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Aliases for RPL39 Gene

Aliases for RPL39 Gene

  • Ribosomal Protein L39 2 3 5
  • 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 Metabolism and Viral mRNA Translation. 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

No data available for 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
GH0XF120734 1.3 Ensembl ENCODE 10.9 -944.4 -944416 3.9 PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF143 FOS SP3 RPL39 C1GALT1C1 LOC100128546 PA2G4P1
GH0XF119869 1.1 ENCODE 11 -79.7 -79658 3.5 PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF263 SP3 UPF3B EEF1A1P30 RPL39 RNF113A NDUFA1
GH0XF119572 1.1 ENCODE 10.9 +217.2 217191 3.0 WRNIP1 ARID4B SIN3A ZNF2 SP3 REST KAT8 SREBF1 ZNF610 SMARCA4 CXorf56 RPL39 GC0XP119575 GC0XP119576 UBE2A
GH0XF120243 1.1 ENCODE 10.9 -453.2 -453203 1.9 ARNT CREB3L1 WRNIP1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 NKAPP1 CXorf56 UPF3B LINC01402 EEF1A1P30 RPL39 RHOXF1
- 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
ENSR00000481616 459 3601 PKNOX1 ATF1 ARID4B SIN3A DMAP1 ZNF2 YY1 GTF3C2 GLIS2 ELK1

Genomic Location for RPL39 Gene

119,786,504 bp from pter
119,791,659 bp from pter
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

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 ribosomal protein L39e family.
  • Belongs to the ribosomal protein L39e 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

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , 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 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 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

Transcripts for RPL39 Gene

mRNA/cDNA for RPL39 Gene

Unigene Clusters for RPL39 Gene

Ribosomal protein L39:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry 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 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:

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 and mRNA Expression by UniProt/SwissProt 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 -- 35
  • 100 (a)
-- 35
  • 100 (a)
-- 35
  • 100 (a)
RPL39 34
  • 93.46 (n)
(Pan troglodytes)
Mammalia LOC100614664 34
  • 99.35 (n)
RPL39 35
  • 98 (a)
(Bos Taurus)
Mammalia RPL39 34 35 35
  • 94.77 (n)
(Rattus norvegicus)
Mammalia Rpl39 34
  • 90.85 (n)
(Mus musculus)
Mammalia Rpl39 34 16 35
  • 89.54 (n)
(Gallus gallus)
Aves RPL39 34 35
  • 83.66 (n)
(Anolis carolinensis)
Reptilia -- 35
  • 96 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia rpl39 34
  • 79.08 (n)
(Danio rerio)
Actinopterygii rpl39 34 35
  • 81.7 (n)
fruit fly
(Drosophila melanogaster)
Insecta RpL39 35
  • 73 (a)
(Caenorhabditis elegans)
Secernentea rpl-39 35
  • 75 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPL39 35
  • 63 (a)
(Hordeum vulgare)
Liliopsida Hv.8290 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6039 35
  • 84 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5449 34
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
rs10156961 -- 119,792,681(+) aagaa(A/G)aagta intron-variant, upstream-variant-2KB
rs111736742 -- 119,786,513(+) AAAGA(A/T)AGGCC utr-variant-3-prime
rs112173203 -- 119,786,584(+) ACACG(C/T)CGAAA utr-variant-3-prime
rs112273494 -- 119,790,027(+) AATGC(A/C)ATCAA intron-variant, upstream-variant-2KB
rs112964621 -- 119,791,087(+) AAACG(C/T)CCTCT intron-variant, upstream-variant-2KB

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. (Biochim. Biophys. Acta 1996) 2 3 4 22 64
  2. Primary structures and sequence analysis of human ribosomal proteins L39 and S27. (PMID: 8908372) Tsui S.K.W. … Lee C.Y. (Biochem. Mol. Biol. Int. 1996) 3 4 22 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. The human ribosomal protein genes: sequencing and comparative analysis of 73 genes. (PMID: 11875025) Yoshihama M. … Kenmochi N. (Genome Res. 2002) 3 4 64
  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 64

Products for RPL39 Gene

Sources for RPL39 Gene

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