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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 Metabolism. 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

Regulatory Elements for RPL39 Gene

Enhancers for RPL39 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XH119789 1.1 ENCODE 0.7 +0.4 396 3.7 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 SP3 ZHX2 REST KAT8 EEF1A1P30 NKAP CUL4B UPF3B RNF113A GC0XM119788 RPL39 SNORA69 GC0XM119789
GH0XH119808 0.9 ENCODE 0.4 -17.5 -17512 0.9 HDAC1 PKNOX1 ATF1 TBL1XR1 ARNT CHAMP1 TCF12 GATA2 EGR1 SIRT6 UPF3B LOC100422368 RPL39
GH0XH119821 0.8 Ensembl ENCODE 0.3 -30.2 -30195 1.5 FOXA2 RFX1 FOXK2 NBN ELF1 ATF7 FOXJ2 RNF113A NDUFA1 UPF3B LOC100422368 RPL39
GH0XH119788 0.2 Ensembl 0.7 +3.6 3559 0.2 GC0XM119789 RPL39 SNORA69 GC0XM119788
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RPL39 on UCSC Golden Path with GeneCards custom track

Promoters for RPL39 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000248375 259 3201 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 SP3 ZHX2 REST KAT8

Genomic Locations for RPL39 Gene

Genomic Locations for RPL39 Gene
5,156 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

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 IEA,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:0002227 innate immune response in mucosa IDA 12860195
GO:0006364 rRNA processing TAS --
GO:0006412 translation IEA,TAS 8764829
GO:0006413 translational initiation TAS --
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

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 33 34 34
  • 94.77 (n)
(Rattus norvegicus)
Mammalia Rpl39 33
  • 90.85 (n)
(Mus musculus)
Mammalia Rpl39 33 16 34
  • 89.54 (n)
(Gallus gallus)
Aves RPL39 33 34
  • 83.66 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 96 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia rpl39 33
  • 79.08 (n)
(Danio rerio)
Actinopterygii rpl39 33 34
  • 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)
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)

Paralogs for RPL39 Gene

Paralogs for RPL39 Gene

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

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 Sequence Context AA Info Type
rs1000190599 -- 119,792,176(+) GTTGC(C/T)AATCA intron-variant, upstream-variant-2KB
rs1000635674 -- 119,786,515(+) AGAAA(A/G)GCCTT utr-variant-3-prime
rs1001146601 -- 119,787,285(+) CCTGG(A/C)CTCGC intron-variant, downstream-variant-500B
rs1001330920 -- 119,790,299(+) TTTCT(A/G)CTCCA intron-variant, upstream-variant-2KB
rs1001440055 -- 119,786,903(+) TTTAA(A/T)AACTA intron-variant, downstream-variant-500B

Variation tolerance for RPL39 Gene

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

Relevant External Links for RPL39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Relevant External Links for RPL39

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 60
  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 60
  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 60
  4. The human ribosomal protein genes: sequencing and comparative analysis of 73 genes. (PMID: 11875025) Yoshihama M … Kenmochi N (Genome research 2002) 3 4 60
  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 60

Products for RPL39 Gene

Sources for RPL39 Gene

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