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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RPL39 Gene

protein-coding   GIFtS: 53
GCID: GC0XM118920

ribosomal protein L39

 Explore 4 diseases affiliated with
RPL39 via our new
 Human Malady Compendium 
Biological research products
for RPL39
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Ribosomal Protein L391 2
L391 2
60S Ribosomal Protein L392

External Ids:    HGNC: 103501   Entrez Gene: 61702   Ensembl: ENSG000001989187   OMIM: 6019045   UniProtKB: P628913   

Export aliases for RPL39 gene to outside databases

Previous GC identifers: GC0XM113738 GC0XM115906 GC0XM116895 GC0XM117674 GC0XM118702 GC0XM118804 GC0XM108414


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for RPL39:
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)

Gene Wiki entry for RPL39


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.1  NT_011786.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RPL39 gene promoter:
         RP58   NCX/Ncx   CUTL1   GATA-1   GATA-2   Ik-2   FOXJ2 (long isoform)   FOXJ2   Ik-1   En-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for RPL39

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RPL39


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xq24   Ensembl cytogenetic band:  Xq24   HGNC cytogenetic band: Xq24

RPL39 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPL39 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM118920:  view genomic region     (about GC identifiers)

Start:
118,920,467 bp from pter      End:
118,925,606 bp from pter
Size:
5,140 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: RL39_HUMAN, P62891 (See protein sequence)
Recommended Name: 60S ribosomal protein L39  
Size: 51 amino acids; 6407 Da
Miscellaneous: This protein is the smallest and one of the most basic of the proteins in liver ribosomes (By
similarity)
Secondary accessions: P02404 P39025 Q9BYF2

Explore the universe of human proteins at neXtProt for RPL39: NX_P62891

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P62891

  • RPL39 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_000991.1  
    ENSEMBL proteins: 
     ENSP00000355315  
    Reactome Protein details: P62891
    Human Recombinant Protein Products: 
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    Uscn Proteins for RPL39

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005829cytosol TAS--
    GO:0022625cytosolic large ribosomal subunit TAS8764829


    RPL39 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    RPL39 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR020083 Ribosomal_L39_CS
     IPR000077 Ribosomal_L39
     IPR023626 Ribosomal_L39e_dom

    Graphical View of Domain Structure for InterPro Entry P62891

    ProtoNet protein and cluster: P62891

    UniProtKB/Swiss-Prot: RL39_HUMAN, P62891
    Similarity: Belongs to the ribosomal protein L39e family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate RPL39:
    hsa-miR-556-3p
    SwitchGear 3'UTR luciferase reporter plasmidRPL39 3' UTR sequence
    Inhib. RNA
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003723RNA binding TAS8764829
    GO:0003735structural constituent of ribosome TAS8764829


    RPL39 for ontologies           About GeneDecksing


    2 GenomeRNAi human phenotypes for RPL39:
     Nuclear 60S biogenesis defects  Nucleoplasmic pre-40S maturati 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Synthesis of PB1-F2
    8/26 pathways (see all 26)
    Viral Protein Synthesis1.00
    Cytoplasmic Ribosomal Proteins0.86
    Viral mRNA Translation1.00
    CFTR translational fidelity (class I mutations)0.83
    Influenza Viral RNA Transcription and Replication1.00
    SMG6 Cleaves mRNA with Premature Termination Codon0.80
    Synthesis of nascent polypeptide containing signal sequence1.00
    L13a-mediated translational silencing of Ceruloplasmin expression0.79
    2Metabolism of mRNA
    Metabolism of mRNA1.00
    Metabolism of RNA0.92
    3Disease
    Disease1.00
    4Generic Transcription Pathway
    Gene Expression0.46
    5Asparagine N-linked glycosylation
    Metabolism of proteins0.15

    Pathway sources
    See GeneCards unified pathways
    Show all pathways


    1 GeneGo (Thomson Reuters) Pathway for RPL39
        CFTR translational fidelity (class I mutations)

    1 BioSystems Pathway for RPL39 
        Cytoplasmic Ribosomal Proteins

    5/28        Reactome Pathways for RPL39 (see all 28)
        Nonsense Mediated Decay Independent of the Exon Junction Complex
    Nonsense-Mediated Decay
    Translation
    SRP-dependent cotranslational protein targeting to membrane
    Eukaryotic Translation Initiation


    1         Kegg Pathway  (Kegg details for RPL39):
        Ribosome


    RPL39 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RPL39

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/51 Interacting proteins for RPL39 (ENSP000003553154) via UniProtKB, MINT, STRING, and/or I2D (see all 51)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RPL30ENSP000002870384STRING: ENSP00000287038
    RPL4ENSP000003114304STRING: ENSP00000311430
    RPL27AENSP000003460154STRING: ENSP00000346015
    RPL5ENSP000003593454STRING: ENSP00000359345
    RPL38ENSP000003098304STRING: ENSP00000309830
    About this table

    Gene Ontology (GO): 5/13 biological process terms (GO ID links to tree view) (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000184nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS--
    GO:0006412translation TAS--
    GO:0006413translational initiation TAS--
    GO:0006414translational elongation TAS--
    GO:0006415translational termination TAS--


    RPL39 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RPL39
    Search CenterWatch for drugs/clinical trials and news about RPL39 / RL39 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RPL39 gene: 
    NM_001000.2  

    Unigene Clusters for RPL39:

    Ribosomal protein L39
    Hs.300141  [show with all ESTs], Hs.558387  [show with all ESTs]
    Unigene Representative Sequences: CD556052, BU566074
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000477403 ENST00000468844 ENST00000361575(uc004erx.1)

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate RPL39:
    hsa-miR-556-3p
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    Inhib. RNA
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    Additional cDNA sequence: BC070205.1 

    24/35 DOTS entries (see all 35):

    DT.95137965  DT.100741480  DT.92038448  DT.95120025  DT.100859048  DT.97800524  DT.91914786  DT.100741485 
    DT.100741503  DT.120990764  DT.121304871  DT.91942842  DT.95331017  DT.98131909  DT.100638469  DT.100741512 
    DT.121355960  DT.91769537  DT.100741475  DT.100741499  DT.100741505  DT.102822622  DT.121304859  DT.121304893 

    24/1120 AceView cDNA sequences (see all 1120):

    BE220782 BE910355 F27699 BM705322 BM741688 BM836269 BU543568 AI805128 
    AJ573240 F24404 CB108196 F30375 BU186971 BI859684 T49725 BE122893 
    N29613 NM_001000 AW020426 F28164 C14339 BM768382 D55370 AA507131 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RPL39 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TTACCATATC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    RPL39 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Endoderm-like cells (Generation of hepato...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See RPL39 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RPL39

    SOURCE GeneReport for Unigene clusters: Hs.300141 Hs.558387
        SABiosciences Custom PCR Arrays for RPL39
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    In Situ
    Assay Products:
     

     
    Search Advanced Cell Diagnostics for RNAscope RNA in situ hybridization assays for RPL39

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for RPL39 gene from 8/28 species (see all 28)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves RPL391 ribosomal protein L39 83.66(n)
    98.04(a)
      374132  NM_204272.1  NP_989603.1 
    lizard
    (Anolis carolinensis)
    Reptilia RPL39L6
    --
    96(a)
    1 → many
    GL343950.1(105218-107398)
    African clawed frog
    (Xenopus laevis)
    Amphibia 480473812   -- 79.88(n)    48047381 
    zebrafish
    (Danio rerio)
    Actinopterygii CK400694.12   -- 78.47(n)    CK400694.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta RpL396
    Ribosomal protein L39
    73(a)
    1 → many
    2R(19949376-19949952)
    worm
    (Caenorhabditis elegans)
    Secernentea rpl-396
    60S ribosomal protein L39
    75(a)
    1 → many
    V(7775719-7776067)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT3G021906
    AT4G319856
    (see all 3)
    60S ribosomal protein L39-1
    (see all 3)
    73(a)
    71(a)
    (see all 3)
    many ↔ many
    many ↔ many
    (see all 3)
    3(405816-406401)
    4(15469895-15470559)
    rice
    (Oryza sativa)
    Liliopsida --
    --
    60S ribosomal protein L39, putative, expressed
    78(a)
    76(a)
    many ↔ many
    many ↔ many
    2(33908132-33908773)
    6(4032796-4033130)


    ENSEMBL Gene Tree for RPL39 (if available)
    TreeFam Gene Tree for RPL39 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RPL39 gene
    RPL39L2  
    2 SIMAP similar genes for RPL39 using alignment to 1 protein entry:     RL39_HUMAN:
    RPL39P5    RPL39L

    RPL39 for paralogs           About GeneDecksing


    5/44 Pseudogenes.org Pseudogenes for RPL39 (see all 44)
    PGOHUM00000238541 PGOHUM00000261108 PGOHUM00000239510 PGOHUM00000248489 PGOHUM00000247747


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/122 NCBI SNPs in RPL39 are shown (see all 122    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs558502321,2
    C,F,--118920006(+) CGTGGT/CGGCTC 1 -- ds50011Minor allele frequency- C:0.34NS 116
    rs1810642101,2
    --118920031(+) AACACC/TTTGGG 1 -- ds50010--------
    rs1864002761,2
    --118920093(+) AACATG/TGTGAA 1 -- ds50010--------
    rs563098831,2
    C,F,--118920298(+) AAAATAAAAT/
            
    TTACA
    1 -- ds50011Minor allele frequency- -:0.27NS 130
    rs1420877351,2
    C,--118920397(+) TACTGG/TATAGT 1 -- ds50010--------
    rs1908597971,2
    --118920514(+) ACCAAC/TGTGTT 1 -- ut310--------
    rs1121732031,2
    C,--118920547(+) ACACGT/CCGAAA 1 -- ut312Minor allele frequency- C:0.02CSA NS 132
    rs2010004801,2
    --118920599(+) TGATCA/GTGACC 1 -- ut310--------
    rs791924371,2
    C,F,--118920652(+) TTATAG/AACCCA 2 /L syn13Minor allele frequency- A:0.05NA WA 4552
    rs1391395621,2
    C,F,--118920677(+) CAATGT/CCTCCT 2 /R syn11Minor allele frequency- C:0.00NA 4548

    HapMap Linkage Disequilibrium report for RPL39 (118920467 - 118925606 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for RPL39: --
    Locus Specific Mutation Databases (LSDB): RPL39

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RPL39
    DNA2.0 Custom Variant and Variant Library Synthesis for RPL39

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    RPL39 for disorders           About GeneDecksing

    OMIM gene information: 601904    OMIM disorders: --

    4 diseases for RPL39:    About MalaCards
    pure red-cell aplasia    diamond-blackfan anemia    anemia    malaria

    1 disease from the University of Copenhagen DISEASES database for RPL39:
    Diamond-Blackfan anemia

    Export disorders for RPL39 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for RPL39 gene, integrated from 9 sources (see all 15):
    (articles sorted by number of sources associating them with RPL39)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning of a cDNA encoding human ribosomal protein L39. (PubMed id 8764829)1, 2, 3, 9 Otsuka S.... Itakura M. (1996)
    2. Primary structures and sequence analysis of human ribosomal proteins L39 and S27. (PubMed id 8908372)1, 2, 9 Tsui S.K.W.... Lee C.Y. (1996)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    4. The human ribosomal protein genes: sequencing and comparative analysis of 73 genes. (PubMed id 11875025)1, 2 Yoshihama M.... Kenmochi N. (2002)
    5. A complete map of the human ribosomal protein genes: assignment of 80 genes to the cytogenetic map and implications for human disorders. (PubMed id 11401437)1, 2 Uechi T.... Kenmochi N. (2001)
    6. A high-throughput approach for measuring temporal chan ges in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (2012)
    7. The molecular mechanics of eukaryotic translation. (PubMed id 15189156)1 Kapp L.D. and Lorsch J.R. (2004)
    8. Regulated release of L13a from the 60S ribosomal subunit as a mechanism of transcript-specific translational control. (PubMed id 14567916)1 Mazumder B....Fox P.L. (2003)
    9. Characterization and analysis of posttranslational modifications of the human large cytoplasmic ribosomal subunit proteins by mass spectrometry and Edman sequencing. (PubMed id 12962325)1 Odintsova T.I....Karpova G.G. (2003)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 6170 HGNC: 10350 AceView: RPL39 Ensembl:ENSG00000198918 euGenes: HUgn6170
    ECgene: RPL39 Kegg: 6170 H-InvDB: RPL39

    (According to HUGE)
    About This Section
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for RPL39 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for RPL39 gene:
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