequence rno-miR-880-3p

• Accession: MIMAT0005288
• Previous IDs: rno-miR-880
• Sequence: 47 - uacuccauucauucugaguaga - 68
• Deep sequencing: 991 reads, 31 experiments
• Evidence: experimental; cloned [1], SOLiD [2]
• Predicted targets:
  • TargetScanVert:rno-miR-880-3p
  • miRDB:rno-miR-880-3p
  • microrna.org:rno-miR-880-3p

References

1. 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).
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).