Stem-loop sequence mmu-mir-878

Accession

MI0005548 (change log)

Symbol

MGI:Mir878

Description

Mus musculus miR-878 stem-loop

Gene family

MIPF0000434; mir-878

Literature search

3 open access papers mention mmu-mir-878
(4 sentences)

Stem-loop

   --u  aa g           -   a     a a   guga 
5'    gc  u cuuuaucuagu ugg uguca g cac    a
      ||  | ||||||||||| ||| ||||| | |||    a
3'    cg  a gagauggguca acc acagu c gug    c
   acu  gg g           c   -     a -   aauu 

Deep sequencing

103662 reads, 959 reads per million, 49 experiments

Confidence

Annotation confidence: high

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Comments

This sequence was identified as a miRNA candidate by Berezikov et al. using RAKE and MPSS techniques [1]. Expression was later confirmed by cloning [2].

Genome context

• Coordinates (GRCm38; GCA_000001635.2): chrX: 66801508-66801585 [-]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from mmu-mir-878

• mmu-mir-871: chrX: 66810428-66810504 [-]
• mmu-mir-881: chrX: 66801944-66802021 [-]
• mmu-mir-878: chrX: 66801508-66801585 [-]
• mmu-mir-880: chrX: 66800530-66800607 [-]
• mmu-mir-463: chrX: 66799223-66799297 [-]
• mmu-mir-741: chrX: 66796805-66796875 [-]
• mmu-mir-471: chrX: 66792595-66792661 [-]

Database links

• EntrezGene:Mir878
• MGI:Mir878
• RNAcentral:URS000075C531_10090
• miRBase Tracker:MI0005548

Mature sequence mmu-miR-878-5p

• Accession: MIMAT0004932
• Sequence: 11 - uaucuaguuggaugucaagaca - 32
• Deep sequencing: 84680 reads, 39 experiments
• Evidence: experimental; cloned [2], 454 [3], Illumina [4-5]
• Database links:
  • RNAcentral:URS000033285F_10090
• Predicted targets:
  • TargetScanVert:mmu-miR-878-5p
  • miRDB:mmu-miR-878-5p
  • microrna.org:mmu-miR-878-5p

Mature sequence mmu-miR-878-3p

• Accession: MIMAT0004933
• Sequence: 47 - gcaugacaccacacuggguaga - 68
• Deep sequencing: 18980 reads, 44 experiments
• Evidence: experimental; cloned [2], Illumina [4-5]
• Database links:
  • RNAcentral:URS000055B084_10090
• Predicted targets:
  • TargetScanVert:mmu-miR-878-3p
  • miRDB:mmu-miR-878-3p
  • microrna.org:mmu-miR-878-3p

References

1. PMID:16954537 "Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis" Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J, Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano H, Plasterk R, Cuppen E Genome Res. 16:1289-1298(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:17989215 "RNA sequence analysis defines Dicer's role in mouse embryonic stem cells" Calabrese JM, Seila AC, Yeo GW, Sharp PA Proc Natl Acad Sci U S A. 104:18097-18102(2007).
4. PMID:20215419 "MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing" Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A, Marra MA, Rajkovic A Mol Hum Reprod. 16:463-471(2010).
5. PMID:20413612 "Mammalian microRNAs: experimental evaluation of novel and previously annotated genes" Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel DP Genes Dev. 24:992-1009(2010).