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Aliases for EMG1 Gene

Aliases for EMG1 Gene

  • EMG1, N1-Specific Pseudouridine Methyltransferase 2 3 5
  • 18S RRNA (Pseudouridine(1248)-N1)-Methyltransferase 3 4
  • 18S RRNA Psi1248 Methyltransferase 3 4
  • Ribosome Biogenesis Protein NEP1 3 4
  • C2F 3 4
  • 18S RRNA (Pseudouridine-N1-)-Methyltransferase NEP1 3
  • Ribosomal RNA Small Subunit Methyltransferase NEP1 3
  • EMG1 Nucleolar Protein Homolog (S. Cerevisiae) 2
  • EMG1 Nucleolar Protein Homolog 3
  • Essential For Mitotic Growth 1 3
  • Nucleolar Protein EMG1 Homolog 4
  • Nucleolar Essential Protein 1 3
  • Protein C2f 4
  • EC 2.1.1.- 4
  • Grcc2f 3
  • NEP1 3

External Ids for EMG1 Gene

Previous GeneCards Identifiers for EMG1 Gene

  • GC12P006951
  • GC12P006954
  • GC12P006957
  • GC12P006961
  • GC12P006964
  • GC12P006968
  • GC12P006973
  • GC12P007079
  • GC12P007146

Summaries for EMG1 Gene

Entrez Gene Summary for EMG1 Gene

  • 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]

GeneCards Summary for EMG1 Gene

EMG1 (EMG1, N1-Specific Pseudouridine Methyltransferase) is a Protein Coding gene. Diseases associated with EMG1 include Bowen-Conradi Syndrome. Among its related pathways are rRNA processing in the nucleus and cytosol and Gene Expression. Gene Ontology (GO) annotations related to this gene include methyltransferase activity. An important paralog of this gene is ENSG00000126749.

UniProtKB/Swiss-Prot for EMG1 Gene

  • S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1248 (Psi1248) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. Is not able to methylate uridine at this position (PubMed:20047967). Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 during the formation of pre-ribosomes (By similarity).

Gene Wiki entry for EMG1 Gene

Additional gene information for EMG1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EMG1 Gene

Genomics for EMG1 Gene

GeneHancer (GH) Regulatory Elements for EMG1 Gene

Promoters and enhancers for EMG1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J006940 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 650.4 -17.1 -17123 25.9 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 PTPN6 C12orf57 EMG1 ZNF384 ENSG00000219410 ENSG00000247853 SPSB2 SCARNA12 NCAPD2 ENSG00000256967
GH12J006967 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 -0.9 -864 5.4 FOXA2 PKNOX1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 ENSG00000126749 PHB2 EMG1 ZNF384 CHD4 ENSG00000247853 NOP2 LOC100419825 LOC100420983 LOC100131676
GH12J006975 Promoter 0.7 EPDnew 650.4 +5.0 5001 0.1 SMAD5 POLR2A ETV6 EMG1 ENSG00000126749 GC12P007546
GH12J006923 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12.8 -43.6 -43630 6.8 HDGF SMAD1 ARID4B SIN3A ZNF2 IRF4 YY1 ZNF213 ZNF143 FOS ATN1 ZNF384 LRRC23 CHD4 ENSG00000219410 ENSG00000247853 SCARNA12 ENSG00000126749 PHB2 RPL13P5
GH12J007059 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 10.9 +90.0 89986 2.5 FOXA2 ARID4B SIN3A YY1 ARID2 RXRA NCOA1 MXD4 REST KAT8 PIR40185 PIR61112 PIR53702 PIR45028 PIR50287 GC12P007576 GC12P007575 GC12P007572 GC12P007567 GC12P007561
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EMG1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the EMG1 gene promoter:
  • ATF-2
  • c-Jun
  • STAT1
  • MyoD
  • GR
  • GR-beta
  • GR-alpha
  • SRF

Genomic Locations for EMG1 Gene

Genomic Locations for EMG1 Gene
chr12:6,970,781-6,997,428
(GRCh38/hg38)
Size:
26,648 bases
Orientation:
Plus strand
chr12:7,072,408-7,105,520
(GRCh37/hg19)
Size:
33,113 bases
Orientation:
Plus strand

Genomic View for EMG1 Gene

Genes around EMG1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EMG1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EMG1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EMG1 Gene

Proteins for EMG1 Gene

  • Protein details for EMG1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92979-NEP1_HUMAN
    Recommended name:
    Ribosomal RNA small subunit methyltransferase NEP1
    Protein Accession:
    Q92979
    Secondary Accessions:
    • O00675
    • O00726
    • O00675
    • O00726

    Protein attributes for EMG1 Gene

    Size:
    244 amino acids
    Molecular mass:
    26720 Da
    Quaternary structure:
    • Homodimer.
    • Homodimer.
    SequenceCaution:
    • Sequence=AAB51325.1; Type=Erroneous initiation; Evidence={ECO:0000305};
    • Sequence=AAB51325.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for EMG1 Gene

neXtProt entry for EMG1 Gene

Post-translational modifications for EMG1 Gene

  • Ubiquitination at isoforms=37 and Lys9
  • Modification sites at PhosphoSitePlus

Other Protein References for EMG1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for EMG1 Gene

Domains & Families for EMG1 Gene

Gene Families for EMG1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for EMG1 Gene

Suggested Antigen Peptide Sequences for EMG1 Gene

Graphical View of Domain Structure for InterPro Entry

Q92979

UniProtKB/Swiss-Prot:

NEP1_HUMAN :
  • Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase NEP1 family.
Family:
  • Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase NEP1 family.
genes like me logo Genes that share domains with EMG1: view

Function for EMG1 Gene

Molecular function for EMG1 Gene

UniProtKB/Swiss-Prot Function:
S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1248 (Psi1248) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. Is not able to methylate uridine at this position (PubMed:20047967). Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 during the formation of pre-ribosomes (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + pseudouridine(1248) in human 18S rRNA = S-adenosyl-L-homocysteine + N(1)-methylpseudouridine(1248) in human 18S rRNA.

Enzyme Numbers (IUBMB) for EMG1 Gene

Phenotypes From GWAS Catalog for EMG1 Gene

Gene Ontology (GO) - Molecular Function for EMG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding ISS --
GO:0005515 protein binding IPI 25416956
GO:0008168 methyltransferase activity IEA --
GO:0019843 rRNA binding IBA --
GO:0070037 rRNA (pseudouridine) methyltransferase activity IBA,IDA 20047967
genes like me logo Genes that share ontologies with EMG1: view
genes like me logo Genes that share phenotypes with EMG1: view

Human Phenotype Ontology for EMG1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for EMG1 Gene

MGI Knock Outs for EMG1:
  • Emg1 Emg1<tm1Hdin>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EMG1

Clone Products

  • Addgene plasmids for EMG1

No data available for miRNA , Transcription Factor Targets and HOMER Transcription for EMG1 Gene

Localization for EMG1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EMG1 Gene

Nucleus, nucleolus.

Gene Ontology (GO) - Cellular Components for EMG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus ISS,IBA --
GO:0005737 cytoplasm ISS --
GO:0032040 small-subunit processome IBA --
genes like me logo Genes that share ontologies with EMG1: view

No data available for Subcellular locations from COMPARTMENTS and Subcellular locations from the Human Protein Atlas (HPA) for EMG1 Gene

Pathways & Interactions for EMG1 Gene

genes like me logo Genes that share pathways with EMG1: view

Gene Ontology (GO) - Biological Process for EMG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA --
GO:0006364 rRNA processing TAS --
GO:0032259 methylation IEA --
GO:0042274 ribosomal small subunit biogenesis ISS --
GO:0070475 rRNA base methylation IBA --
genes like me logo Genes that share ontologies with EMG1: view

No data available for SIGNOR curated interactions for EMG1 Gene

Drugs & Compounds for EMG1 Gene

(1) Drugs for EMG1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma 0

(1) Additional Compounds for EMG1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with EMG1: view

Transcripts for EMG1 Gene

mRNA/cDNA for EMG1 Gene

(2) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(6) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for EMG1 Gene

EMG1 nucleolar protein homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EMG1

Clone Products

  • Addgene plasmids for EMG1

Alternative Splicing Database (ASD) splice patterns (SP) for EMG1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b
SP1: - - - -
SP2: - - - - -
SP3: - -
SP4: -
SP5: -
SP6: - -
SP7: -
SP8: -

Relevant External Links for EMG1 Gene

GeneLoc Exon Structure for
EMG1
ECgene alternative splicing isoforms for
EMG1

Expression for EMG1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EMG1 Gene

Protein differential expression in normal tissues from HIPED for EMG1 Gene

This gene is overexpressed in Tlymphocyte (17.3) and Peripheral blood mononuclear cells (12.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for EMG1 Gene



Protein tissue co-expression partners for EMG1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of EMG1 Gene:

EMG1

SOURCE GeneReport for Unigene cluster for EMG1 Gene:

Hs.744040

Phenotype-based relationships between genes and organs from Gene ORGANizer for EMG1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • reproductive
  • skeleton
Regions:
Head and neck:
  • brain
  • chin
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • nose
  • skull
Pelvis:
  • testicle
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • skin
genes like me logo Genes that share expression patterns with EMG1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES for EMG1 Gene

Orthologs for EMG1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for EMG1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia EMG1 33
  • 99.45 (n)
dog
(Canis familiaris)
Mammalia EMG1 33
  • 89.34 (n)
cow
(Bos Taurus)
Mammalia EMG1 33
  • 88.52 (n)
rat
(Rattus norvegicus)
Mammalia Emg1 33
  • 85.66 (n)
mouse
(Mus musculus)
Mammalia Emg1 16 33
  • 84.97 (n)
chicken
(Gallus gallus)
Aves EMG1 33
  • 73.74 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia emg1 33
  • 71.19 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.25562 33
zebrafish
(Danio rerio)
Actinopterygii zgc:136360 33
  • 62.93 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.389 33
fruit fly
(Drosophila melanogaster)
Insecta CG3527 33
  • 62.42 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002808 33
  • 57.73 (n)
worm
(Caenorhabditis elegans)
Secernentea CELE_Y39A1A.14 33
  • 57.37 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR686C 33
  • 53.86 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes EMG1 33
  • 52.53 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C01914g 33
  • 51.08 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G57000 33
  • 53.3 (n)
rice
(Oryza sativa)
Liliopsida Os02g0290400 33
  • 55.12 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes mra1 33
  • 54.74 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02428 33
  • 54.43 (n)
sea squirt
(Ciona savignyi)
Ascidiacea Cin.4032 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4032 33
Species where no ortholog for EMG1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for EMG1 Gene

ENSEMBL:
Gene Tree for EMG1 (if available)
TreeFam:
Gene Tree for EMG1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for EMG1: view image

Paralogs for EMG1 Gene

Paralogs for EMG1 Gene

genes like me logo Genes that share paralogs with EMG1: view

Variants for EMG1 Gene

Sequence variations from dbSNP and Humsavar for EMG1 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs74435397 pathogenic, Bowen-Conradi syndrome, Bowen-Conradi syndrome (BWCNS) [MIM:211180] 6,974,427(+) A/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs36061201 likely-benign, not provided 6,970,961(+) G/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs11064480 benign, not specified 6,971,024(+) C/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1000141659 -- 6,975,547(+) A/C intron_variant
rs1000224637 -- 6,982,231(+) G/A/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for EMG1 Gene

Variant ID Type Subtype PubMed ID
nsv1035811 CNV gain 25217958
nsv1047373 CNV gain 25217958
nsv509453 CNV insertion 20534489

Variation tolerance for EMG1 Gene

Gene Damage Index Score: 2.52; 44.04% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EMG1 Gene

Human Gene Mutation Database (HGMD)
EMG1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
EMG1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EMG1 Gene

Disorders for EMG1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for EMG1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, and GeneCards

Disorder Aliases PubMed IDs
bowen-conradi syndrome
  • bwcns
- elite association - COSMIC cancer census association via MalaCards
Search EMG1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NEP1_HUMAN
  • Bowen-Conradi syndrome (BWCNS) [MIM:211180]: A combination of malformations characterized in newborns by low birth weight, microcephaly, mild joint restriction, a prominent nose, micrognathia, fifth finger clinodactyly, and rocker-bottom feet. The syndrome is transmitted as an autosomal recessive trait. The prognosis is poor, with all infants dying within the first few months of life. {ECO:0000269 PubMed:19463982}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for EMG1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with EMG1: view

No data available for Genatlas for EMG1 Gene

Publications for EMG1 Gene

  1. Nep1p (Emg1p), a novel protein conserved in eukaryotes and archaea, is involved in ribosome biogenesis. (PMID: 11935223) Eschrich D … Entian KD (Current genetics 2002) 2 3 4 22 58
  2. Mutation of a gene essential for ribosome biogenesis, EMG1, causes Bowen-Conradi syndrome. (PMID: 19463982) Armistead J … Triggs-Raine B (American journal of human genetics 2009) 2 3 4 58
  3. Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination. (PMID: 9074930) Ansari-Lari MA … Gibbs RA (Genome research 1997) 2 3 4 58
  4. The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase. (PMID: 20047967) Wurm JP … Wöhnert J (Nucleic acids research 2010) 3 4 58
  5. Evaluating new candidate SNPs as low penetrance risk factors in sporadic breast cancer: a two-stage Spanish case-control study. (PMID: 18950845) Vega A … Carracedo A (Gynecologic oncology 2009) 3 44 58

Products for EMG1 Gene

Sources for EMG1 Gene

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