Stem-loop sequence rno-mir-409a

Accession

MI0003550 (change log)

Previous IDs

rno-mir-409

Description

Rattus norvegicus miR-409 stem-loop

Gene family

MIPF0000018; mir-154

Literature search

9 open access papers mention rno-mir-409a
(17 sentences)

Stem-loop

        u       a    ac         -    - auc 
5' gguac cggagag gguu  ccgagcaac uuug c   u
   ||||| ||||||| ||||  ||||||||| |||| |    
3' cuaug gcuuuuc ccaa  ggcucguug aagc g   g
        -       c    gu         u    a gag 

Deep sequencing

234943 reads, 145 reads per million, 455 experiments

Confidence

Annotation confidence: high

Feedback: Do you believe this miRNA is real?

Genome context

• Coordinates (Rnor_6.0; GCA_000001895.4): chr6: 133893419-133893495 [+]
• Overlapping transcripts:

  antisense

  ENSRNOT00000053696 ; Mir3581-201; exon 1

Clustered miRNAs

< 10kb from rno-mir-409a

• 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:Mir409
• miRBase Tracker:MI0003550

Mature sequence rno-miR-409a-5p

• Accession: MIMAT0003204
• Previous IDs: rno-miR-409-5p
• Sequence: 14 - agguuacccgagcaacuuugcau - 36
• Deep sequencing: 29678 reads, 343 experiments
• Evidence: experimental; SOLiD [2]
• Predicted targets:
  • TargetScanVert:rno-miR-409a-5p
  • miRDB:rno-miR-409a-5p
  • microrna.org:rno-miR-409a-5p

Mature sequence rno-miR-409a-3p

• Accession: MIMAT0003205
• Previous IDs: rno-miR-409-3p
• Sequence: 47 - aauguugcucggugaacccc - 66
• Deep sequencing: 205188 reads, 452 experiments
• Evidence: experimental; SOLiD [2]
• Predicted targets:
  • TargetScanVert:rno-miR-409a-3p
  • miRDB:rno-miR-409a-3p
  • microrna.org:rno-miR-409a-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: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).