NELFE negative elongation factor complex member E [Homo sapiens (human)] - Gene

Summary

Official Symbol: NELFEprovided by HGNC
Official Full Name: negative elongation factor complex member Eprovided by HGNC
Primary source: HGNC:HGNC:13974
See related: Ensembl:ENSG00000204356 MIM:154040; AllianceGenome:HGNC:13974
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: RD; RDP; RDBP; D6S45; NELF-E
Summary: The protein encoded by this gene is part of a complex termed negative elongation factor (NELF) which represses RNA polymerase II transcript elongation. This protein bears similarity to nuclear RNA-binding proteins; however, it has not been demonstrated that this protein binds RNA. The protein contains a tract of alternating basic and acidic residues, largely arginine (R) and aspartic acid (D). The gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 52.1), ovary (RPKM 20.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.33

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (31952087..31958971, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (31805292..31812176, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (31919864..31926748, complement)

Chromosome 6 - NC_000006.12 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?

Dependency of NELF-E-SLUG-KAT2B epigenetic axis in breast cancer carcinogenesis.
Title: Dependency of NELF-E-SLUG-KAT2B epigenetic axis in breast cancer carcinogenesis.
Genome-wide chromatin contacts of super-enhancer-associated lncRNA identify LINC01013 as a regulator of fibrosis in the aortic valve.
Title: Genome-wide chromatin contacts of super-enhancer-associated lncRNA identify LINC01013 as a regulator of fibrosis in the aortic valve.
Overexpression of NELFE contributes to gastric cancer progression via Wnt/beta-catenin signaling-mediated activation of CSNK2B expression.
Title: Overexpression of NELFE contributes to gastric cancer progression via Wnt/β-catenin signaling-mediated activation of CSNK2B expression.
NELF complex fosters BRCA1 and RAD51 recruitment to DNA damage sites and modulates sensitivity to PARP inhibition.
Title: NELF complex fosters BRCA1 and RAD51 recruitment to DNA damage sites and modulates sensitivity to PARP inhibition.
NELFE-Dependent MYC Signature Identifies a Unique Cancer Subtype in Hepatocellular Carcinoma.
Title: NELFE-Dependent MYC Signature Identifies a Unique Cancer Subtype in Hepatocellular Carcinoma.
NELFE expression was increased in pancreatic cancer (PC) tissues compared with the paired normal tissues. NELFE expression was upregulated in PC cells when compared with normal pancreatic cells. Knockdown of NELFE inhibited the proliferation, invasion and migration of PC cells. NELFE activates the Wnt/betacatenin signaling pathway and epithelialtomesenchymal transition by decreasing the stabilization of NDRG2 mRNA in PC.
Title: NELFE promoted pancreatic cancer metastasis and the epithelial‑to‑mesenchymal transition by decreasing the stabilization of NDRG2 mRNA.
define two mutually exclusive complexes CBC-NELF-E and CBC-ARS2-PHAX, which likely act in respectively earlier and later phases of transcription
Title: Structural basis for mutually exclusive co-transcriptional nuclear cap-binding complexes with either NELF-E or ARS2.
A positively charged face of NELF-AC is involved in RNA binding, whereas the opposite face of the NELF-AC subcomplex binds NELF-B. NELF-B is predicted to form a HEAT repeat fold, also binds RNA in vivo, and anchors the subunit NELF-E, which is confirmed to bind RNA in vivo.
Title: Architecture and RNA binding of the human negative elongation factor.
novel actions of BRD4 and of NELF-E in GR-controlled gene induction have been uncovered.
Title: Kinetically Defined Mechanisms and Positions of Action of Two New Modulators of Glucocorticoid Receptor-regulated Gene Induction.
Following NELF-E knockdown or tumor necrosis factor alpha stimulation, promoter-proximal RNAP II levels increase up to 3-fold, and there is a dramatic increase in RNAP II levels within the HIV genome.
Title: Negative elongation factor is required for the maintenance of proviral latency but does not induce promoter-proximal pausing of RNA polymerase II on the HIV long terminal repeat.

Submit: New GeneRIF Correction See all GeneRIFs (24)

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

EBI GWAS Catalog

Description
Genetic factors in nonsmokers with age-related macular degeneration revealed through genome-wide gene-environment interaction analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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Replication interactions

Interaction	Pubs
Knockdown of NELF-E by shRNA enhances HIV-1 transcription in latently infected cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	NELF represses HIV-1 transcription by pausing the RNA polymerase II complex	PubMed
	tat	NELF associates with HIV-1 Tat as part of the HIV-1 transcription elongation complex	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

RH46865 (e-PCR)
- UniSTS:13369

D6S45 (e-PCR)
- UniSTS:147295

HUEST-L03411 (e-PCR)
- UniSTS:264061

RH70616 (e-PCR)
- UniSTS:32381

SHGC-12705 (e-PCR)
- UniSTS:38784

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	NAS Non-traceable Author Statement more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription elongation by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription elongation by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of ERK1 and ERK2 cascade	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein modification process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of NELF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of NELF complex	IDA Inferred from Direct Assay more info	PubMed
part_of NELF complex	IPI Inferred from Physical Interaction more info	PubMed
is_active_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: negative elongation factor E

Names: RD RNA-binding protein; RNA-binding protein RD; major histocompatibility complex gene RD; negative elongation factor polypeptide E; nuclear protein

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.