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    EMG1 EMG1, N1-specific pseudouridine methyltransferase [ Homo sapiens (human) ]

    Gene ID: 10436, updated on 13-Oct-2018

    Summary

    Official Symbol
    EMG1provided by HGNC
    Official Full Name
    EMG1, N1-specific pseudouridine methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:16912
    See related
    Ensembl:ENSG00000126749 MIM:611531; Vega:OTTHUMG00000168968; Vega:OTTHUMG00000188247
    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
    C2F; NEP1; Grcc2f
    Summary
    This gene encodes an essential, conserved eukaryotic protein that methylates pseudouridine in 18S rRNA. The related protein in yeast is a component of the small subunit processome and is essential for biogenesis of the ribosomal 40S subunit. A mutation in this gene has been associated with Bowen-Conradi syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
    Expression
    Ubiquitous expression in appendix (RPKM 11.6), lymph node (RPKM 11.5) and 25 other tissues See more
    Orthologs

    Genomic context

    See EMG1 in Genome Data Viewer
    Location:
    12p13.31
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (6970781..6997428)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (7079944..7085165)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene MIR200C and MIR141 host gene Neighboring gene microRNA 141 Neighboring gene small Cajal body-specific RNA 12 Neighboring gene prohibitin 2 Neighboring gene lysophosphatidylcholine acyltransferase 3 Neighboring gene ribosomal protein L37 pseudogene 20 Neighboring gene zinc finger protein 655 pseudogene

    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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, EMG1 nucleolar protein homolog (EMG1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with EMG1 is increased by RRE PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystem (from REACTOME)
      Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystemIn humans, a 47S precursor rRNA (pre-rRNA) is transcribed by RNA polymerase I from rRNA-encoding genes (rDNA) at the boundary of the fibrillar center and the dense fibrillar components of the nucleol...
    • Ribosome biogenesis in eukaryotes, organism-specific biosystem (from KEGG)
      Ribosome biogenesis in eukaryotes, organism-specific biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
    • Ribosome biogenesis in eukaryotes, conserved biosystem (from KEGG)
      Ribosome biogenesis in eukaryotes, conserved biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
    • rRNA modification in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
      rRNA modification in the nucleus and cytosol, organism-specific biosystemHuman ribosomal RNAs (rRNAs) contain about 200 residues that are enzymatically modified after transcription in the nucleolus (Maden and Khan 1977, Maden 1988, Maden and Hughes 1997, reviewed in Herna...
    • rRNA processing, organism-specific biosystem (from REACTOME)
      rRNA processing, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...
    • rRNA processing in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
      rRNA processing in the nucleus and cytosol, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ60792

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding HDA PubMed 
    RNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    rRNA (pseudouridine) methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    rRNA (pseudouridine) methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    rRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    blastocyst development IEA
    Inferred from Electronic Annotation
    more info
     
    nucleologenesis IEA
    Inferred from Electronic Annotation
    more info
     
    rRNA base methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    rRNA processing ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    rRNA processing TAS
    Traceable Author Statement
    more info
     
    ribosomal small subunit biogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleolus IDA
    Inferred from Direct Assay
    more info
     
    nucleolus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
     
    nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    small-subunit processome IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    ribosomal RNA small subunit methyltransferase NEP1
    Names
    18S rRNA (pseudouridine(1248)-N1)-methyltransferase
    18S rRNA (pseudouridine-N1-)-methyltransferase NEP1
    18S rRNA Psi1248 methyltransferase
    EMG1 nucleolar protein homolog
    essential for mitotic growth 1
    nucleolar essential protein 1
    ribosome biogenesis protein NEP1

    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_021408.2 RefSeqGene

      Range
      5001..10223
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001320049.1NP_001306978.1  ribosomal RNA small subunit methyltransferase NEP1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AI394112, BC055314, BP315329, DC403138
      UniProtKB/Swiss-Prot
      Q92979
      Conserved Domains (1) summary
      pfam03587
      Location:45187
      EMG1; EMG1/NEP1 methyltransferase
    2. NM_006331.7NP_006322.4  ribosomal RNA small subunit methyltransferase NEP1 isoform 1

      See identical proteins and their annotated locations for NP_006322.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AI394112, BC055314, DC403138
      Consensus CDS
      CCDS73430.1
      UniProtKB/Swiss-Prot
      Q92979
      Related
      ENSP00000470560.1, OTTHUMP00000276024, ENST00000599672.5, OTTHUMT00000401804
      Conserved Domains (1) summary
      pfam03587
      Location:45238
      EMG1; EMG1/NEP1 methyltransferase

    RNA

    1. NR_135131.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon and contains three alternate 3' exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK298745, DC403138
      Related
      ENST00000607161.5, OTTHUMT00000476749

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

      Range
      6970781..6997428
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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