Stem-loop sequence rno-mir-199a

Accession

MI0000941 (change log)

Description

Rattus norvegicus miR-199a stem-loop

Gene family

MIPF0000040; mir-199

Literature search

67 open access papers mention rno-mir-199a
(253 sentences)

Stem-loop

   uggaagcuu    aga    -    c   gcc       u        c   --uca  ac 
5'          cugg   uccu gcuc guc   ccagugu cagacuac ugu     gg  a
            ||||   |||| |||| |||   ||||||| |||||||| |||     ||   
3'          gacc   ggga cggg cag   gguuaca gucugaug aca     cc  a
   -------ac    ---    a    u   auu       c        -   uguug  gu 

Deep sequencing

1537961 reads, 904 reads per million, 491 experiments

Confidence

Annotation confidence: high

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Genome context

• Coordinates (Rnor_6.0; GCA_000001895.4): chr13: 80125487-80125596 [+]
• Overlapping transcripts:

  sense

  ENSRNOT00000044190 ; rno-mir-199a-201; 3'UTR (exon 1)

  antisense

  ENSRNOT00000064219 ; Dnm3-204; intron 14

  ENSRNOT00000068490 ; Dnm3-201; intron 15

  ENSRNOT00000047799 ; Dnm3-202; intron 15

  ENSRNOT00000067653 ; Dnm3-203; intron 15

  ENSRNOT00000041058 ; Dnm3-205; intron 15

Clustered miRNAs

< 10kb from rno-mir-199a

• rno-mir-199a: chr13: 80125487-80125596 [+]
• rno-mir-214: chr13: 80130905-80131014 [+]
• rno-mir-3120: chr13: 80130909-80131025 [-]

Database links

• EntrezGene:Mir199a
• miRBase Tracker:MI0000941

Mature sequence rno-miR-199a-5p

• Accession: MIMAT0000872
• Previous IDs: rno-miR-199a
• Sequence: 31 - cccaguguucagacuaccuguuc - 53
• Deep sequencing: 201438 reads, 478 experiments
• Evidence: experimental; cloned [1], SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-199a-5p
  • miRDB:rno-miR-199a-5p
  • microrna.org:rno-miR-199a-5p

Mature sequence rno-miR-199a-3p

• Accession: MIMAT0004738
• Sequence: 70 - acaguagucugcacauugguua - 91
• Deep sequencing: 1336503 reads, 489 experiments
• Evidence: experimental; cloned [2], SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-199a-3p
  • miRDB:rno-miR-199a-3p
  • microrna.org:rno-miR-199a-3p

References

1. PMID:16766679 "Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes" Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N, Imai H Genes Dev. 20:1732-1743(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: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).