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

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; AllianceGenome:HGNC:16912
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: mouse all
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Genomic context

Location:: 12p13.31

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (6970913..6997428)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (6984388..7010891)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (7080076..7105520)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Our findings further indicate that in Bowen-Conradi syndrome, nuclear disassembly of the import complex and release of EMG1D86G lead to its nuclear aggregation and degradation, resulting in the reduced nucleolar recruitment of the RNA methyltransferase and defects in the biogenesis of the small ribosomal subunit.
Title: Effects of the Bowen-Conradi syndrome mutation in EMG1 on its nuclear import, stability and nucleolar recruitment.
Mutation of a gene essential for ribosome biogenesis, EMG1, causes Bowen-Conradi syndrome.
Title: Mutation of a gene essential for ribosome biogenesis, EMG1, causes Bowen-Conradi syndrome.
Observational study of gene-disease association. (HuGE Navigator)
Title: Evaluating new candidate SNPs as low penetrance risk factors in sporadic breast cancer: a two-stage Spanish case-control study.

Submit: New GeneRIF Correction

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

Associated conditions

Description	Tests
Bowen-Conradi syndrome MedGen: C1859405 OMIM: 211180 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D12S397 (e-PCR), detects polymorphism
- UniSTS:77882

SHGC-33346 (e-PCR)
- UniSTS:73094

MARC_5237-5238:996690168:1 (e-PCR)
- UniSTS:269469

RH11325 (e-PCR)
- UniSTS:77219

RH26657 (e-PCR)
- UniSTS:86499

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables rRNA (pseudouridine) methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables rRNA (pseudouridine) methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables rRNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in blastocyst development	IEA Inferred from Electronic Annotation more info
involved_in nucleologenesis	IEA Inferred from Electronic Annotation more info
involved_in rRNA base methylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in rRNA processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in ribosomal small subunit biogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in ribosomal small subunit biogenesis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in chromosome	IDA Inferred from Direct Assay more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of small-subunit processome	IBA Inferred from Biological aspect of Ancestor more info
part_of small-subunit processome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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)

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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

NG_021408.2 RefSeqGene

Range

5133..14156

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001320049.2 → NP_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)

AC006512, AI394112, BC055314, BP315329, DC403138

UniProtKB/Swiss-Prot

Q92979

Conserved Domains (1) summary

pfam03587
Location:45 → 187

EMG1; EMG1/NEP1 methyltransferase
NM_006331.8 → NP_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)

AC006512, AI394112, BC055314, DC403138

Consensus CDS

CCDS73430.1

UniProtKB/Swiss-Prot

O00675, O00726, Q92979

UniProtKB/TrEMBL

A8K6D2

Related

ENSP00000470560.1, ENST00000599672.6

Conserved Domains (1) summary

cd18088
Location:43 → 238

Nep1-like; 18S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1

RNA

NR_135131.2 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