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Aliases for MIR539 Gene

Subcategory (RNA class) for MIR539 Gene


Quality Score for this RNA gene is


Aliases for MIR539 Gene

  • MicroRNA 539 2 3 5
  • Hsa-Mir-539 3
  • Mir-539 3
  • MIRN539 3

External Ids for MIR539 Gene

ORGUL Members for MIR539 Gene

Previous HGNC Symbols for MIR539 Gene

  • MIRN539

Previous GeneCards Identifiers for MIR539 Gene

  • GC14P100826
  • GC14P100916
  • GC14P101517
  • GC14P101546
  • GC14P101580
  • GC14P101620
  • GC14P101648
  • GC14P101681
  • GC14P101719
  • GC14P101761
  • GC14P101819
  • GC14P101959
  • GC14P102156
  • GC14P101258
  • GC14P101868
  • GC14P102188
  • GC14P102357
  • GC14P102527
  • GC14P102707
  • GC14P102880
  • GC14P103051

Summaries for MIR539 Gene

Entrez Gene Summary for MIR539 Gene

  • microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

GeneCards Summary for MIR539 Gene

MIR539 (MicroRNA 539) is an RNA Gene, and is affiliated with the miRNA class. Diseases associated with MIR539 include Autism Spectrum Disorder.

Additional gene information for MIR539 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MIR539 Gene

Genomics for MIR539 Gene

GeneHancer (GH) Regulatory Elements for MIR539 Gene

Promoters and enhancers for MIR539 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14J101287 Enhancer 1 ENCODE 9.5 +241.6 241600 2.5 FOXA2 MLX ZFP64 ARID4B ZNF48 ETS1 YY1 NFKBIZ RXRA SP5 MEG3 MIR1185-2 MIR381 MIR487B MIR539 MIR544A MIR889 MIR655 MIR1185-1 MIR300
GH14J101333 Enhancer 0.9 ENCODE 8.9 +287.7 287736 2.2 FOXA2 ARID4B YY1 NFKBIZ RXRA SP5 PPARG NFIL3 MIER3 RCOR2 ENSG00000258460 GC14M101304 MIR381 MIR487B MIR539 MIR544A MIR655 MIR889 MIR376C MIR1185-1
GH14J101215 Enhancer 0.8 ENCODE 9.9 +169.4 169403 2.8 FOXA2 ARID4B RAD21 ZNF48 ZSCAN9 RARA CREM RXRA CEBPB NR2F2 LOC100128373 SNORD113-3 SNORD113-8 SNORD113-9 SNORD113-4 SNORD113-6 SNORD113-7 MIR543 ENSG00000222185 ENSG00000222095
GH14J101004 Enhancer 0.7 Ensembl ENCODE 10.9 -42.2 -42236 1.9 GATA3 MNT MYC TCF7L2 MIR134 MIR487A MIR154 MIR323B MIR485 MIR377 MIR496 MIR376C MIR1185-1 MIR1185-2
GH14J101096 Enhancer 0.7 FANTOM5 ENCODE 10.7 +51.0 51027 3.2 ATF4 POLR2A JUN MAFK RTL1 LOC105370670 MEG9 MIR369 MIR409 MIR410 MIR412 MIR541 MIR656 MIR154
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around MIR539 on UCSC Golden Path with GeneCards custom track

Genomic Locations for MIR539 Gene

Genomic Locations for MIR539 Gene
78 bases
Plus strand
78 bases
Plus strand

Genomic View for MIR539 Gene

Genes around MIR539 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MIR539 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MIR539 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MIR539 Gene

Proteins for MIR539 Gene

Post-translational modifications for MIR539 Gene

No Post-translational modifications

No data available for DME Specific Peptides for MIR539 Gene

Domains & Families for MIR539 Gene

Gene Families for MIR539 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with MIR539: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for MIR539 Gene

Function for MIR539 Gene

Animal Model Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for MIR539 Gene

Localization for MIR539 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for MIR539 Gene

Pathways & Interactions for MIR539 Gene

SuperPathways for MIR539 Gene

No Data Available

Interacting Proteins for MIR539 Gene

Gene Ontology (GO) - Biological Process for MIR539 Gene


No data available for Pathways by source and SIGNOR curated interactions for MIR539 Gene

Drugs & Compounds for MIR539 Gene

No Compound Related Data Available

Transcripts for MIR539 Gene

mRNA/cDNA for MIR539 Gene

(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :
(3) RNA Central transcripts :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for MIR539 Gene

No ASD Table

Relevant External Links for MIR539 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for MIR539 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MIR539 Gene

NURSA nuclear receptor signaling pathways regulating expression of MIR539 Gene:

genes like me logo Genes that share expression patterns with MIR539: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for MIR539 Gene

Orthologs for MIR539 Gene

This gene was present in the common ancestor of mammals.

Orthologs for MIR539 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ptr-mir-539 34
  • 100 (a)
(Bos Taurus)
Mammalia bta-mir-539 34
  • 96 (a)
(Canis familiaris)
Mammalia cfa-mir-539 34
  • 95 (a)
(Mus musculus)
Mammalia Mir539 34
  • 92 (a)
Species where no ortholog for MIR539 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for MIR539 Gene

Gene Tree for MIR539 (if available)
Gene Tree for MIR539 (if available)

Paralogs for MIR539 Gene

No data available for Paralogs for MIR539 Gene

Variants for MIR539 Gene

Sequence variations from dbSNP and Humsavar for MIR539 Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs1000942364 -- 101,046,276(+) G/A upstream_transcript_variant
rs1002444581 -- 101,046,676(+) T/C upstream_transcript_variant
rs1003662338 -- 101,045,775(+) T/C upstream_transcript_variant
rs1006688709 -- 101,047,488(+) G/C downstream_transcript_variant
rs1006923333 -- 101,047,203(+) A/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for MIR539 Gene

Variant ID Type Subtype PubMed ID
nsv565860 CNV gain 21841781
nsv565859 CNV gain 21841781
nsv1040993 CNV gain 25217958
esv3635521 CNV gain 21293372

Additional Variant Information for MIR539 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for MIR539 Gene

Disorders for MIR539 Gene

MalaCards: The human disease database

(1) MalaCards diseases for MIR539 Gene - From: miR2Disease

Disorder Aliases PubMed IDs
autism spectrum disorder
  • asd
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for MIR539

genes like me logo Genes that share disorders with MIR539: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MIR539 Gene

Publications for MIR539 Gene

  1. Androgen receptor promotes melanoma metastasis via altering the miRNA-539-3p/USP13/MITF/AXL signals. (PMID: 27869170) Wang Y … Chang C (Oncogene 2017) 3 58
  2. Long non-coding RNA LOC100129148 functions as an oncogene in human nasopharyngeal carcinoma by targeting miR-539-5p. (PMID: 28328537) Sun KY … Zhou XH (Aging 2017) 3 58
  3. miR-539 inhibits FSCN1 expression and suppresses hepatocellular carcinoma migration and invasion. (PMID: 28393215) Liu Y … Li X (Oncology reports 2017) 3 58
  4. miR-539 inhibits prostate cancer progression by directly targeting SPAG5. (PMID: 27037000) Zhang H … Xu Y (Journal of experimental & clinical cancer research : CR 2016) 3 58
  5. microRNA-539 suppresses tumor growth and tumorigenesis and overcomes arsenic trioxide resistance in hepatocellular carcinoma. (PMID: 27717846) Zhu C … Jiang M (Life sciences 2016) 3 58

Products for MIR539 Gene

Sources for MIR539 Gene

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