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

    Gene ID: 5986, updated on 14-Nov-2024

    Summary

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    Official Symbol
    RFNGprovided by HGNC
    Official Full Name
    RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:9974
    See related
    Ensembl:ENSG00000169733 MIM:602578; AllianceGenome:HGNC:9974
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to enable O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity. Predicted to be involved in regulation of Notch signaling pathway. Predicted to act upstream of or within positive regulation of Notch signaling pathway. Predicted to be located in Golgi membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 13.6), fat (RPKM 12.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RFNG in Genome Data Viewer
    Location:
    17q25.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (82047902..82051811, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (82915060..82918969, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (80005778..80009687, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9184 Neighboring gene DCXR divergent transcript Neighboring gene dicarbonyl and L-xylulose reductase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80009332-80010001 Neighboring gene G protein pathway suppressor 1 Neighboring gene dihydrouridine synthase 1 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80022320-80023048 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9189 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9190 Neighboring gene MPRA-validated peak3028 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80038893-80039778 Neighboring gene fatty acid synthase Neighboring gene small nucleolar RNA, C/D box 134

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Radical fringe negatively modulates Notch signaling in postmitotic neurons of the rat brain. Mikami T, et al. Brain Res Mol Brain Res, 2001 Jan 31. PMID 11165380
    2. Genomic structure, mapping, and expression analysis of the mammalian Lunatic, Manic, and Radical fringe genes. Moran JL, et al. Mamm Genome, 1999 Jun. PMID 10341080
    3. A family of mammalian Fringe genes implicated in boundary determination and the Notch pathway. Johnston SH, et al. Development, 1997 Jun. PMID 9187150
    4. Large-scale concatenation cDNA sequencing. Yu W, et al. Genome Res, 1997 Apr. PMID 9110174, Free PMC Article
    5. A "double adaptor" method for improved shotgun library construction. Andersson B, et al. Anal Biochem, 1996 Apr 5. PMID 8619474

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in animal organ morphogenesis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in pattern specification process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of Notch signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of Notch signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of Notch signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    beta-1,3-N-acetylglucosaminyltransferase radical fringe
    Names
    O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase
    radical fringe homolog
    NP_002908.1
    XP_011521889.1
    XP_054172829.1

    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.

    mRNA and Protein(s)

    1. NM_002917.2 → NP_002908.1  beta-1,3-N-acetylglucosaminyltransferase radical fringe

      See identical proteins and their annotated locations for NP_002908.1

      Status: VALIDATED

      Source sequence(s)
      AC135056, AF038196, AF108139, AK094016, BC014495, BF435018
      Consensus CDS
      CCDS32773.1
      UniProtKB/Swiss-Prot
      O00588, Q9Y644
      UniProtKB/TrEMBL
      B4DEC8
      Related
      ENSP00000307971.4, ENST00000310496.9
      Conserved Domains (1) summary
      pfam02434
      Location:55 → 305
      Fringe; Fringe-like

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      82047902..82051811 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011523587.3 → XP_011521889.1  beta-1,3-N-acetylglucosaminyltransferase radical fringe isoform X1

      UniProtKB/TrEMBL
      B4DXP6, F5H3H7
      Related
      ENSP00000402931.3, ENST00000429557.7
      Conserved Domains (1) summary
      pfam02434
      Location:1 → 179
      Fringe; Fringe-like

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      82915060..82918969 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316854.1 → XP_054172829.1  beta-1,3-N-acetylglucosaminyltransferase radical fringe isoform X1

      UniProtKB/TrEMBL
      F5H3H7
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y644.3 GenPept UniProtKB/Swiss-Prot:Q9Y644

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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