Stem-loop sequence rno-mir-543

Accession

MI0003525 (change log)

Description

Rattus norvegicus miR-543 stem-loop

Gene family

MIPF0000110; mir-329

Literature search

4 open access papers mention rno-mir-543
(16 sentences)

Stem-loop

         u  u       u  -     --      -    uu 
5' ggugcu aa gagaagu gc ccgcg  uguuuu ucgc  u
   |||||| || ||||||| || |||||  |||||| ||||  a
3' cuacga uu uucuuca cg ggcgc  acaaag agug  u
         c  u       -  u     uu      c    ua 

Deep sequencing

17917 reads, 4.73 reads per million, 296 experiments

Confidence

Annotation confidence: high

Feedback: Do you believe this miRNA is real?

Genome context

• Coordinates (Rnor_6.0; GCA_000001895.4): chr6: 133866660-133866739 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from rno-mir-543

• 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 [+]
• rno-mir-495: chr6: 133868288-133868367 [+]
• rno-mir-667: chr6: 133869570-133869661 [+]
• rno-mir-376c: chr6: 133872439-133872522 [+]
• rno-mir-376b: chr6: 133873095-133873180 [+]
• rno-mir-3595: chr6: 133873587-133873706 [-]
• rno-mir-376a: chr6: 133873605-133873686 [+]
• rno-mir-300: chr6: 133874152-133874230 [+]
• rno-mir-381: chr6: 133876615-133876675 [+]

Database links

• EntrezGene:Mir543
• miRBase Tracker:MI0003525

Mature sequence rno-miR-543-5p

• Accession: MIMAT0004787
• Previous IDs: rno-miR-543
• Sequence: 14 - aaguugcccgcguguuuuucg - 34
• Deep sequencing: 1908 reads, 161 experiments
• Evidence: experimental; cloned [2], SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-543-5p
  • miRDB:rno-miR-543-5p
  • microrna.org:rno-miR-543-5p

Mature sequence rno-miR-543-3p

• Accession: MIMAT0003175
• Previous IDs: rno-miR-543;rno-miR-543*
• Sequence: 49 - aaacauucgcggugcacuucu - 69
• Deep sequencing: 16000 reads, 285 experiments
• Evidence: experimental; SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-543-3p
  • miRDB:rno-miR-543-3p
  • microrna.org:rno-miR-543-3p

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).