Stem-loop sequence dme-mir-4

Accession

MI0000122 (change log)

Description

Drosophila melanogaster miR-4 stem-loop

Gene family

MIPF0000305; mir-4

Literature search

6 open access papers mention dme-mir-4
(21 sentences)

Stem-loop

    ug    u gu   uu    c   c   cuuag      u 
5' u  caau a  uuc  uggu guc agc     gugauu u
   |  |||| |  |||  |||| ||| |||     |||||| u
3' g  guug u  aag  acca cag ucg     uacugg c
    gu    c ug   uu    a   a   --aaa      c 

Deep sequencing

32680 reads, 1.84e+03 reads per million, 45 experiments

Confidence

Annotation confidence: high

Feedback: Do you believe this miRNA is real?

Genome context

• Coordinates (Release_6; GCA_000001215.4): chr2R: 19661289-19661369 [-]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from dme-mir-4

• dme-mir-309: chr2R: 19661706-19661774 [-]
• dme-mir-3: chr2R: 19661595-19661663 [-]
• dme-mir-286: chr2R: 19661422-19661521 [-]
• dme-mir-4: chr2R: 19661289-19661369 [-]
• dme-mir-5: chr2R: 19661158-19661226 [-]
• dme-mir-6-1: chr2R: 19661003-19661084 [-]
• dme-mir-6-2: chr2R: 19660869-19660942 [-]
• dme-mir-6-3: chr2R: 19660716-19660795 [-]

Database links

• RNAcentral:URS000079406B_7227
• miRBase Tracker:MI0000122

Mature sequence dme-miR-4-5p

• Accession: MIMAT0020785
• Sequence: 14 - cuuuggucguccagccuuagguga - 37
• Deep sequencing: 5536 reads, 30 experiments
• Evidence: not experimental
• Database links:
  • RNAcentral:URS00003805C8_7227

Mature sequence dme-miR-4-3p

• Accession: MIMAT0000109
• Previous IDs: dme-miR-4
• Sequence: 49 - auaaagcuagacaaccauuga - 69
• Deep sequencing: 27144 reads, 41 experiments
• Evidence: experimental; cloned [1,3], Northern [1-3], 454 [4-5], Illumina [5]
• Database links:
  • RNAcentral:URS000030D462_7227
• Predicted targets:
  • TargetScanFly:dme-miR-4
  • microrna.org:dme-miR-4-3p

References

1. PMID:11679670 "Identification of novel genes coding for small expressed RNAs" Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T Science. 294:853-858(2001).
2. PMID:12812784 "Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-Complex gene activity" Sempere LF, Sokol NS, Dubrovsky EB, Berger EM, Ambros V Dev Biol. 259:9-18(2003).
3. PMID:12919683 "The small RNA profile during Drosophila melanogaster development" Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J, Tuschl T Dev Cell. 5:337-350(2003).
4. PMID:17989254 "Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs" Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC Genome Res. 17:1850-1864(2007).
5. PMID:17989255 "Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes" Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M Genome Res. 17:1865-1879(2007).