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Aliases for RPL39 Gene

Aliases for RPL39 Gene

  • Ribosomal Protein L39 2 3 5
  • Large Ribosomal Subunit Protein EL39 3 4
  • Ribosomal Protein L39 Pseudogene 42 2
  • 60S Ribosomal Protein L39 3
  • RPL39_23_1806 3
  • RPL39P42 3
  • L39 3

External Ids for RPL39 Gene

Previous HGNC Symbols for RPL39 Gene

  • RPL39P42

Previous GeneCards Identifiers for RPL39 Gene

  • GC0XM113738
  • GC0XM115906
  • GC0XM116895
  • GC0XM117674
  • GC0XM118702
  • GC0XM118804
  • GC0XM118920
  • GC0XM108414

Summaries for RPL39 Gene

Entrez Gene Summary for RPL39 Gene

  • Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the S39E family of ribosomal proteins. It is located in the cytoplasm. In rat, the protein is the smallest, and one of the most basic, proteins of the ribosome. This gene is co-transcribed with the U69 small nucleolar RNA gene, which is located in its second intron. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

GeneCards Summary for RPL39 Gene

RPL39 (Ribosomal Protein L39) is a Protein Coding gene. Diseases associated with RPL39 include Lacrimal Gland Adenocarcinoma. Among its related pathways are Viral mRNA Translation and Influenza Viral RNA Transcription and Replication. Gene Ontology (GO) annotations related to this gene include RNA binding and structural constituent of ribosome. An important paralog of this gene is RPL39L.

Gene Wiki entry for RPL39 Gene

Additional gene information for RPL39 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RPL39 Gene

Genomics for RPL39 Gene

GeneHancer (GH) Regulatory Elements for RPL39 Gene

Promoters and enhancers for RPL39 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
GH0XJ119789 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 +0.4 395 3.7 PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B SP3 ZHX2 RPL39 EEF1A1P30 NKAP CUL4B UPF3B RNF113A GC0XM119789 GC0XM119788 SNORA69
GH0XJ119674 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 3.7 +107.0 106955 20.2 HDGF PKNOX1 SMAD1 ARNT ZFP64 ARID4B FEZF1 IRF4 YY1 POLR2B SEPT6 NKAPP1 EEF1A1P30 CUL4B NKAP NKRF UPF3B MIR766 CXorf56 SLC25A5-AS1
GH0XJ119808 Enhancer 0.9 ENCODE 0.4 -17.5 -17512 0.9 PKNOX1 ATF1 ARNT NCOA2 TCF12 FOS ATF7 NCOA1 MBD2 GMEB1 UPF3B LOC100422368 RPL39
GH0XJ119821 Enhancer 0.8 Ensembl ENCODE 0.3 -30.2 -30194 1.5 SP1 FOXA2 RFX1 FOXK2 NBN ATF7 ELF1 ZNF384 LOC100422368 NDUFA1 RNF113A UPF3B RPL39
GH0XJ119788 Enhancer 0.2 Ensembl 0.7 +3.6 3558 0.2 GC0XM119789 SNORA69 GC0XM119788 RPL39
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RPL39 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RPL39 gene promoter:
  • GATA-2
  • NCX
  • GATA-1
  • Ik-2
  • En-1
  • RP58
  • CUTL1
  • FOXJ2 (long isoform)
  • FOXJ2
  • Ik-1

Genomic Locations for RPL39 Gene

Genomic Locations for RPL39 Gene
5,156 bases
Minus strand
5,140 bases
Minus strand

Genomic View for RPL39 Gene

Genes around RPL39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPL39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPL39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPL39 Gene

Proteins for RPL39 Gene

  • Protein details for RPL39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    60S ribosomal protein L39
    Protein Accession:
    Secondary Accessions:
    • P02404
    • P39025
    • Q9BYF2

    Protein attributes for RPL39 Gene

    51 amino acids
    Molecular mass:
    6407 Da
    Quaternary structure:
    • Interacts with IMPACT.
    • This protein is the smallest and one of the most basic of the proteins in liver ribosomes.

    Three dimensional structures from OCA and Proteopedia for RPL39 Gene

neXtProt entry for RPL39 Gene

Post-translational modifications for RPL39 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RPL39 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RPL39 Gene

Domains & Families for RPL39 Gene

Gene Families for RPL39 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Ribosomal proteins

Protein Domains for RPL39 Gene

Suggested Antigen Peptide Sequences for RPL39 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the eukaryotic ribosomal protein eL39 family.
  • Belongs to the eukaryotic ribosomal protein eL39 family.
genes like me logo Genes that share domains with RPL39: view

Function for RPL39 Gene

Gene Ontology (GO) - Molecular Function for RPL39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding TAS 8764829
GO:0003735 structural constituent of ribosome TAS 8764829
genes like me logo Genes that share ontologies with RPL39: view
genes like me logo Genes that share phenotypes with RPL39: view

Animal Model Products

miRNA for RPL39 Gene

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RPL39 Gene

Localization for RPL39 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RPL39 gene
Compartment Confidence
extracellular 5
cytosol 5
nucleus 1

Gene Ontology (GO) - Cellular Components for RPL39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 12860195
GO:0005622 intracellular IEA --
GO:0005829 cytosol TAS --
GO:0005840 ribosome IEA --
GO:0022625 cytosolic large ribosomal subunit TAS 8764829
genes like me logo Genes that share ontologies with RPL39: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for RPL39 Gene

Pathways & Interactions for RPL39 Gene

genes like me logo Genes that share pathways with RPL39: view

Pathways by source for RPL39 Gene

1 KEGG pathway for RPL39 Gene
1 GeneGo (Thomson Reuters) pathway for RPL39 Gene

Gene Ontology (GO) - Biological Process for RPL39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS --
GO:0002181 cytoplasmic translation IDA 25957688
GO:0002227 innate immune response in mucosa IDA 12860195
GO:0006364 rRNA processing TAS --
GO:0006412 translation TAS 8764829
genes like me logo Genes that share ontologies with RPL39: view

No data available for SIGNOR curated interactions for RPL39 Gene

Drugs & Compounds for RPL39 Gene

No Compound Related Data Available

Transcripts for RPL39 Gene

mRNA/cDNA for RPL39 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(1120) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RPL39 Gene

Ribosomal protein L39:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RPL39 Gene

No ASD Table

Relevant External Links for RPL39 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RPL39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RPL39 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of RPL39 Gene:


SOURCE GeneReport for Unigene cluster for RPL39 Gene:


Evidence on tissue expression from TISSUES for RPL39 Gene

  • Eye(4.6)
  • Intestine(4.5)
  • Heart(4.4)
  • Muscle(4.1)
  • Nervous system(2.8)
  • Blood(2.7)
  • Lymph node(2.6)
  • Spleen(2.6)
  • Lung(2.5)
  • Pancreas(2.5)
  • Thyroid gland(2.5)
  • Adrenal gland(2.4)
  • Bone marrow(2.4)
  • Liver(2.4)
  • Skin(2.3)
  • Kidney(2.1)
  • Stomach(2)
genes like me logo Genes that share expression patterns with RPL39: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPL39 Gene

Orthologs for RPL39 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RPL39 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia -- 34
  • 100 (a)
-- 34
  • 100 (a)
-- 34
  • 100 (a)
RPL39 33
  • 93.46 (n)
(Pan troglodytes)
Mammalia LOC100614664 33
  • 99.35 (n)
RPL39 34
  • 98 (a)
(Bos Taurus)
Mammalia RPL39 34 34 33
  • 94.77 (n)
(Rattus norvegicus)
Mammalia Rpl39 33
  • 90.85 (n)
(Mus musculus)
Mammalia Rpl39 16 34 33
  • 89.54 (n)
(Gallus gallus)
Aves RPL39 34 33
  • 83.66 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 96 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia rpl39 33
  • 79.08 (n)
(Danio rerio)
Actinopterygii rpl39 34 33
  • 81.7 (n)
fruit fly
(Drosophila melanogaster)
Insecta RpL39 34
  • 73 (a)
(Caenorhabditis elegans)
Secernentea rpl-39 34
  • 75 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPL39 34
  • 63 (a)
(Hordeum vulgare)
Liliopsida Hv.8290 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6039 34
  • 84 (a)
Cin.5449 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5449 33
Species where no ortholog for RPL39 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)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for RPL39 Gene

Gene Tree for RPL39 (if available)
Gene Tree for RPL39 (if available)
Evolutionary constrained regions (ECRs) for RPL39: view image

Paralogs for RPL39 Gene

Paralogs for RPL39 Gene

(2) SIMAP similar genes for RPL39 Gene using alignment to 1 proteins:

  • RL39_HUMAN
genes like me logo Genes that share paralogs with RPL39: view

Variants for RPL39 Gene

Sequence variations from dbSNP and Humsavar for RPL39 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1000190599 -- 119,792,176(-) C/T upstream_transcript_variant
rs1000635674 -- 119,786,515(-) G/A 3_prime_UTR_variant
rs1001146601 -- 119,787,285(-) C/A intron_variant
rs1001330920 -- 119,790,299(-) G/A intron_variant
rs1001440055 -- 119,786,903(-) A/T intron_variant

Variation tolerance for RPL39 Gene

Residual Variation Intolerance Score: 58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RPL39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for RPL39 Gene

Disorders for RPL39 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RPL39 Gene - From: DISEASES

Disorder Aliases PubMed IDs
lacrimal gland adenocarcinoma
  • adenocarcinoma of lacrimal gland
- elite association - COSMIC cancer census association via MalaCards
Search RPL39 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RPL39

genes like me logo Genes that share disorders with RPL39: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RPL39 Gene

Publications for RPL39 Gene

  1. Molecular cloning of a cDNA encoding human ribosomal protein L39. (PMID: 8764829) Otsuka S … Itakura M (Biochimica et biophysica acta 1996) 2 3 4 22 58
  2. Primary structures and sequence analysis of human ribosomal proteins L39 and S27. (PMID: 8908372) Tsui SK … Lee CY (Biochemistry and molecular biology international 1996) 3 4 22 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. The human ribosomal protein genes: sequencing and comparative analysis of 73 genes. (PMID: 11875025) Yoshihama M … Kenmochi N (Genome research 2002) 3 4 58
  5. A complete map of the human ribosomal protein genes: assignment of 80 genes to the cytogenetic map and implications for human disorders. (PMID: 11401437) Uechi T … Kenmochi N (Genomics 2001) 3 4 58

Products for RPL39 Gene

Sources for RPL39 Gene

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