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LFNG Gene

protein-coding   GIFtS: 65
GCID: GC07P002552

LFNG O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase

(Previous names: lunatic fringe (Drosophila) homolog, lunatic fringe homolog...)
  See LFNG-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
LFNG O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase1 2     Lunatic Fringe Homolog (Drosophila)1
EC 2.4.1.2223 8     Beta-1,3-N-Acetylglucosaminyltransferase Lunatic Fringe2
SCDO32 5     O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase3
Lunatic Fringe (Drosophila) Homolog1     

External Ids:    HGNC: 65601   Entrez Gene: 39552   Ensembl: ENSG000001060037   OMIM: 6025765   UniProtKB: Q8NES33   

Export aliases for LFNG gene to outside databases

Previous GC identifers: GC07P002201 GC07P002303 GC07P002302 GC07P002330 GC07P002524 GC07P002469


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for LFNG Gene:
This gene is a member of the fringe gene family which also includes radical and manic fringe genes. They all
encode evolutionarily conserved glycosyltransferases that act in the Notch signaling pathway to define boundaries
during embryonic development. While their genomic structure is distinct from other glycosyltransferases, fringe
proteins have a fucose-specific beta-1,3-N-acetylglucosaminyltransferase activity that leads to elongation of
O-linked fucose residues on Notch, which alters Notch signaling. This gene product is predicted to be a
single-pass type II Golgi membrane protein but it may also be secreted and proteolytically processed like the
related proteins in mouse and Drosophila (PMID: 9187150). Mutations in this gene have been associated with
autosomal recessive spondylocostal dysostosis 3. Multiple transcript variants encoding different isoforms have
been found for this gene. (provided by RefSeq, Oct 2009)

GeneCards Summary for LFNG Gene:
LFNG (LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase) is a protein-coding gene. Diseases associated with LFNG include spondylocostal dysostosis 3, and lfng-related spondylocostal dysostosis, autosomal recessive. GO annotations related to this gene include O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity. An important paralog of this gene is MFNG.

UniProtKB/Swiss-Prot: LFNG_HUMAN, Q8NES3
Function: Glycosyltransferase that initiates the elongation of O-linked fucose residues attached to EGF-like
repeats in the extracellular domain of Notch molecules. Decreases the binding of JAGGED1 to NOTCH2 but not that
of DELTA1. Essential mediator of somite segmentation and patterning (By similarity)

Gene Wiki entry for LFNG 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000007.13  NC_018918.2  NT_007819.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the LFNG gene promoter:
         GR   SREBP-1c   GR-beta   SREBP-1b   GATA-2   c-Ets-1   HEN1   SREBP-1a   GR-alpha   Pax-4a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for LFNG

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat LFNG


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

Entrez Gene cytogenetic band: 7p22.2   Ensembl cytogenetic band:  7p22.3   HGNC cytogenetic band: 7p22.3

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

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07P002552:  view genomic region     (about GC identifiers)

Start:
2,552,163 bp from pter      End:
2,568,811 bp from pter
Size:
16,649 bases      Orientation:
plus strand

1 alternative location:
Chr7+,CRA_TCAG 2,600,032-2,616,654     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: LFNG_HUMAN, Q8NES3 (See protein sequence)
Recommended Name: Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe  
Size: 379 amino acids; 41773 Da
Cofactor: Manganese (By similarity)
Secondary accessions: B3KTY6 B5MCR5 O00589 Q96C39 Q9UJW5
Alternative splicing: 4 isoforms:  Q8NES3-1   Q8NES3-2   Q8NES3-3   Q8NES3-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for LFNG: NX_Q8NES3

Explore proteomics data for LFNG at MOPED

Post-translational modifications: 

  • A soluble form may be derived from the membrane form by proteolytic processing (Potential)1
  • Glycosylation2 at Asn167
  • Selected DME Specific Peptides for LFNG (Q8NES3) (see all 13)
     DDDNYVN  RLPDDCT  QVTLSYG  FIAVKTT 


    See LFNG Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001035257.1  NP_001035258.1  NP_001159827.1  NP_002295.1  

    ENSEMBL proteins: 
     ENSP00000385764   ENSP00000384786   ENSP00000222725   ENSP00000352579   ENSP00000343095  
    Reactome Protein details: Q8NES3

    LFNG Human Recombinant Protein Products:

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    Novus Biologicals LFNG Protein
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    Cloud-Clone Corp. Proteins for LFNG

     
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    B3GT: Beta 3-glycosyltransferases

    2 InterPro protein domains:
     IPR017374 Fringe
     IPR003378 Fringe-like

    Graphical View of Domain Structure for InterPro Entry Q8NES3

    ProtoNet protein and cluster: Q8NES3

    1 Blocks protein domain: IPB003378 Fringe-like

    UniProtKB/Swiss-Prot: LFNG_HUMAN, Q8NES3
    Similarity: Belongs to the glycosyltransferase 31 family


    Find genes that share domains with LFNG           About GenesLikeMe


    (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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: LFNG_HUMAN, Q8NES3
    Function: Glycosyltransferase that initiates the elongation of O-linked fucose residues attached to EGF-like
    repeats in the extracellular domain of Notch molecules. Decreases the binding of JAGGED1 to NOTCH2 but not that
    of DELTA1. Essential mediator of somite segmentation and patterning (By similarity)
    Catalytic activity: Transfers a beta-D-GlcNAc residue from UDP-D-GlcNAc to the fucose residue of a fucosylated
    protein acceptor

         Genatlas biochemistry entry for LFNG:
    lunatic fringe,putative regulator of developmental processes through regulation of the sensitivity of NOTCH
    receptor genes for their specific ligands,essential mediator of somite segmentation and patterning

         Enzyme Number (IUBMB): EC 2.4.1.2221 2

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0016757transferase activity, transferring glycosyl groups ----
    GO:0033829O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity ISS--
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with LFNG           About GenesLikeMe


    Phenotypes:
         14 MGI mutant phenotypes (inferred from 7 alleles(MGI details for Lfng):
     cardiovascular system  embryogenesis  endocrine/exocrine gland  growth/size/body  hearing/vestibular/ear 
     hematopoietic system  limbs/digits/tail  mortality/aging  nervous system  no phenotypic analysis 
     reproductive system  respiratory system  skeleton  vision/eye 

    Find genes that share phenotypes with LFNG           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for LFNG: Lfngtm1Rjo Lfngtm1.2Egan Lfngtm1Seco

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LFNG
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for LFNG
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for LFNG

    miRNA
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    miRTarBase miRNAs that target LFNG:
    hsa-mir-181a-5p (MIRT025038), hsa-mir-335-5p (MIRT018104), hsa-mir-132-3p (MIRT021806)

    Block miRNA regulation of human, mouse, rat LFNG using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate LFNG (see all 41):
    hsa-miR-345 hsa-miR-3938 hsa-miR-640 hsa-miR-429 hsa-miR-513a-5p hsa-miR-146a hsa-miR-3667-5p hsa-miR-1276
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat LFNG

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    GenScript: all cDNA clones in your preferred vector (see all 4): LFNG (NM_001040167)
    Sino Biological Human cDNA Clone for LFNG
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for LFNG
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LFNG

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LFNG


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    LFNG_HUMAN, Q8NES3: Golgi apparatus membrane; Single-pass type II membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    golgi apparatus5
    endoplasmic reticulum1
    lysosome1
    plasma membrane1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region NAS10341080
    GO:0016020membrane ----
    GO:0030173integral component of Golgi membrane IEA--

    Find genes that share ontologies with LFNG           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for LFNG About   (see all 6)  
    See pathways by source

    SuperPathContained pathways About
    1Notch signaling pathway (KEGG)
    Notch signaling pathway0.84
    Delta-Notch Signaling Pathway0.33
    Notch Signaling Pathway0.84
    Notch Signaling0.30
    2Pre-NOTCH Expression and Processing
    Pre-NOTCH Expression and Processing0.62
    Pre-NOTCH Processing in Golgi0.00
    3Signaling by NOTCH1 PEST Domain Mutants in Cancer
    Signaling by NOTCH0.64
    4Signaling by GPCR
    Signal Transduction0.58
    5Development NOTCH1 mediated pathway for NF KB activity modulation
    Development Notch Signaling Pathway0.50


    Find genes that share SuperPaths with LFNG           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for LFNG
        Notch Signaling

    1 GeneGo (Thomson Reuters) Pathway for LFNG
        Development Notch Signaling Pathway

    2 BioSystems Pathways for LFNG
        Notch Signaling Pathway
    Delta-Notch Signaling Pathway


    1 Reactome Pathway for LFNG
        Pre-NOTCH Processing in Golgi


    2 Kegg Pathways  (Kegg details for LFNG):
        Other types of O-glycan biosynthesis
    Notch signaling pathway

        Pathway & Disease-focused RT2 Profiler PCR Arrays including LFNG: 
              Notch Signaling Targets in human mouse rat
              Glycosylation in human mouse rat
              Signal Transduction PathwayFinder in human mouse rat
              Notch Signaling Pathway in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for LFNG

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

    Selected Interacting proteins for LFNG (Q8NES33 ENSP000002227254) via UniProtKB, MINT, STRING, and/or I2D (see all 26)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NOTCH2Q047213, ENSP000002566464I2D: score=1 STRING: ENSP00000256646
    NOTCH1P465313, ENSP000002775414I2D: score=1 STRING: ENSP00000277541
    B4GALT1ENSP000003690554STRING: ENSP00000369055
    ATP2A1ENSP000003495954STRING: ENSP00000349595
    ATP2A3ENSP000003530724STRING: ENSP00000353072
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001541ovarian follicle development IEA--
    GO:0001756somitogenesis IEA--
    GO:0007143female meiosis IEA--
    GO:0007219Notch signaling pathway TAS--
    GO:0007386compartment pattern specification IEA--

    Find genes that share ontologies with LFNG           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for LFNG



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for LFNG gene (4 alternative transcripts): 
    NM_001040167.1  NM_001040168.1  NM_001166355.1  NM_002304.2  

    Unigene Cluster for LFNG:

    LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase
    Hs.159142  [show with all ESTs]
    Unigene Representative Sequence: NM_001040167
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000402506(uc021zyw.1) ENST00000402045(uc021zyx.1) ENST00000222725(uc003smf.3)
    ENST00000359574(uc003smg.3) ENST00000493850 ENST00000338732
    miRNA
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    Block miRNA regulation of human, mouse, rat LFNG using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate LFNG (see all 41):
    hsa-miR-345 hsa-miR-3938 hsa-miR-640 hsa-miR-429 hsa-miR-513a-5p hsa-miR-146a hsa-miR-3667-5p hsa-miR-1276
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    Additional mRNA sequence: 

    AF193612.1 AK096284.1 BC014851.1 U94354.1 

    5 DOTS entries:

    DT.75176778  DT.305349  DT.106093  DT.91705271  DT.95082690 

    Selected AceView cDNA sequences (see all 33):

    AW771962 BM549606 BQ015362 AA583350 BX100485 AA805132 BM797222 BG422267 
    BE713110 AI143535 BC014851 BF031445 D20171 AF193612 CA305967 BG164143 
    AW151924 AI569874 BF110401 AK096284 BE839963 BM854210 U94354 BG325616 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for LFNG    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12
    SP1:              -     -                                                                     
    SP2:                    -                                                           -         
    SP3:                                                                                          
    SP4:                                                                                          


    ECgene alternative splicing isoforms for LFNG

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    LFNG expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCTCACCTGT
    LFNG Expression
    About this image


    LFNG expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 10) fully expand
     
     Brain (Nervous System)    fully expand to see all 10 entries
             Thalamus
             Oligodendrocyte progenitor cells
     
     Mesoderm (Gastrulation Derivatives)
             Paraxial Mesoderm Cells Paraxial Mesoderm
     
     Paraxial Mesoderm (Gastrulation Derivatives)
             Paraxial Mesoderm Cells Paraxial Mesoderm
     
     Tooth (Integumentary System)    fully expand to see all 3 entries
             Inner Enamel Epithelial Cells Dental Enamel
     
     Epithelial Cells
             Inner Enamel Epithelial Cells Dental Enamel
    LFNG Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LFNG Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.159142
        Pathway & Disease-focused RT2 Profiler PCR Arrays including LFNG: 
              Notch Signaling Targets in human mouse rat
              Glycosylation in human mouse rat
              Signal Transduction PathwayFinder in human mouse rat
              Notch Signaling Pathway in human mouse rat

    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LFNG

    (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)
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    This gene was present in the common ancestor of animals.

    Orthologs for LFNG gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lfng1 , 5 LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase1, 5 84.66(n)1
    88.36(a)1
      5 (79.15 cM)5
    168481  NM_008494.31  NP_032520.11 
     1406073415 
    chicken
    (Gallus gallus)
    Aves LFNG1 LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase 78.81(n)
    76.49(a)
      395790  NM_204948.1  NP_990279.1 
    lizard
    (Anolis carolinensis)
    Reptilia LFNG6
    LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminylt...
    71(a)
    1 ↔ 1
    GL343340.1(209013-250732)
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3978552 lunatic fringe 77.31(n)    U77640.1 
    zebrafish
    (Danio rerio)
    Actinopterygii lfng2 lunatic fringe homolog 77.27(n)   30158  AY007434.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta fng3 dorsal/ventral pattern formation,
    imaginal disc more
    46(a)   3 78A1   --


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LFNG gene
    MFNG2  RFNG2  
    2 SIMAP similar genes for LFNG using alignment to 1 protein entry:     LFNG_HUMAN:
    RFNG    MFNG

    Find genes that share paralogs with LFNG           About GenesLikeMe



    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for LFNG (see all 519)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0258504
    Spondylocostal dysostosis 3, autosomal recessive (SCDO3)4--see VAR_0258502 F L mis40--------
    rs1048940241,2
    Cpathogenic12612772(+) CGCTTA/CATCGA 8 L F mis10--------
    rs58819281,2
    C--2554451(+) GTCTG-/TCCA  
            
    TCCAT
    1 -- int10--------
    rs1995823771,2
    C--2554451(+) GTCTG-/TCC   
       ATCCA
    TCCAT
    1 -- int10--------
    rs1480725181,2
    C--2554654(+) TGTCT-/ATC   
       CATCC
    ATCCA
    1 -- int10--------
    rs720618121,2
    C--2554655(+) GTCTA-/TCCATCCATCCAT
    CCATCCATCCATCTG
    TCCAT
    1 -- int10--------
    rs102764921,2
    C--2554674(+) CATCCA/GTCCAT 1 -- int1 tfbs30--------
    rs570328821,2
    C--2556676(+) CCCTT-/TGTCCT 2 -- int1 us2k12Minor allele frequency- T:0.25NA CSA 4
    rs2015743731,2
    --2566954(+) GTGCC-/TGTGCG
            
    TGTGC
    4 -- cds10--------
    rs710265261,2
    C--2566976(+) GTGTG-/CATGTG/CGT
    GTG
    /CGTGTGTG
    TGTGT
    12 -- cds1 ut31 int11NA 2

    HapMap Linkage Disequilibrium report for LFNG (2552163 - 2568811 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for LFNG (see all 14):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2733856CNV Deletion23290073
    esv2733857CNV Deletion23290073
    esv5169CNV Duplication18987735
    esv2575091CNV Insertion19546169
    nsv887298CNV Loss21882294
    dgv7117n71CNV Loss21882294
    dgv7118n71CNV Loss21882294
    nsv887297CNV Loss21882294
    nsv471216CNV Loss18288195
    nsv830887CNV Loss17160897

    Human Gene Mutation Database (HGMD): LFNG
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing LFNG
    DNA2.0 Custom Variant and Variant Library Synthesis for LFNG

    (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.)
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    OMIM gene information: 602576   
    OMIM disorders: 609813  
    UniProtKB/Swiss-Prot: LFNG_HUMAN, Q8NES3
  • Spondylocostal dysostosis 3 (SCDO3) [MIM:609813]: An autosomal recessive condition of variable severity
    associated with vertebral and rib segmentation defects. The main skeletal malformations include fusion of
    vertebrae, hemivertebrae, fusion of certain ribs, and other rib malformations. Deformity of the chest and spine
    (severe scoliosis, kyphoscoliosis and lordosis) is a natural consequence of the malformation and leads to a
    dwarf-like appearance. As the thorax is small, infants frequently have respiratory insufficiency and repeated
    respiratory infections resulting in life-threatening complications in the first year of life. Note=The disease is
    caused by mutations affecting the gene represented in this entry

  • 6 diseases for LFNG:    
    About MalaCards
    spondylocostal dysostosis 3    lfng-related spondylocostal dysostosis, autosomal recessive    spondylocostal dysostosis    spondylocostal dysostosis 1
    dysostosis    spondylocostal dysostosis, autosomal recessive

    1 disease from the University of Copenhagen DISEASES database for LFNG:
    Spondylocostal dysostosis

    Find genes that share disorders with LFNG           About GenesLikeMe

    GeneTests: LFNG
    GeneReviews: LFNG

    Export disorders for LFNG 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)
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    PubMed articles for LFNG gene, integrated from 10 sources (see all 22):
    (articles sorted by number of sources associating them with LFNG)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A family of mammalian Fringe genes implicated in boundary determination and the Notch pathway. (PubMed id 9187150)1, 2, 3 Johnston S.H....Vogt T.F. (Development 1997)
    2. Mutation of the LUNATIC FRINGE gene in humans causes spondylocostal dysostosis with a severe vertebral phenotype. (PubMed id 16385447)1, 2, 9 Sparrow D.B.... Dunwoodie S.L. (Am. J. Hum. Genet. 2006)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis. (PubMed id 12110169)1, 2 Cole S.E.... Vogt T.F. (Dev. Cell 2002)
    5. Manic fringe and lunatic fringe modify different sites of the Notch2 extracellular region, resulting in different signaling modulation. (PubMed id 11346656)1, 2 Shimizu K.... Hirai H. (J. Biol. Chem. 2001)
    6. Mapping of the human Lunatic Fringe (LFNG) gene to 7p22 and Manic Fringe (MFNG) to 22q12. (PubMed id 9878264)1, 3 Egan S....Scherer S.W. (Genomics 1998)
    7. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    8. Lunatic fringe deficiency cooperates with the Met/Caveolin gene amplicon to induce basal-like breast cancer. (PubMed id 22624713)1 Xu K....Egan S.E. (Cancer Cell 2012)
    9. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
    10. Mutation of the fucose-specific beta1,3 N-acetylglucosaminyltransferase LFNG results in abnormal formation of the spine. (PubMed id 19061953)1 Dunwoodie S.L. (Biochim. Biophys. Acta 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 3955 HGNC: 6560 AceView: LFNG Ensembl:ENSG00000106003 euGenes: HUgn3955
    ECgene: LFNG Kegg: 3955 H-InvDB: LFNG

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for LFNG Pharmacogenomics, SNPs, Pathways
    GGDBhttp://jcggdb.jp/rcmg/ggdb/Homolog?cat=symbol&symbol=B3GNT1
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=LFNG[genesymbol]
    Functional Glycomics Gateway - GTasehttp://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/viewGlycoEnzyme.jsp?gbpId=gt_hum_551

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

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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