Stem-loop sequence rno-mir-500

Accession

MI0006153 (change log)

Description

Rattus norvegicus miR-500 stem-loop

Gene family

MIPF0000139; mir-500

Literature search

10 open access papers mention rno-mir-500
(51 sentences)

Stem-loop

   -cc  c     -         uau ug     uuag   uau 
5'    cc ucucu aauccuugc   c  ggugc    ugc   c
      || ||||| |||||||||   |  |||||    |||   u
3'    gg agaga uugggaacg   g  ccacg    acg   c
   agu  a     c         --- gu     --ua   uaa 

Deep sequencing

12259 reads, 0.208 reads per million, 481 experiments

Confidence

Annotation confidence: high

Feedback: Do you believe this miRNA is real?

Genome context

• Coordinates (Rnor_6.0; GCA_000001895.4): chrX: 16121332-16121411 [+]
• Overlapping transcripts:

  sense

  ENSRNOT00000054385 ; Mir500-201; exon 1

Clustered miRNAs

< 10kb from rno-mir-500

• rno-mir-362: chrX: 16117170-16117234 [+]
• rno-mir-3560: chrX: 16117863-16117974 [-]
• rno-mir-501: chrX: 16117874-16117957 [+]
• rno-mir-500: chrX: 16121332-16121411 [+]

Database links

• EntrezGene:Mir500
• miRBase Tracker:MI0006153

Mature sequence rno-miR-500-5p

• Accession: MIMAT0017311
• Previous IDs: rno-miR-500*
• Sequence: 11 - aauccuugcuaucugggugcuuag - 34
• Deep sequencing: 244 reads, 146 experiments
• Evidence: experimental; SOLiD [2]
• Predicted targets:
  • TargetScanVert:rno-miR-500-5p
  • miRDB:rno-miR-500-5p

Mature sequence rno-miR-500-3p

• Accession: MIMAT0005321
• Previous IDs: rno-miR-500
• Sequence: 49 - aaugcaccugggcaaggguuca - 70
• Deep sequencing: 12014 reads, 480 experiments
• Evidence: experimental; cloned [1], SOLiD [2]
• Predicted targets:
  • TargetScanVert:rno-miR-500-3p
  • miRDB:rno-miR-500-3p
  • microrna.org:rno-miR-500-3p

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).