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Aliases for RPL3 Gene

Aliases for RPL3 Gene

  • Ribosomal Protein L3 2 3 5
  • Large Ribosomal Subunit Protein UL3 3 4
  • HIV-1 TAR RNA-Binding Protein B 3 4
  • TARBP-B 3 4
  • 60S Ribosomal Protein L3 3
  • ASC-1 3
  • L3 3

External Ids for RPL3 Gene

Previous GeneCards Identifiers for RPL3 Gene

  • GC22M036323
  • GC22M037951
  • GC22M038033
  • GC22M038046
  • GC22M039710
  • GC22M039717
  • GC22M039719
  • GC22M039721
  • GC22M039723
  • GC22M039728
  • GC22M039821
  • GC22M040108
  • GC22M039333
  • GC22M039835
  • GC22M039847
  • GC22M039942
  • GC22M040631
  • GC22M041078
  • GC22M041476
  • GC22M041884

Summaries for RPL3 Gene

Entrez Gene Summary for RPL3 Gene

  • Ribosomes, the complexes 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 L3P family of ribosomal proteins and it is located in the cytoplasm. The protein can bind to the HIV-1 TAR mRNA, and it has been suggested that the protein contributes to tat-mediated transactivation. This gene is co-transcribed with several small nucleolar RNA genes, which are located in several of this gene's introns. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. 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 RPL3 Gene

RPL3 (Ribosomal Protein L3) is a Protein Coding gene. Diseases associated with RPL3 include Diamond-Blackfan Anemia. Among its related pathways are Viral mRNA Translation and Influenza Viral RNA Transcription and Replication. Gene Ontology (GO) annotations related to this gene include structural constituent of ribosome. An important paralog of this gene is RPL3L.

UniProtKB/Swiss-Prot for RPL3 Gene

  • The L3 protein is a component of the large subunit of cytoplasmic ribosomes.

Gene Wiki entry for RPL3 Gene

Additional gene information for RPL3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RPL3 Gene

Genomics for RPL3 Gene

GeneHancer (GH) Regulatory Elements for RPL3 Gene

Promoters and enhancers for RPL3 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
GH22J039315 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 688.2 +2.4 2393 5.9 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 ZNF143 SP3 NFYC ZFP41 SSRP1 RPL3 PIR31798 SNORD43 SNORD139 GC22M042958 GC22M042591 GC22M042519 CBX7 DDX17 SNORD83B
GH22J039518 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 42.1 -204.0 -203994 12.3 MLX DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 SP3 ATF4 ENSG00000272834 RPL3 TAB1 ENSG00000230912 SNORD83B ENSG00000228274 CBY1 CBX6 TNRC6B
GH22J040175 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 25.5 -857.5 -857546 5.6 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 TNRC6B EP300 ENSG00000272834 RPL3 SNORD83B ATF4 PIR61047 RPL7P52
GH22J038567 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 21.1 +751.0 751001 4.7 PKNOX1 GLI4 ZNF2 YY1 ZNF213 E2F8 KLF7 ATF7 RUNX3 ZNF263 LOC105373031 DMC1 FAM227A DDX17 SNORD83B RPL3 JOSD1 TAB1 PLA2G6 ENSG00000230149
GH22J039308 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 23.2 +10.1 10056 4.3 HDGF PKNOX1 MLX ARNT ZFP64 SIN3A FEZF1 ZNF2 IRF4 POLR2B DDX17 RPL3 SYNGR1 APOBEC3A ENSG00000230149 SNORD83B ENSG00000273076 ENSG00000272669 ENSG00000225450 TAB1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RPL3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RPL3 gene promoter:
  • ATF6
  • CUTL1
  • AML1a
  • Bach2
  • STAT1alpha
  • STAT1
  • ER-alpha
  • STAT2
  • STAT1beta

Genomic Locations for RPL3 Gene

Genomic Locations for RPL3 Gene
7,508 bases
Minus strand
7,508 bases
Minus strand

Genomic View for RPL3 Gene

Genes around RPL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPL3 Gene

Proteins for RPL3 Gene

  • Protein details for RPL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    60S ribosomal protein L3
    Protein Accession:
    Secondary Accessions:
    • B2RDV9
    • Q15548
    • Q5I0G0

    Protein attributes for RPL3 Gene

    403 amino acids
    Molecular mass:
    46109 Da
    Quaternary structure:
    • Component of the large ribosomal subunit (Probable). Interacts with METTL18 (PubMed:23349634). Interacts with DHX33 (PubMed:26100019).

    Three dimensional structures from OCA and Proteopedia for RPL3 Gene

neXtProt entry for RPL3 Gene

Post-translational modifications for RPL3 Gene

  • Ubiquitination at posLast=366366, posLast=300300, Lys286, and posLast=3939
  • Modification sites at PhosphoSitePlus

Other Protein References for RPL3 Gene

No data available for DME Specific Peptides for RPL3 Gene

Domains & Families for RPL3 Gene

Gene Families for RPL3 Gene

Human Protein Atlas (HPA):
  • FDA approved drug targets
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted secreted proteins
  • Ribosomal proteins

Protein Domains for RPL3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the universal ribosomal protein uL3 family.
  • Belongs to the universal ribosomal protein uL3 family.
genes like me logo Genes that share domains with RPL3: view

Function for RPL3 Gene

Molecular function for RPL3 Gene

UniProtKB/Swiss-Prot Function:
The L3 protein is a component of the large subunit of cytoplasmic ribosomes.
GENATLAS Biochemistry:
60S ribosomal protein L3

Phenotypes From GWAS Catalog for RPL3 Gene

Gene Ontology (GO) - Molecular Function for RPL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding TAS,IBA --
GO:0003735 structural constituent of ribosome NAS,IEA 12962325
GO:0005515 protein binding IPI 23349634
GO:0008097 5S rRNA binding IEA --
genes like me logo Genes that share ontologies with RPL3: view
genes like me logo Genes that share phenotypes with RPL3: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RPL3 Gene

Localization for RPL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPL3 Gene

Nucleus, nucleolus. Cytoplasm.

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 RPL3 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoli (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RPL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IEA,HDA 21630459
GO:0005730 nucleolus IDA 16963496
GO:0005737 cytoplasm HDA,IEA 16791210
GO:0005829 cytosol IDA,TAS --
genes like me logo Genes that share ontologies with RPL3: view

Pathways & Interactions for RPL3 Gene

genes like me logo Genes that share pathways with RPL3: view

Pathways by source for RPL3 Gene

1 KEGG pathway for RPL3 Gene
1 GeneGo (Thomson Reuters) pathway for RPL3 Gene

Gene Ontology (GO) - Biological Process for RPL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000027 ribosomal large subunit assembly IBA --
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS --
GO:0006364 rRNA processing TAS --
GO:0006412 translation NAS,IEA 12962325
GO:0006413 translational initiation TAS --
genes like me logo Genes that share ontologies with RPL3: view

No data available for SIGNOR curated interactions for RPL3 Gene

Drugs & Compounds for RPL3 Gene

(6) Drugs for RPL3 Gene - From: DrugBank and FDA Approved Drugs

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Omacetaxine mepesuccinate Approved, Investigational Pharma Target, antagonist 0
Xanthinol Approved, Withdrawn Pharma Target, binder 0
Synribo Approved October 2012 Pharma 0
Alpha-Hydroxy-Beta-Phenyl-Propionic Acid Experimental Pharma Target 0
Anisomycin Experimental Pharma Target JNK agonist, potent and specific, JNK, SAPK and p38 activator 0
genes like me logo Genes that share compounds with RPL3: view

Transcripts for RPL3 Gene

mRNA/cDNA for RPL3 Gene

Unigene Clusters for RPL3 Gene

Ribosomal protein L3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RPL3 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b · 3c · 3d ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b · 6c · 6d ^ 7a · 7b · 7c ^ 8a · 8b · 8c ^ 9 ^ 10a · 10b ^ 11 ^
SP1: - - - - - -
SP2: -
SP3: - - -
SP4: - - - - -
SP5: - -
SP6: - - - - - - - - - - - - - -
SP7: - - -
SP8: - - - - -
SP9: - - -
SP10: - - -
SP11: -

ExUns: 12a · 12b

Relevant External Links for RPL3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RPL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RPL3 Gene

Protein differential expression in normal tissues from HIPED for RPL3 Gene

This gene is overexpressed in Nasal epithelium (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RPL3 Gene

Protein tissue co-expression partners for RPL3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RPL3 Gene:


SOURCE GeneReport for Unigene cluster for RPL3 Gene:


Evidence on tissue expression from TISSUES for RPL3 Gene

  • Intestine(5)
  • Liver(5)
  • Lung(5)
  • Muscle(5)
  • Skin(5)
  • Nervous system(5)
  • Eye(4.9)
  • Pancreas(4.9)
  • Blood(4.7)
  • Kidney(4.7)
  • Stomach(4.6)
  • Bone(4.4)
  • Thyroid gland(4.2)
  • Heart(3.6)
  • Lymph node(2.9)
  • Adrenal gland(2.8)
  • Bone marrow(2.8)
  • Gall bladder(2.7)
  • Spleen(2.7)
genes like me logo Genes that share expression patterns with RPL3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPL3 Gene

Orthologs for RPL3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RPL3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RPL3 33
  • 99.65 (n)
(Monodelphis domestica)
Mammalia RPL3 34
  • 96 (a)
(Ornithorhynchus anatinus)
Mammalia RPL3 34
  • 95 (a)
(Canis familiaris)
Mammalia RPL3 34 33
  • 91.56 (n)
(Bos Taurus)
Mammalia RPL3 34 33
  • 90.49 (n)
(Rattus norvegicus)
Mammalia Rpl3 33
  • 89.74 (n)
(Mus musculus)
Mammalia Rpl3 16 34 33
  • 89.16 (n)
(Gallus gallus)
Aves RPL3 34 33
  • 84.62 (n)
(Anolis carolinensis)
Reptilia RPL3 34
  • 95 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia rpl3 33
  • 81.22 (n)
Str.6702 33
African clawed frog
(Xenopus laevis)
Amphibia rpl3-prov 33
(Danio rerio)
Actinopterygii rpl3 34 33
  • 80.31 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8466 33
fruit fly
(Drosophila melanogaster)
Insecta RpL3 34 35 33
  • 72.04 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003556 33
  • 67.87 (n)
(Caenorhabditis elegans)
Secernentea rpl-3 34 33
  • 69.17 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADR206W 33
  • 66.67 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F16511g 33
  • 63.04 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPL3 36 34 33
  • 62.86 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons RPL3B 33
  • 65.36 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.7639 33
(Hordeum vulgare)
Liliopsida Hv.977 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 74 (a)
Cin.3689 33
bread mold
(Neurospora crassa)
Ascomycetes NCU06843 33
  • 68.55 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rpl302 33
  • 64.59 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3689 33
Species where no ortholog for RPL3 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RPL3 Gene

Gene Tree for RPL3 (if available)
Gene Tree for RPL3 (if available)
Evolutionary constrained regions (ECRs) for RPL3: view image

Paralogs for RPL3 Gene

Paralogs for RPL3 Gene

(2) SIMAP similar genes for RPL3 Gene using alignment to 10 proteins:

  • B4DN06_HUMAN
  • G5E9G0_HUMAN
  • H7C3M2_HUMAN
  • H7C422_HUMAN
  • Q49AJ9_HUMAN
  • Q96QL0_HUMAN
  • Q9BT63_HUMAN
genes like me logo Genes that share paralogs with RPL3: view

Variants for RPL3 Gene

Sequence variations from dbSNP and Humsavar for RPL3 Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1000169001 -- 39,318,975(-) G/A intron_variant
rs1000192525 -- 39,316,190(-) G/A intron_variant
rs1000218282 -- 39,314,088(-) C/A intron_variant
rs1000404930 -- 39,314,290(-) G/A intron_variant
rs1000428722 -- 39,316,470(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RPL3 Gene

Variant ID Type Subtype PubMed ID
nsv589033 CNV loss 21841781
nsv834198 CNV loss 17160897
nsv964632 CNV duplication 23825009
nsv966110 CNV duplication 23825009
nsv979677 CNV duplication 23825009

Variation tolerance for RPL3 Gene

Residual Variation Intolerance Score: 15.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.48; 28.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RPL3 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 for RPL3 Gene

Disorders for RPL3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RPL3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
diamond-blackfan anemia
  • diamond-blackfan anemia 1
- elite association - COSMIC cancer census association via MalaCards
Search RPL3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RPL3

genes like me logo Genes that share disorders with RPL3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RPL3 Gene

Publications for RPL3 Gene

  1. A map of 75 human ribosomal protein genes. (PMID: 9582194) Kenmochi N … Page DC (Genome research 1998) 2 3 4 58
  2. Molecular cloning and characterization of a TAR-binding nuclear factor from T cells. (PMID: 7576925) Reddy TR … Wong-Staal F (AIDS research and human retroviruses 1995) 3 4 22 58
  3. The DHX33 RNA Helicase Promotes mRNA Translation Initiation. (PMID: 26100019) Zhang Y … Weber J (Molecular and cellular biology 2015) 3 4 58
  4. A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. (PMID: 23349634) Cloutier P … Coulombe B (PLoS genetics 2013) 3 4 58
  5. Genes associated with telomerase activity levels in esophageal carcinoma cell lines. (PMID: 16364039) Bergqvist M … Paulsson-Karlsson Y (Diseases of the esophagus : official journal of the International Society for Diseases of the Esophagus 2006) 3 22 58

Products for RPL3 Gene

Sources for RPL3 Gene