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Aliases for LFNG Gene

Aliases for LFNG Gene

  • LFNG O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase 2 3 5
  • EC 2.4.1.222 4 58
  • Beta-1,3-N-Acetylglucosaminyltransferase Lunatic Fringe 3
  • O-Fucosylpeptide 3-Beta-N-Acetylglucosaminyltransferase 4
  • Lunatic Fringe (Drosophila) Homolog 2
  • Lunatic Fringe Homolog (Drosophila) 2
  • SCDO3 3

External Ids for LFNG Gene

Previous GeneCards Identifiers for LFNG Gene

  • GC07P002201
  • GC07P002303
  • GC07P002302
  • GC07P002330
  • GC07P002524
  • GC07P002469
  • GC07P002552

Summaries for LFNG Gene

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, Autosomal Recessive and Spondylocostal Dysostosis 3. Among its related pathways are Other types of O-glycan biosynthesis and Pre-NOTCH Expression and Processing. GO annotations related to this gene include transferase activity, transferring glycosyl groups and O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity. An important paralog of this gene is RFNG.

UniProtKB/Swiss-Prot for LFNG Gene

  • 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

Additional gene information for LFNG Gene

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

Genomics for LFNG Gene

Regulatory Elements for LFNG Gene

Enhancers for LFNG Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07H002520 2 FANTOM5 Ensembl ENCODE dbSUPER 21.5 +14.2 14248 13 HDGF PKNOX1 FOXA2 ARID4B SIN3A ZBTB7B ZNF143 FOS SP5 JUNB LFNG BRAT1 IQCE MIR4648
GH07H002626 2 FANTOM5 Ensembl ENCODE dbSUPER 16.1 +122.1 122096 16 HDGF FOXA2 PKNOX1 MLX ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 TTYH3 LFNG AMZ1 CHST12 BRAT1 EIF3B IQCE SNX8
GH07H002756 2 FANTOM5 Ensembl ENCODE dbSUPER 11.7 +248.1 248065 8 HDGF PKNOX1 FOXA2 ARNT ZFP64 SIN3A ZNF2 ZNF766 CBX5 ZNF143 CHST12 GNA12 BRAT1 AMZ1 LFNG EIF3B TTYH3 SNX8 GC07M002729 PIR32151
GH07H002507 1.8 FANTOM5 Ensembl ENCODE dbSUPER 11.6 -1.8 -1812 6 ELF3 FOXA2 PTBP1 ARID4B KLF17 THRB RARA ZNF766 GLIS2 ZNF366 LFNG BRAT1 GRIFIN
GH07H002862 2 FANTOM5 Ensembl ENCODE dbSUPER 10.3 +351.4 351380 2 PKNOX1 FOXA2 ARID4B ZBTB7B ZNF766 ZNF143 FOS SP5 ZHX2 JUNB GNA12 LFNG MRM2 TTYH3 LOC100131264
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LFNG on UCSC Golden Path with GeneCards custom track

Genomic Location for LFNG Gene

Chromosome:
7
Start:
2,512,529 bp from pter
End:
2,529,177 bp from pter
Size:
16,649 bases
Orientation:
Plus strand

Genomic View for LFNG Gene

Genes around LFNG on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for LFNG Gene

Proteins for LFNG Gene

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

    Protein Symbol:
    Q8NES3-LFNG_HUMAN
    Recommended name:
    Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe
    Protein Accession:
    Q8NES3
    Secondary Accessions:
    • B3KTY6
    • B5MCR5
    • O00589
    • Q96C39
    • Q9UJW5

    Protein attributes for LFNG Gene

    Size:
    379 amino acids
    Molecular mass:
    41773 Da
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LFNG Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LFNG Gene

Selected DME Specific Peptides for LFNG Gene

Q8NES3:
  • CHVDDDNY
  • ALSCKMA
  • TLSYGMFENKRN
  • FIAVKTT
  • SRGLALKMSPWAS
  • FWFATGGAGFC
  • DDDNYVN
  • LFHSHLENLQ
  • CKMAVEYD
  • QVTLSYG
  • LYPDTPWCP
  • RLPDDCT
  • GKPSLDRP

Post-translational modifications for LFNG Gene

  • A soluble form may be derived from the membrane form by proteolytic processing.
  • Glycosylation at posLast=167167
  • Modification sites at PhosphoSitePlus

Domains & Families for LFNG Gene

Gene Families for LFNG Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for LFNG Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for LFNG Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8NES3

UniProtKB/Swiss-Prot:

LFNG_HUMAN :
  • Belongs to the glycosyltransferase 31 family.
Family:
  • Belongs to the glycosyltransferase 31 family.
genes like me logo Genes that share domains with LFNG: view

Function for LFNG Gene

Molecular function for LFNG Gene

GENATLAS Biochemistry:
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
UniProtKB/Swiss-Prot CatalyticActivity:
Transfers a beta-D-GlcNAc residue from UDP-D-GlcNAc to the fucose residue of a fucosylated protein acceptor.
UniProtKB/Swiss-Prot 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).

Enzyme Numbers (IUBMB) for LFNG Gene

Phenotypes From GWAS Catalog for LFNG Gene

Gene Ontology (GO) - Molecular Function for LFNG Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0016740 transferase activity IEA --
GO:0016757 transferase activity, transferring glycosyl groups IEA --
GO:0033829 O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity ISS --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LFNG: view
genes like me logo Genes that share phenotypes with LFNG: view

Human Phenotype Ontology for LFNG Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LFNG Gene

MGI Knock Outs for LFNG:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for LFNG
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
  • R&D Systems cDNA Clones for LFNG (Lunatic Fringe/LFNG)

No data available for Transcription Factor Targets and HOMER Transcription for LFNG Gene

Localization for LFNG Gene

Subcellular locations from UniProtKB/Swiss-Prot for LFNG Gene

Golgi apparatus membrane; Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LFNG gene
Compartment Confidence
extracellular 5
golgi apparatus 4
nucleus 3
plasma membrane 2
endoplasmic reticulum 1
lysosome 1

Gene Ontology (GO) - Cellular Components for LFNG Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region NAS 10341080
GO:0005794 Golgi apparatus IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030173 integral component of Golgi membrane IEA --
genes like me logo Genes that share ontologies with LFNG: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LFNG Gene

Pathways & Interactions for LFNG Gene

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

Pathways by source for LFNG Gene

1 GeneGo (Thomson Reuters) pathway for LFNG Gene
1 Qiagen pathway for LFNG Gene

SIGNOR curated interactions for LFNG Gene

Activates:
Inactivates:
Is activated by:

Gene Ontology (GO) - Biological Process for LFNG Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001541 ovarian follicle development IEA --
GO:0001756 somitogenesis ISS --
GO:0002315 marginal zone B cell differentiation ISS --
GO:0007275 multicellular organism development IEA --
GO:0007386 compartment pattern specification IEA --
genes like me logo Genes that share ontologies with LFNG: view

Drugs & Compounds for LFNG Gene

No Compound Related Data Available

Transcripts for LFNG Gene

Unigene Clusters for LFNG Gene

LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for LFNG
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more
  • R&D Systems cDNA Clones for LFNG (Lunatic Fringe/LFNG)

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

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

Relevant External Links for LFNG Gene

GeneLoc Exon Structure for
LFNG
ECgene alternative splicing isoforms for
LFNG

Expression for LFNG Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LFNG Gene

This gene is overexpressed in Whole Blood (x6.5) and Pancreas (x5.5).

Protein differential expression in normal tissues from HIPED for LFNG Gene

This gene is overexpressed in Heart (31.8), Stomach (20.5), and Pancreas (13.9).

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



Protein tissue co-expression partners for LFNG Gene

NURSA nuclear receptor signaling pathways regulating expression of LFNG Gene:

LFNG

SOURCE GeneReport for Unigene cluster for LFNG Gene:

Hs.159142

Evidence on tissue expression from TISSUES for LFNG Gene

  • Kidney(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LFNG Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • immune
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeleton
Organs:
Head and neck:
  • brain
  • head
  • jaw
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • skull
  • tooth
Thorax:
  • chest wall
  • lung
  • rib
  • rib cage
  • sternum
Pelvis:
  • pelvis
Limb:
  • digit
  • finger
  • hand
  • upper limb
General:
  • blood vessel
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with LFNG: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for LFNG Gene

Orthologs for LFNG Gene

This gene was present in the common ancestor of animals.

Orthologs for LFNG Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LFNG 33 34
  • 98.94 (n)
dog
(Canis familiaris)
Mammalia LFNG 33 34
  • 91.18 (n)
cow
(Bos Taurus)
Mammalia LFNG 33 34
  • 89.36 (n)
rat
(Rattus norvegicus)
Mammalia Lfng 33
  • 85.45 (n)
mouse
(Mus musculus)
Mammalia Lfng 33 16 34
  • 84.66 (n)
oppossum
(Monodelphis domestica)
Mammalia LFNG 34
  • 70 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LFNG 34
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves LFNG 34 33
  • 78.81 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LFNG 34
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lfng 33
  • 69.5 (n)
Str.16143 33
African clawed frog
(Xenopus laevis)
Amphibia LOC397855 33
zebrafish
(Danio rerio)
Actinopterygii lfng 33 34
  • 70.81 (n)
fruit fly
(Drosophila melanogaster)
Insecta fng 35 34
  • 46 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 44 (a)
ManyToMany
-- 34
  • 43 (a)
ManyToMany
-- 34
  • 42 (a)
ManyToMany
-- 34
  • 41 (a)
ManyToMany
-- 34
  • 40 (a)
ManyToMany
-- 34
  • 40 (a)
ManyToMany
-- 34
  • 40 (a)
ManyToMany
-- 34
  • 40 (a)
ManyToMany
-- 34
  • 39 (a)
ManyToMany
-- 34
  • 39 (a)
ManyToMany
-- 34
  • 38 (a)
ManyToMany
-- 34
  • 37 (a)
ManyToMany
-- 34
  • 35 (a)
ManyToMany
-- 34
  • 35 (a)
ManyToMany
-- 34
  • 34 (a)
ManyToMany
-- 34
  • 34 (a)
ManyToMany
-- 34
  • 33 (a)
ManyToMany
Species where no ortholog for LFNG was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LFNG Gene

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

Paralogs for LFNG Gene

Paralogs for LFNG Gene

(2) SIMAP similar genes for LFNG Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with LFNG: view

Variants for LFNG Gene

Sequence variations from dbSNP and Humsavar for LFNG Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs104894024 Pathogenic, Spondylocostal dysostosis 3, autosomal recessive (SCDO3) [MIM:609813] 2,525,301(+) CGCTT(A/C/T)ATCGA upstream-variant-2KB, reference, synonymous-codon, missense
rs141008352 Likely benign 2,524,746(+) CGGGT(A/G)AGCCC intron-variant
rs147266260 Likely benign 2,525,444(+) AACTA(C/T)GTCAA upstream-variant-2KB, reference, synonymous-codon
rs151012354 Likely benign 2,525,504(+) GTCTA(C/T)GTCGG upstream-variant-2KB, reference, synonymous-codon
rs139864844 Uncertain significance 2,525,310(+) GAGTC(C/T)GGCAG upstream-variant-2KB, reference, synonymous-codon

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

Variant ID Type Subtype PubMed ID
esv2575091 CNV insertion 19546169
esv2733856 CNV deletion 23290073
esv2733857 CNV deletion 23290073
esv3446190 CNV duplication 20981092
esv5169 OTHER sequence alteration 18987735
nsv471216 CNV loss 18288195
nsv605861 CNV loss 21841781
nsv605862 CNV loss 21841781
nsv823981 CNV gain 20364138
nsv830887 CNV loss 17160897
nsv950792 CNV deletion 24416366

Variation tolerance for LFNG Gene

Residual Variation Intolerance Score: 81% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.80; 16.88% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LFNG Gene

Human Gene Mutation Database (HGMD)
LFNG
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LFNG

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LFNG Gene

Disorders for LFNG Gene

MalaCards: The human disease database

(5) MalaCards diseases for LFNG Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
spondylocostal dysostosis 3, autosomal recessive
  • spondylocostal dysostosis
spondylocostal dysostosis 3
  • spondylocostal dysostosis 3, autosomal recessive
spondylocostal dysostosis, autosomal recessive
  • costovertebral dysplasia
lfng-related spondylocostal dysostosis, autosomal recessive
  • spondylocostal dysostosis, autosomal recessive 3
dysostosis
  • dysostoses
- elite association - COSMIC cancer census association via MalaCards
Search LFNG in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

LFNG_HUMAN
  • Spondylocostal dysostosis 3, autosomal recessive (SCDO3) [MIM:609813]: A 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. {ECO:0000269 PubMed:16385447}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for LFNG

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LFNG
genes like me logo Genes that share disorders with LFNG: view

No data available for Genatlas for LFNG Gene

Publications for LFNG Gene

  1. Mutation of the LUNATIC FRINGE gene in humans causes spondylocostal dysostosis with a severe vertebral phenotype. (PMID: 16385447) Sparrow DB … Dunwoodie SL (American journal of human genetics 2006) 3 4 22 60
  2. A family of mammalian Fringe genes implicated in boundary determination and the Notch pathway. (PMID: 9187150) Johnston SH … Vogt TF (Development (Cambridge, England) 1997) 2 3 4 60
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  4. Clock regulatory elements control cyclic expression of Lunatic fringe during somitogenesis. (PMID: 12110169) Cole SE … Vogt TF (Developmental cell 2002) 3 4 60
  5. Manic fringe and lunatic fringe modify different sites of the Notch2 extracellular region, resulting in different signaling modulation. (PMID: 11346656) Shimizu K … Hirai H (The Journal of biological chemistry 2001) 3 4 60

Products for LFNG Gene

Sources for LFNG Gene

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