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LFNG LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase [ Homo sapiens (human) ]

Gene ID: 3955, updated on 12-Oct-2019

Summary

Official Symbol
LFNGprovided by HGNC
Official Full Name
LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:6560
See related
Ensembl:ENSG00000106003 MIM:602576
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SCDO3
Summary
This gene is a member of the glycosyltransferase 31 gene family. Members of this gene family, which also includes the MFNG (GeneID: 4242) and RFNG (GeneID: 5986) genes, 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, these 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. The protein encoded by this gene 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. [provided by RefSeq, May 2018]
Expression
Ubiquitous expression in skin (RPKM 16.6), stomach (RPKM 14.0) and 23 other tissues See more
Orthologs

Genomic context

See LFNG in Genome Data Viewer
Location:
7p22.3
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (2512529..2529177)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (2552163..2568811)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986758 Neighboring gene uncharacterized LOC107986759 Neighboring gene nonconserved acetylation island sequence 106 enhancer Neighboring gene microRNA 4648 Neighboring gene BRCA1 associated ATM activator 1 Neighboring gene IQ motif containing E Neighboring gene uncharacterized LOC107986760

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from BioSystems

  • Gene regulatory network modelling somitogenesis, organism-specific biosystem (from WikiPathways)
    Gene regulatory network modelling somitogenesis, organism-specific biosystemReaction scheme of the proposed gene regulatory network (GRN). The scheme details the full GRN for one cell and part of a neighboring cell for those reactions that involve ligand-receptor interactio...
  • Notch Signaling Pathway, organism-specific biosystem (from WikiPathways)
    Notch Signaling Pathway, organism-specific biosystemThe Notch signaling pathway is an evolutionarily conserved, intercellular signaling mechanism essential for proper embryonic development in all metazoan organisms in the Animal kingdom. The Notch pro...
  • Notch signaling pathway, organism-specific biosystem (from KEGG)
    Notch signaling pathway, organism-specific biosystemThe Notch signaling pathway is an evolutionarily conserved, intercellular signaling mechanism essential for proper embryonic development in all metazoan organisms in the Animal kingdom. The Notch pro...
  • Notch signaling pathway, conserved biosystem (from KEGG)
    Notch signaling pathway, conserved biosystemThe Notch signaling pathway is an evolutionarily conserved, intercellular signaling mechanism essential for proper embryonic development in all metazoan organisms in the Animal kingdom. The Notch pro...
  • Other types of O-glycan biosynthesis, organism-specific biosystem (from KEGG)
    Other types of O-glycan biosynthesis, organism-specific biosystemO-linked glycosylation is the attachment of monosaccharides to the hydroxyl groups of amino acids, mostly serine and threonine, and is found in eukaryotes, archaea and bacteria. O-glycans exhibit div...
  • Other types of O-glycan biosynthesis, conserved biosystem (from KEGG)
    Other types of O-glycan biosynthesis, conserved biosystemO-linked glycosylation is the attachment of monosaccharides to the hydroxyl groups of amino acids, mostly serine and threonine, and is found in eukaryotes, archaea and bacteria. O-glycans exhibit div...
  • Pre-NOTCH Expression and Processing, organism-specific biosystem (from REACTOME)
    Pre-NOTCH Expression and Processing, organism-specific biosystemIn humans and other mammals the NOTCH gene family has four members, NOTCH1, NOTCH2, NOTCH3 and NOTCH4, encoded on four different chromosomes. Their transcription is developmentally regulated and tiss...
  • Pre-NOTCH Processing in Golgi, organism-specific biosystem (from REACTOME)
    Pre-NOTCH Processing in Golgi, organism-specific biosystemNOTCH undergoes final posttranslational processing in the Golgi apparatus (Lardelli et al. 1994, Blaumueller et al. 1997, Weinmaster et al. 1991, Weinmaster et al. 1992, Uyttendaele et al. 1996). Mov...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by NOTCH, organism-specific biosystem (from REACTOME)
    Signaling by NOTCH, organism-specific biosystemThe Notch Signaling Pathway (NSP) is a highly conserved pathway for cell-cell communication. NSP is involved in the regulation of cellular differentiation, proliferation, and specification. For exam...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
molecular_function ND
No biological Data available
more info
 
Process Evidence Code Pubs
T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
animal organ morphogenesis NAS
Non-traceable Author Statement
more info
PubMed 
compartment pattern specification IEA
Inferred from Electronic Annotation
more info
 
marginal zone B cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of Notch signaling pathway involved in somitogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
ovarian follicle development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein binding IEA
Inferred from Electronic Annotation
more info
 
protein O-linked fucosylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein O-linked fucosylation ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of Notch signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of Notch signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of somitogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
somitogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
extracellular region NAS
Non-traceable Author Statement
more info
PubMed 
extracellular vesicle HDA PubMed 
integral component of Golgi membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
beta-1,3-N-acetylglucosaminyltransferase lunatic fringe
NP_001035257.1
NP_001035258.1
NP_001159827.1
NP_002295.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008109.2 RefSeqGene

    Range
    12246..21649
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001040167.2NP_001035257.1  beta-1,3-N-acetylglucosaminyltransferase lunatic fringe isoform a precursor

    See identical proteins and their annotated locations for NP_001035257.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC092488, BC014851, BM854210, U94354
    Consensus CDS
    CCDS34587.1
    UniProtKB/Swiss-Prot
    Q8NES3
    Related
    ENSP00000222725.5, ENST00000222725.10
    Conserved Domains (1) summary
    pfam02434
    Location:110358
    Fringe; Fringe-like
  2. NM_001040168.2NP_001035258.1  beta-1,3-N-acetylglucosaminyltransferase lunatic fringe isoform b precursor

    See identical proteins and their annotated locations for NP_001035258.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an alternate 3' terminal exon compared to variant 1. The resulting protein (isoform b) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC092488, AF193612, U94354
    Consensus CDS
    CCDS34586.1
    UniProtKB/Swiss-Prot
    Q8NES3
    Related
    ENSP00000352579.3, ENST00000359574.7
    Conserved Domains (1) summary
    pfam02434
    Location:110358
    Fringe; Fringe-like
  3. NM_001166355.1NP_001159827.1  beta-1,3-N-acetylglucosaminyltransferase lunatic fringe isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate start codon, compared to variant 1. The encoded protein (isoform c) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK096284, BC014851
    Consensus CDS
    CCDS55081.1
    UniProtKB/Swiss-Prot
    Q8NES3
    Related
    ENSP00000385764.1, ENST00000402506.5
    Conserved Domains (1) summary
    pfam02434
    Location:72287
    Fringe; Fringe-like
  4. NM_002304.2NP_002295.1  beta-1,3-N-acetylglucosaminyltransferase lunatic fringe isoform d

    See identical proteins and their annotated locations for NP_002295.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple differences, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate start codon, compared to variant 1. The encoded protein (isoform d) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK096284, BC014851
    Consensus CDS
    CCDS55082.1
    UniProtKB/Swiss-Prot
    Q8NES3
    Related
    ENSP00000384786.1, ENST00000402045.5
    Conserved Domains (1) summary
    pfam02434
    Location:16229
    Fringe; Fringe-like

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

    Range
    2512529..2529177
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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