Stem-loop sequence rno-mir-379

Accession

MI0003541 (change log)

Description

Rattus norvegicus miR-379 stem-loop

Gene family

MIPF0000126; mir-379

Literature search

5 open access papers mention rno-mir-379
(19 sentences)

Stem-loop

   u  uuc   c    g    a       ga       -  uua 
5'  gg   cug agag uggu gacuaug  acguagg cg   u
    ||   ||| |||| |||| |||||||  ||||||| ||   g
3'  cc   gac ucuc auca cugguac  uguaucc gu   u
   a  uau   -    a    c       aa       a  cuu 

Deep sequencing

114069 reads, 56.6 reads per million, 422 experiments

Confidence

Annotation confidence: high

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Genome context

• Coordinates (Rnor_6.0; GCA_000001895.4): chr6: 133857700-133857784 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from rno-mir-379

• rno-mir-379: chr6: 133857700-133857784 [+]
• rno-mir-411: chr6: 133858849-133858924 [+]
• rno-mir-299b: chr6: 133859295-133859412 [-]
• rno-mir-299a: chr6: 133859324-133859386 [+]
• rno-mir-3579: chr6: 133860473-133860585 [-]
• rno-mir-380: chr6: 133860490-133860566 [+]
• rno-mir-323: chr6: 133861199-133861284 [+]
• rno-mir-758: chr6: 133861498-133861575 [+]
• rno-mir-329: chr6: 133862168-133862264 [+]
• rno-mir-494: chr6: 133864370-133864452 [+]
• rno-mir-679: chr6: 133864564-133864700 [+]
• rno-mir-1193: chr6: 133864698-133864817 [+]
• rno-mir-666: chr6: 133866523-133866621 [+]
• rno-mir-543: chr6: 133866660-133866739 [+]

Database links

• EntrezGene:Mir379
• miRBase Tracker:MI0003541

Mature sequence rno-miR-379-5p

• Accession: MIMAT0003192
• Previous IDs: rno-miR-379
• Sequence: 16 - ugguagacuauggaacguagg - 36
• Deep sequencing: 46297 reads, 382 experiments
• Evidence: experimental; cloned [2], SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-379-5p
  • miRDB:rno-miR-379-5p
  • microrna.org:rno-miR-379-5p

Mature sequence rno-miR-379-3p

• Accession: MIMAT0004791
• Previous IDs: rno-miR-379*
• Sequence: 52 - cuauguaacaugguccacuaac - 73
• Deep sequencing: 67556 reads, 400 experiments
• Evidence: experimental; cloned [2], SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-379-3p
  • miRDB:rno-miR-379-3p
  • microrna.org:rno-miR-379-3p

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).