Stem-loop sequence rno-mir-541

Accession

MI0003527 (change log)

Description

Rattus norvegicus miR-541 stem-loop

Gene family

MIPF0000213; mir-541

Literature search

5 open access papers mention rno-mir-541
(5 sentences)

Stem-loop

       a  u     aag        a    g     a uccaaga 
5' gcca aa cagag   ggauucug uguu gucac c       a
   |||| || |||||   |||||||| |||| ||||| |       u
3' cggu uu gucuc   ccuaagac acaa cggug g       u
       a  c     aua        -    g     a uaaaauu 

Deep sequencing

443679 reads, 981 reads per million, 480 experiments

Confidence

Annotation confidence: high

Feedback: Do you believe this miRNA is real?

Genome context

• Coordinates (Rnor_6.0; GCA_000001895.4): chr6: 133892655-133892744 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from rno-mir-541

• rno-mir-3592: chr6: 133884161-133884276 [-]
• rno-mir-382: chr6: 133884178-133884257 [+]
• rno-mir-134: chr6: 133884547-133884619 [+]
• rno-mir-668: chr6: 133885141-133885208 [+]
• rno-mir-485: chr6: 133885299-133885377 [+]
• rno-mir-154: chr6: 133888586-133888669 [+]
• rno-mir-496: chr6: 133889283-133889361 [+]
• rno-mir-377: chr6: 133890690-133890761 [+]
• rno-mir-541: chr6: 133892655-133892744 [+]
• rno-mir-409b: chr6: 133893418-133893497 [-]
• rno-mir-409a: chr6: 133893419-133893495 [+]
• rno-mir-412: chr6: 133893571-133893640 [+]
• rno-mir-3578: chr6: 133893672-133893788 [-]
• rno-mir-369: chr6: 133893693-133893771 [+]
• rno-mir-410: chr6: 133893997-133894072 [+]
• rno-mir-3072: chr6: 133898795-133898905 [+]

Database links

• EntrezGene:Mir541
• miRBase Tracker:MI0003527

Mature sequence rno-miR-541-5p

• Accession: MIMAT0003177
• Previous IDs: rno-miR-541
• Sequence: 14 - aagggauucugauguuggucacacu - 38
• Deep sequencing: 443251 reads, 480 experiments
• Evidence: experimental; cloned [2], SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-541-5p
  • miRDB:rno-miR-541-5p
  • microrna.org:rno-miR-541-5p

Mature sequence rno-miR-541-3p

• Accession: MIMAT0017213
• Previous IDs: rno-miR-541*
• Sequence: 56 - aguggcgaacacagaauccauac - 78
• Deep sequencing: 427 reads, 133 experiments
• Evidence: experimental; SOLiD [3]
• Predicted targets:
  • TargetScanVert:rno-miR-541-3p
  • miRDB:rno-miR-541-3p

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).