Stem-loop sequence hsa-mir-539

Accession

MI0003514 (change log)

Symbol

HGNC:MIR539

Description

Homo sapiens miR-539 stem-loop

Gene family

MIPF0000018; mir-154

Literature search

27 open access papers mention hsa-mir-539
(87 sentences)

Stem-loop

        ug          a      g    -    - uuu 
5' auacu  aggagaaauu uccuug ugug uucg c   a
   |||||  |||||||||| |||||| |||| |||| |   u
3' uauga  uuuucuuuaa aggaac auac aagu g   u
        gu          c      -    u    a uau 

Deep sequencing

6103 reads, 4.76 reads per million, 105 experiments

Confidence

Annotation confidence: high

Feedback: Do you believe this miRNA is real?

Genome context

• Coordinates (GRCh38; GCA_000001405.15): chr14: 101047321-101047398 [+]
• Overlapping transcripts:

  antisense

  OTTHUMT00000414335 ; BEGAIN-006; intron 1

  ENST00000554140 ; BEGAIN-006; intron 1

Clustered miRNAs

< 10kb from hsa-mir-539

• hsa-mir-376c: chr14: 101039690-101039755 [+]
• hsa-mir-376a-2: chr14: 101040069-101040148 [+]
• hsa-mir-654: chr14: 101040219-101040299 [+]
• hsa-mir-376b: chr14: 101040436-101040535 [+]
• hsa-mir-376a-1: chr14: 101040782-101040849 [+]
• hsa-mir-300: chr14: 101041363-101041445 [+]
• hsa-mir-1185-1: chr14: 101042977-101043062 [+]
• hsa-mir-1185-2: chr14: 101044198-101044283 [+]
• hsa-mir-381: chr14: 101045920-101045994 [+]
• hsa-mir-487b: chr14: 101046455-101046538 [+]
• hsa-mir-539: chr14: 101047321-101047398 [+]
• hsa-mir-889: chr14: 101047901-101047979 [+]
• hsa-mir-544a: chr14: 101048658-101048748 [+]
• hsa-mir-655: chr14: 101049550-101049646 [+]
• hsa-mir-487a: chr14: 101052446-101052525 [+]
• hsa-mir-382: chr14: 101054306-101054381 [+]
• hsa-mir-134: chr14: 101054687-101054759 [+]
• hsa-mir-668: chr14: 101055258-101055323 [+]
• hsa-mir-485: chr14: 101055419-101055491 [+]
• hsa-mir-323b: chr14: 101056219-101056300 [+]

Database links

• EntrezGene:MIR539
• HGNC:MIR539
• RNAcentral:URS0000759CA5_9606
• miRBase Tracker:MI0003514

Mature sequence hsa-miR-539-5p

• Accession: MIMAT0003163
• Previous IDs: hsa-miR-539
• Sequence: 9 - ggagaaauuauccuuggugugu - 30
• Deep sequencing: 1545 reads, 90 experiments
• Evidence: experimental; cloned [1,3], miRAP-cloned [2]
• Predicted targets:
  • TargetMiner:hsa-miR-539-5p
  • TargetScanVert:hsa-miR-539-5p
  • miRDB:hsa-miR-539-5p
  • microrna.org:hsa-miR-539-5p

Mature sequence hsa-miR-539-3p

• Accession: MIMAT0022705
• Sequence: 49 - aucauacaaggacaauuucuuu - 70
• Deep sequencing: 4555 reads, 102 experiments
• Evidence: not experimental
• Database links:
  • RNAcentral:URS000039607D_9606
• Predicted targets:
  • TargetMiner:hsa-miR-539-3p
  • TargetScanVert:hsa-miR-539-3p
  • miRDB:hsa-miR-539-3p

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:16973894 "Mouse microRNA profiles determined with a new and sensitive cloning method" Takada S, Berezikov E, Yamashita Y, Lagos-Quintana M, Kloosterman WP, Enomoto M, Hatanaka H, Fujiwara S, Watanabe H, Soda M, Choi YL, Plasterk RH, Cuppen E, Mano H Nucleic Acids Res. 34:e115(2006).
3. 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).