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

MRPL39 Gene

protein-coding   GIFtS: 52
GCID: GC21M026957

Mitochondrial Ribosomal Protein L39

  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Mitochondrial Ribosomal Protein L391 2     MRP-L392 3
MRPL52 3 5     MRP-L52 3
39S Ribosomal Protein L5, Mitochondrial2 3     RPML52 3
C21orf922 3     39S Ribosomal Protein L39, Mitochondrial2
L39mt2 3     PRED222
L5mt2 3     PRED662

External Ids:    HGNC: 140271   Entrez Gene: 541482   Ensembl: ENSG000001547197   OMIM: 6118455   UniProtKB: Q9NYK53   

Export aliases for MRPL39 gene to outside databases

Previous GC identifers: GC21M023536 GC21M025879 GC21M012361


(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 MRPL39 Gene:
Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the
mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit.
They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is
reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain
a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and
sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a
39S subunit protein. Two transcript variants encoding distinct isoforms have been described. A pseudogene
corresponding to this gene is found on chromosome 5q. (provided by RefSeq, Jul 2008)

GeneCards Summary for MRPL39 Gene: 
MRPL39 (mitochondrial ribosomal protein L39) is a protein-coding gene. Diseases associated with MRPL39 include tuberculosis. GO annotations related to this gene include molecular_function and nucleotide binding. An important paralog of this gene is TARS2.

Gene Wiki entry for MRPL39 Gene


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000021.8  NC_018932.2  NT_011512.11  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for MRPL39
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidMRPL39 promoter sequence
   Search SABiosciences Chromatin IP Primers for MRPL39

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat MRPL39


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

Entrez Gene cytogenetic band: 21q21.3   Ensembl cytogenetic band:  21q21.3   HGNC cytogenetic band: 21q11.2-q21

MRPL39 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MRPL39 gene location

GeneLoc information about chromosome 21         GeneLoc Exon Structure

GeneLoc location for GC21M026957:  view genomic region     (about GC identifiers)

Start:
26,957,968 bp from pter      End:
26,979,829 bp from pter
Size:
21,862 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: RM39_HUMAN, Q9NYK5 (See protein sequence)
Recommended Name: 39S ribosomal protein L39, mitochondrial  
Size: 338 amino acids; 38712 Da
Subcellular location: Mitochondrion
Caution: Ref.1 indicates C21orf8 as a synonym for this orf, this is incorrect, C21orf8 is already assigned to
another chromosome 21 region
Caution: It is uncertain whether Met-1 or Met-6 is the initiator
Sequence caution: Sequence=AAF44696.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=AAQ13505.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAA91177.1;
Type=Frameshift; Positions=72;
Secondary accessions: C9JYA5 Q32Q74 Q5QTR3 Q96Q65 Q9BSQ7 Q9BZV6 Q9NX44
Alternative splicing: 2 isoforms:  Q9NYK5-1   Q9NYK5-2   

Explore the universe of human proteins at neXtProt for MRPL39: NX_Q9NYK5

Explore proteomics data for MRPL39 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9NYK5

  • MRPL39 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    MRPL39 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_059142.2  NP_542984.2  

    ENSEMBL proteins: 
     ENSP00000284967   ENSP00000305682   ENSP00000404426  

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    Cloud-Clone Corp. Proteins for MRPL39 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion ----
    GO:0005761mitochondrial ribosome NAS11167009

    MRPL39 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    MRPL: Mitochondrial ribosomal proteins / large subunits

    3 InterPro protein domains:
     IPR012675 Beta-grasp_dom
     IPR015552 Ribosomal_L39_mit
     IPR018163 Thr/Ala-tRNA-synth_IIc_edit

    Graphical View of Domain Structure for InterPro Entry Q9NYK5

    ProtoNet protein and cluster: Q9NYK5

    UniProtKB/Swiss-Prot: RM39_HUMAN, Q9NYK5
    Similarity: To the N-terminal of threonyl-tRNA synthetases


    MRPL39 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003674molecular_function ND--
         
    MRPL39 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for MRPL39:
     Synthetic lethal with Ras 

    Animal Models:
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for MRPL39

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    5/252 Interacting proteins for MRPL39 (Q9NYK52, 3 ENSP000003056824) via UniProtKB, MINT, STRING, and/or I2D (see all 252)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ICT1Q141972, 3, ENSP000003015854MINT-8079030 I2D: score=1 STRING: ENSP00000301585
    USP32Q8NFA03, ENSP000003008964I2D: score=2 STRING: ENSP00000300896
    PUF60Q9UHX13I2D: score=5 
    RPL3P390233I2D: score=3 
    PAN2Q504Q33I2D: score=2 
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--

    MRPL39 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 MRPL39 (RM39)

    Search CenterWatch for drugs/clinical trials and news about MRPL39 / RM39

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for MRPL39 gene (2 alternative transcripts): 
    NM_017446.3  NM_080794.3  

    Unigene Cluster for MRPL39:

    Mitochondrial ribosomal protein L39
    Hs.420696  [show with all ESTs]
    Unigene Representative Sequence: BX648335
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000352957(uc002ylo.3) ENST00000307301(uc002yln.3) ENST00000419219

    miRNA
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    Additional mRNA sequence: 

    AF109357.1 AF239727.1 AF270511.1 AK000458.1 AK225878.1 BC004896.2 BC107719.1 BX648335.1 

    9 DOTS entries:

    DT.416474  DT.121138158  DT.101968028  DT.70103684  DT.95376051  DT.100786544  DT.100025654  DT.120831587 
    DT.92432375 

    24/171 AceView cDNA sequences (see all 171):

    AW661737 BE278484 CR614734 W93466 AA426183 BF111473 AI263419 AI470380 
    CR598909 CD365644 AI306121 AA424729 AV706014 AI193223 AF239727 CA418845 
    BU601241 AF270511 AA417020 BG536708 AI207266 AI276282 F09765 AI150612 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for MRPL39    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11
    SP1:                                                                              
    SP2:                                      -                                       
    SP3:        -                                                                     


    ECgene alternative splicing isoforms for MRPL39

    (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

    MRPL39 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTTTAATTTA
    MRPL39 Expression
    About this image


    See MRPL39 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for MRPL39

    SOURCE GeneReport for Unigene cluster: Hs.420696

    UniProtKB/Swiss-Prot: RM39_HUMAN, Q9NYK5
    Tissue specificity: Isoform 1 is ubiquitously expressed. Isoform 2 is heart-specific

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    In Situ
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    (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 animals and fungi.

    Orthologs for MRPL39 gene from 8/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Mrpl391 , 5 mitochondrial ribosomal protein L391, 5 83.63(n)1
    86.23(a)1
      16 (46.92 cM)5
    273931  NM_017404.41  NP_059100.31 
     847175765 
    chicken
    (Gallus gallus)
    Aves MRPL391 mitochondrial ribosomal protein L39 71.94(n)
    70.97(a)
      418475  XM_416683.3  XP_416683.1 
    lizard
    (Anolis carolinensis)
    Reptilia MRPL396
    Uncharacterized protein
    63(a)
    1 ↔ 1
    3(148331621-148356539)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.166282 Xenopus laevis transcribed sequence with moderate similarity more 73.33(n)    BX855294.1 
    zebrafish
    (Danio rerio)
    Actinopterygii mrpl391 mitochondrial ribosomal protein L39 54.54(n)
    51.15(a)
      334588  NM_199915.2  NP_956209.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta mRpL53
    mRpL391
    protein biosynthesis threonine-tRNA
    ligase3
    mitochondrial ribosomal protein L391
    39(a)3
    49.21(n)1
    42.91(a)1
      71B13
    396271  NM_079351.31  NP_524075.21 
    worm
    (Caenorhabditis elegans)
    Secernentea tars-16
    Threonine--tRNA ligase, cytoplasmic
    9(a)
    possible ortholog
    II(11691326-11695657)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes THS16
    Threonyl-tRNA synthetase, essential cytoplasmic pr...
    8(a)
    1 → many
    IX(212499-214703)


    ENSEMBL Gene Tree for MRPL39 (if available)
    TreeFam Gene Tree for MRPL39 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for MRPL39 gene
    TARS22  TARSL22  TARS2  

    MRPL39 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for MRPL39
    PGOHUM00000235246


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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

    10/619 SNPs in MRPL39 are shown (see all 619)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 21 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0520414
    ----see VAR_0520412 S P mis40--------
    rs573731691,2
    C,F--26957700(+) TGTTCG/AGCAAA 2 -- ds50013Minor allele frequency- A:0.06WA CSA 122
    rs124820561,2
    C,F,H--26957749(+) TTAGAA/CATTAC 2 -- ds500117Minor allele frequency- C:0.12NS EA NA 2224
    rs1425134841,2
    C,F--26958045(+) TGTTGC/TTTTAC 3 T A ut31 mis11Minor allele frequency- T:0.00NA 4496
    rs2001878391,2
    --26958103(+) ATAAAC/TACTTT 2 -- int10--------
    rs1395963401,2
    C--26958334(+) CAGCCA/GTAAAA 2 -- int10--------
    rs99740621,2
    C,F,H--26958607(+) CAGCAT/ATCAAG 2 -- int15Minor allele frequency- A:0.00NS EA WA 526
    rs1861267901,2
    --26958665(+) AATTCA/GGCCTA 2 -- int10--------
    rs1452287741,2
    --26958666(+) ATTCAA/GCCTAA 2 -- int10--------
    rs791442221,2
    F--26958726(+) ATTCTC/GTTCTA 2 -- int11Minor allele frequency- G:0.03NA 120

    HapMap Linkage Disequilibrium report for MRPL39 (26957968 - 26979829 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for MRPL39:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv510501CNV Loss20534489

    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing MRPL39
    DNA2.0 Custom Variant and Variant Library Synthesis for MRPL39

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 611845    OMIM disorders: --

    2 diseases for MRPL39:    About MalaCards
    tuberculosis    


    MRPL39 for disorders           About GeneDecksing

    Genetic Association Database (GAD): MRPL39
    Human Genome Epidemiology (HuGE) Navigator: MRPL39 (1 document)

    Export disorders for MRPL39 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 MRPL39 gene, integrated from 9 sources (see all 25):
    (articles sorted by number of sources associating them with MRPL39)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The human mitochondrial ribosomal protein genes: mapping of 54 genes to the chromosomes and implications for human disorders. (PubMed id 11543634)1, 2, 3 Kenmochi N....Tanaka T. (2001)
    2. Genetic variants in nuclear-encoded mitochondrial gen es influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (2010)
    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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    5. Heart-specific splice-variant of a human mitochondrial ribosomal protein (mRNA processing; tissue specific splicing). (PubMed id 11167009)1, 2 Spirina O....Fischel-Ghodsian N. (2000)
    6. Mammalian mitochondrial ribosomal proteins (2). Amino acid sequencing, characterization, and identification of corresponding gene sequences. (PubMed id 10593885)1, 2 O'Brien T.W.... Graack H.R. (1999)
    7. Quantitative study of the interactome of PKCz involved in the EGF-induced tumor cell chemotaxis. (PubMed id 23402259)1 Chen R....Zhang N. (2013)
    8. The SOX2-interactome in brain cancer cells identifies the requirement of MSI2 and USP9X for the growth of brain tumor cells. (PubMed id 23667531)1 Cox J.L....Rizzino A. (2013)
    9. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    10. Biochemical and phosphoproteomic analysis of the helix -loop-helix protein E47. (PubMed id 22354994)1 Teachenor R....Murre C. (2012)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 54148 HGNC: 14027 AceView: MRPL39 Ensembl:ENSG00000154719 euGenes: HUgn54148
    ECgene: MRPL39 H-InvDB: MRPL39

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for MRPL39 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for MRPL39 gene:
    Search GeneIP for patents involving MRPL39

    GeneCards and IP:
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