Stem-loop sequence rno-mir-17-1

Accession

MI0000845 (change log)

Previous IDs

rno-mir-17

Description

Rattus norvegicus miR-17-1 stem-loop

Gene family

MIPF0000001; mir-17

Literature search

72 open access papers mention rno-mir-17-1
(564 sentences)

Stem-loop

        g         -        a  g     guagu    u 
5' gucag auaauguca aagugcuu ca ugcag     ggug g
   ||||| ||||||||| |||||||| || |||||     ||||  
3' caguc uguuacggu uucacgga gu acguc     cuac u
        g         g        a  g     ---au    g 

Deep sequencing

105039 reads, 42.6 reads per million, 495 experiments

Confidence

Annotation confidence: high

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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): chr15: 100179879-100179962 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from rno-mir-17-1

• rno-mir-17-1: chr15: 100179879-100179962 [+]
• rno-mir-18a: chr15: 100180015-100180110 [+]
• rno-mir-19a: chr15: 100180162-100180243 [+]
• rno-mir-20a: chr15: 100180334-100180418 [+]
• rno-mir-19b-1: chr15: 100180464-100180550 [+]
• rno-mir-92a-1: chr15: 100180586-100180663 [+]

Database links

• EntrezGene:Mir17-1
• miRBase Tracker:MI0000845

Mature sequence rno-miR-17-5p

• Accession: MIMAT0000786
• Previous IDs: rno-miR-17
• Sequence: 14 - caaagugcuuacagugcagguag - 36
• Deep sequencing: 192321 reads, 492 experiments
• Evidence: experimental; cloned [1-2], SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-17-5p
  • miRDB:rno-miR-17-5p
  • microrna.org:rno-miR-17-5p

Mature sequence rno-miR-17-1-3p

• Accession: MIMAT0004710
• Previous IDs: rno-miR-17-3p
• Sequence: 51 - acugcagugaaggcacuugugg - 72
• Deep sequencing: 8924 reads, 472 experiments
• Evidence: experimental; cloned [2], SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-17-1-3p
  • miRDB:rno-miR-17-1-3p
  • microrna.org:rno-miR-17-1-3p

References

1. PMID:15345052 "Microarray analysis of microRNA expression in the developing mammalian brain" Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P, Constantine-Paton M, Horvitz HR Genome Biol. 5:R68(2004).
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).