Stem-loop sequence rno-mir-20b

Accession

MI0003554 (change log)

Description

Rattus norvegicus miR-20b stem-loop

Gene family

MIPF0000001; mir-17

Literature search

32 open access papers mention rno-mir-20b
(69 sentences)

Stem-loop

   gu       -           g     g   -  uuu 
5'   agugcca aagugcucaua ugcag uag gu   g
     ||||||| ||||||||||| ||||| ||| ||    
3'   ucauggu uucacgagugu acguc auc ca   c
   -c       c           g     -   u  cgu 

Deep sequencing

2670 reads, 0 reads per million, 341 experiments

Confidence

Annotation confidence: high

Feedback: Do you believe this miRNA is real?

Comments

The mature sequence shown here represents the most commonly cloned form from large-scale cloning studies [2]. The ends of the miRNA may be offset with respect to previous annotations.

Genome context

• Coordinates (Rnor_6.0; GCA_000001895.4): chrX: 140117518-140117589 [-]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from rno-mir-20b

• rno-mir-17-2: chrX: 140117891-140117968 [-]
• rno-mir-20b: chrX: 140117518-140117589 [-]
• rno-mir-19b-2: chrX: 140117379-140117474 [-]
• rno-mir-92a-2: chrX: 140117249-140117340 [-]
• rno-mir-363: chrX: 140117098-140117184 [-]

Database links

• EntrezGene:Mir20b
• miRBase Tracker:MI0003554

Mature sequence rno-miR-20b-5p

• Accession: MIMAT0003211
• Previous IDs: rno-miR-20b
• Sequence: 8 - caaagugcucauagugcagguag - 30
• Deep sequencing: 1950 reads, 311 experiments
• Evidence: experimental; SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-20b-5p
  • miRDB:rno-miR-20b-5p
  • microrna.org:rno-miR-20b-5p

Mature sequence rno-miR-20b-3p

• Accession: MIMAT0003212
• Previous IDs: rno-miR-20b*
• Sequence: 46 - acugcagugugagcacuucugg - 67
• Deep sequencing: 719 reads, 205 experiments
• Evidence: experimental; cloned [1-2], SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-20b-3p
  • miRDB:rno-miR-20b-3p
  • microrna.org:rno-miR-20b-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: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: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).