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

NDUFAF3 Gene

protein-coding   GIFtS: 50
GCID: GC03P049057

NADH dehydrogenase (ubiquinone) complex I, assembly factor...

(Previous names: chromosome 3 open reading frame 60, NADH dehydrogenase...)
(Previous symbol: C3orf60)
 Explore 7 diseases affiliated with
NDUFAF3 via our new
 Human Malady Compendium 
Biological research products
for NDUFAF3
    

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

Aliases
NADH Dehydrogenase (Ubiquinone) Complex I, Assembly Factor 31 2     DKFZP564J01231
C3orf601 2 3     MGC105271
2P11 2     Chromosome 3 Open Reading Frame 601
E3-31 2     NADH Dehydrogenase [Ubiquinone] 1 Alpha Subcomplex Assembly Factor 32
NADH Dehydrogenase (Ubiquinone) 1 Alpha Subcomplex, Assembly Factor 31 2     Nuclear Protein E3-32

External Ids:    HGNC: 299181   Entrez Gene: 259152   Ensembl: ENSG000001780577   OMIM: 6129115   UniProtKB: Q9BU613   

Export aliases for NDUFAF3 gene to outside databases

Previous GC identifer: GC03P049034


(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 NDUFAF3:
This gene encodes a mitochondrial complex I assembly protein that interacts with complex I subunits. Mutations in this
gene cause mitochondrial complex I deficiency, a fatal neonatal disorder of the oxidative phosphorylation system.
Alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq, Jul
2009)

UniProtKB/Swiss-Prot: NDUF3_HUMAN, Q9BU61
Function: Essential factor for the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I)

Gene Wiki entry for NDUFAF3 (C3orf60)


(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_000003.11  NC_018914.1  NT_022517.18  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the NDUFAF3 gene promoter:
         E2F-1   E2F   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNDUFAF3 promoter sequence
   Search SABiosciences Chromatin IP Primers for NDUFAF3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NDUFAF3


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

Entrez Gene cytogenetic band: 3p21.31   Ensembl cytogenetic band:  3p21.31   HGNC cytogenetic band: 3p21.31

NDUFAF3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NDUFAF3 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P049057:  view genomic region     (about GC identifiers)

Start:
49,057,892 bp from pter      End:
49,060,928 bp from pter
Size:
3,037 bases      Orientation:
plus 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: NDUF3_HUMAN, Q9BU61 (See protein sequence)
Recommended Name: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 3  
Size: 184 amino acids; 20350 Da
Subunit: Interacts with NDUFAF4, NDUFS2 and NDUFS3
Subcellular location: Nucleus (By similarity). Mitochondrion inner membrane
Alternative splicing: 2 isoforms:  Q9BU61-1   Q9BU61-2   

Explore the universe of human proteins at neXtProt for NDUFAF3: NX_Q9BU61

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9BU61

  • NDUFAF3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (4 alternative transcripts): 
    NP_951032.1  NP_951033.1  NP_951047.1  NP_951056.1  

    ENSEMBL proteins: 
     ENSP00000323003   ENSP00000323076   ENSP00000378843   ENSP00000402465  

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    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005739mitochondrion ----
    GO:0005743mitochondrial inner membrane IDA19463981


    NDUFAF3 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

    NDUFAF3 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR007523 NADH_Ub_cplx-1_asu_assmbl-fac3

    Graphical View of Domain Structure for InterPro Entry Q9BU61

    ProtoNet protein and cluster: Q9BU61


    (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

    Function Summary:

         UniProtKB/Swiss-Prot: NDUF3_HUMAN, Q9BU61
    Function: Essential factor for the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI19463981


    NDUFAF3 for ontologies           About GeneDecksing


    2 GenomeRNAi human phenotypes for NDUFAF3:
     Increased gamma-H2AX phosphory  Low eccentricity cells 


    (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



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for NDUFAF3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 11)

    5/241 Interacting proteins for NDUFAF3 (Q9BU612, 3 ENSP000003230764) via UniProtKB, MINT, STRING, and/or I2D (see all 241)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NDUFS2O753062, 3, ENSP000003569724MINT-8079030 I2D: score=1 STRING: ENSP00000356972
    NDUFS3O754892, 3, ENSP000002637744MINT-8079030 I2D: score=1 STRING: ENSP00000263774
    ICT1Q141972, 3, ENSP000003015854MINT-8079030 I2D: score=1 STRING: ENSP00000301585
    LSM1O151163, ENSP000003105964I2D: score=3 STRING: ENSP00000310596
    GEMP550403, ENSP000002975964I2D: score=2 STRING: ENSP00000297596
    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:0032981mitochondrial respiratory chain complex I assembly IMP19463981


    NDUFAF3 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
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    (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,
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    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 NDUFAF3 gene (5 alternative transcripts): 
    NM_199069.1  NM_199070.1  NM_199073.1  NM_199074.1  NM_199417.1  

    Unigene Cluster for NDUFAF3:

    NADH dehydrogenase (ubiquinone) complex I, assembly factor 3
    Hs.31387  [show with all ESTs]
    Unigene Representative Sequence: BC111004
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000326912 ENST00000326925(uc003cvn.3 uc003cvp.3 uc003cvq.3 uc003cvr.3)
    ENST00000395458 ENST00000451378 ENST00000496152 ENST00000480392

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    Additional cDNA sequence: 

    AL049955.1 BC002873.2 BC111004.1 

    21 DOTS entries:

    DT.100696815  DT.95368369  DT.100052885  DT.40235956  DT.92437665  DT.120852572  DT.100818255  DT.92437662 
    DT.100044240  DT.95152922  DT.100818254  DT.92437664  DT.95162303  DT.120852592  DT.95259889  DT.100818253 
    DT.120852548  DT.100810143  DT.120852558  DT.120852599  DT.120852487 

    24/380 AceView cDNA sequences (see all 380):

    AA443755 BM048755 BI831431 AA714358 BU789687 BI964206 AI817443 AA687168 
    BM905944 BI829966 NM_199073 BU541706 AW005133 CD358942 BU167624 CA450306 
    BQ645068 BG750155 BQ220921 BM507361 AA552562 BI762100 AA534495 BI963892 

    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for NDUFAF3 (see all 6)    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b · 3c · 3d ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c
    SP1:        -     -     -     -     -                                                   
    SP2:              -     -     -     -                                                   
    SP3:                                                                                    
    SP4:                                                                                    
    SP5:                                            -                                       


    ECgene alternative splicing isoforms for NDUFAF3

    (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

    NDUFAF3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AAGGCCGAGT

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

    About this image
    See NDUFAF3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for NDUFAF3

    SOURCE GeneReport for Unigene cluster: Hs.31387
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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 eukaryotes.

    Orthologs for NDUFAF3 gene from 8/23 species (see all 23)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ndufaf31 , 5 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, more1, 5 78.99(n)1
    80.43(a)1
      9 (59.50 cM)5
    667061  NM_023247.11  NP_075736.11 
     1085658665 
    lizard
    (Anolis carolinensis)
    Reptilia NDUFAF36
    --
    55(a)
    1 ↔ 1
    2(187882355-187887544)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.157602 Transcribed sequence with weak similarity to protein more 76.12(n)    137731791 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1531761 zgc:153176 64.6(n)
    63.45(a)
      791133  NM_001080615.1  NP_001074084.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG55691 CG5569 52.49(n)
    41.73(a)
      37783  NM_137996.3  NP_611840.1 
    worm
    (Caenorhabditis elegans)
    Secernentea nuaf-31 Protein NUAF-3 46.43(n)
    40.71(a)
      187686  NM_001028157.2  NP_001023328.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT2G445256
    AT3G601506
    uncharacterized protein
    25(a)
    25(a)
    many → 1
    many → 1
    2(18382070-18383513)
    3(22222105-22223512)
    rice
    (Oryza sativa)
    Liliopsida --
    AGAP003819-PA, putative, expressed
    25(a)
    1 ↔ 1
    10(22564559-22568580)


    ENSEMBL Gene Tree for NDUFAF3 (if available)
    TreeFam Gene Tree for NDUFAF3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for NDUFAF3 gene
    2 SIMAP similar genes for NDUFAF3 using alignment to 1 protein entry:     NDUF3_HUMAN:
    C3orf60    DKFZp564J0123

    NDUFAF3 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for NDUFAF3
    PGOHUM00000259850


    (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

    10/69 NCBI SNPs in NDUFAF3 are shown (see all 69    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2000753981,2
    --49056025(+) ACCGG-/AAAAAA 3 -- us2k1 int10--------
    rs1867949381,2
    --49056214(+) GGGGCC/TCTCCC 3 -- int1 us2k10--------
    rs1479919941,2
    --49056282(+) ACCCGA/GTGGGC 3 -- int1 us2k10--------
    rs1912348501,2
    --49056308(+) CGTCTC/GTTCTC 3 -- int1 us2k10--------
    rs2019931931,2
    --49056327(+) CTCAC-/ATGTTTG 3 -- us2k1 int10--------
    rs1831586061,2
    --49056493(+) TTCTCA/GTTTGA 3 -- us2k1 int10--------
    rs1878918681,2
    --49056600(+) CTCCCA/GGATTC 3 -- us2k1 int10--------
    rs1899782881,2
    --49056647(+) ATTACC/GGGCGC 4 -- us2k1 int10--------
    rs1387669381,2
    --49057200(+) ACCGCG/TCCCGG 7 -- ds5001 int1 us2k10--------
    rs1822899801,2
    --49057204(+) CGCCCA/GGCTCA 7 -- ds5001 int1 us2k10--------

    HapMap Linkage Disequilibrium report for NDUFAF3 (49057892 - 49060928 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for NDUFAF3: --
    Human Gene Mutation Database (HGMD): NDUFAF3

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    (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

    NDUFAF3 for disorders           About GeneDecksing

    OMIM gene information: 612911   
    OMIM disorders: 252010  
    UniProtKB/Swiss-Prot: NDUF3_HUMAN, Q9BU61
  • Defects in NDUFAF3 are a cause of mitochondrial complex I deficiency (MT-C1D) [MIM:252010]. A disorder of the
  • mitochondrial respiratory chain that causes a wide range of clinical disorders, from lethal neonatal disease to
    adult-onset neurodegenerative disorders. Phenotypes include macrocephaly with progressive leukodystrophy, non-specific
    encephalopathy, cardiomyopathy, myopathy, liver disease, Leigh syndrome, Leber hereditary optic neuropathy, and some
    forms of Parkinson disease

    7 diseases for NDUFAF3:    About MalaCards
    mitochondrial complex i deficiency    leber hereditary optic neuropathy    paralytic poliomyelitis    poliomyelitis
    leukodystrophy    neuropathy    parkinson's disease

    Human Genome Epidemiology (HuGE) Navigator: NDUFAF3 (1 document)

    Export disorders for NDUFAF3 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 NDUFAF3 gene, integrated from 9 sources (see all 15):
    (articles sorted by number of sources associating them with NDUFAF3)
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    1. 2P1, a novel male mouse cDNA specifically expressed during meiosis. (PubMed id 12653254)1, 3, 9 Hammami-Hamza S....Finaz C. (2003)
    2. Mutations in NDUFAF3 (C3ORF60), encoding an NDUFAF4 (C6ORF66)- interacting complex I assembly protein, cause fatal neonatal mitochondrial disease. (PubMed id 19463981)1, 2 Saada A....Nijtmans L.G. (2009)
    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. Molecular cloning of a novel alternatively spliced nuclear protein. (PubMed id 9349717)1, 3 Hartmann A.M. and Stamm S. (1997)
    5. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    6. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    7. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    8. A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome. (PubMed id 20186120)1 Richter R....Chrzanowska-Lightowlers Z.M. (2010)
    9. Genetic variants in nuclear-encoded mitochondrial gen es influence AIDS progression. (PubMed id 20877624)1 Hendrickson S.L....O'Brien S.J. (2010)
    10. Protein interaction data set highlighted with human Ras-MAPK/PI3K signaling pathways. (PubMed id 18624398)1 Wang J....He F. (2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 25915 HGNC: 29918 AceView: DKFZP564J0123 Ensembl:ENSG00000178057 euGenes: HUgn25915
    ECgene: NDUFAF3 H-InvDB: NDUFAF3

    (According to HUGE)
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      --

    (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 NDUFAF3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for NDUFAF3 gene:
    Search GeneIP for patents involving NDUFAF3

    GeneCards and IP:
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