Stem-loop sequence rno-mir-23b

Accession

MI0000853 (change log)

Description

Rattus norvegicus miR-23b stem-loop

Gene family

MIPF0000027; mir-23

Literature search

39 open access papers mention rno-mir-23b
(219 sentences)

Stem-loop

   cuca  -u c  -   c   u   --          -  c      gugacu 
5'     cc  g uc ugg ugc ugg  guuccuggca ug ugauuu      u
       ||  | || ||| ||| |||  |||||||||| || ||||||       
3'     gg  c ag acc acg acc  uagggaccgu ac acuaaa      g
   ---c  uu c  u   a   c   au          u  -      auuaga 

Deep sequencing

1490569 reads, 1.21e+03 reads per million, 510 experiments

Confidence

Annotation confidence: high

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Genome context

• Coordinates (Rnor_6.0; GCA_000001895.4): chr17: 823222-823318 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from rno-mir-23b

• rno-mir-23b: chr17: 823222-823318 [+]
• rno-mir-27b: chr17: 823461-823557 [+]
• rno-mir-3074: chr17: 823940-824056 [-]
• rno-mir-24-1: chr17: 823968-824035 [+]

Database links

• EntrezGene:Mir23b
• miRBase Tracker:MI0000853

Mature sequence rno-miR-23b-5p

• Accession: MIMAT0017099
• Previous IDs: rno-miR-23b*
• Sequence: 21 - ggguuccuggcaugcugauuu - 41
• Deep sequencing: 217 reads, 134 experiments
• Evidence: experimental; SOLiD [4]
• Predicted targets:
  • TargetScanVert:rno-miR-23b-5p
  • miRDB:rno-miR-23b-5p

Mature sequence rno-miR-23b-3p

• Accession: MIMAT0000793
• Previous IDs: rno-miR-23b
• Sequence: 58 - aucacauugccagggauuacc - 78
• Deep sequencing: 1490107 reads, 510 experiments
• Evidence: experimental; cloned [1-3], SOLiD [4]
• Predicted targets:
  • TargetScanVert:rno-miR-23b-3p
  • miRDB:rno-miR-23b-3p
  • microrna.org:rno-miR-23b-3p

References

1. PMID:16766679 "Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes" Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N, Imai H Genes Dev. 20:1732-1743(2006).
2. 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).
3. PMID:17805466 "Cloning and identification of novel microRNAs from rat hippocampus" He X, Zhang Q, Liu Y, Pan X Acta Biochim Biophys Sin (Shanghai). 39:708-714(2007).
4. 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).