Stem-loop sequence rno-mir-1

Accession

MI0003489 (change log)

Description

Rattus norvegicus miR-1 stem-loop

Gene family

MIPF0000038; mir-1

Literature search

126 open access papers mention rno-mir-1
(898 sentences)

Stem-loop

                c                ac     ugaaca 
5' ugccuacucagag acauacuucuuuaugu  ccaua      u
   ||||||||||||| ||||||||||||||||  |||||       
3' auggauggguuuu ugugugaagaaaugua  gguau      a
                a                -a     cguaag 

Deep sequencing

527149 reads, 343 reads per million, 403 experiments

Confidence

Annotation confidence: not enough data

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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): chr18: 2054933-2055019 [-]
• Overlapping transcripts:

  antisense

  ENSRNOT00000053646 ; Mir3571-201; exon 1

  ENSRNOT00000018025 ; Mib1-201; intron 12

Clustered miRNAs

< 10kb from rno-mir-1

• rno-mir-1: chr18: 2054933-2055019 [-]
• rno-mir-3571: chr18: 2054922-2055032 [+]
• rno-mir-133a: chr18: 2052478-2052564 [-]
• rno-mir-133c: chr18: 2052459-2052576 [+]

Database links

• EntrezGene:Mir1
• miRBase Tracker:MI0003489

Mature sequence rno-miR-1-5p

• Accession: MIMAT0003162
• Previous IDs: rno-miR-1*
• Sequence: 13 - gcacauacuucuuuauguaccc - 34
• Deep sequencing: 14 reads, 11 experiments
• Evidence: experimental; SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-1-5p
  • miRDB:rno-miR-1-5p
  • microrna.org:rno-miR-1-5p

Mature sequence rno-miR-1-3p

• Accession: MIMAT0003125
• Previous IDs: rno-miR-1
• Sequence: 54 - uggaauguaaagaaguguguau - 75
• Deep sequencing: 527035 reads, 404 experiments
• Evidence: experimental; cloned [2], SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-1-3p
  • miRDB:rno-miR-1-3p
  • microrna.org:rno-miR-1-3p

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).