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

Gene ID: 3955, updated on 13-May-2022

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; AllianceGenome:HGNC:6560
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
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Genomic context

See LFNG in Genome Data Viewer
Location:
7p22.3
Exon count:
13
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (2512529..2529177)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (2625971..2642596)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (2552163..2568811)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene galectin-related inter-fiber protein Neighboring gene uncharacterized LOC107986759 Neighboring gene nonconserved acetylation island sequence 106 enhancer Neighboring gene microRNA 4648 Neighboring gene small nucleolar RNA U13 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 PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in T cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in animal organ morphogenesis NAS
Non-traceable Author Statement
more info
PubMed 
involved_in compartment pattern specification IEA
Inferred from Electronic Annotation
more info
 
involved_in marginal zone B cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of Notch signaling pathway involved in somitogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in ovarian follicle development IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of protein binding IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of Notch signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of Notch signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of somitogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in somitogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
located_in Golgi membrane TAS
Traceable Author Statement
more info
 
located_in extracellular region NAS
Non-traceable Author Statement
more info
PubMed 
located_in extracellular vesicle HDA PubMed 
located_in 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)

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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_001166355.2NP_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_002304.3NP_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 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    2625971..2642596
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)