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 as... See more...

Aliases for NELFE Gene

Aliases for NELFE Gene

  • Negative Elongation Factor Complex Member E 2 3 5
  • Negative Elongation Factor E 3 4
  • RD RNA-Binding Protein 2 3
  • RNA-Binding Protein RD 3 4
  • NELF-E 3 4
  • RDBP 3 4
  • RD 3 4
  • Major Histocompatibility Complex Gene RD 3
  • Negative Elongation Factor Polypeptide E 3
  • RD RNA Binding Protein 2
  • Nuclear Protein 3
  • D6S45 3
  • RDP 3

External Ids for NELFE Gene

Previous HGNC Symbols for NELFE Gene

  • RDBP

Previous GeneCards Identifiers for NELFE Gene

  • GC06M031925
  • GC06M031926

Summaries for NELFE Gene

Entrez Gene Summary for NELFE Gene

  • 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]

GeneCards Summary for NELFE Gene

NELFE (Negative Elongation Factor Complex Member E) is a Protein Coding gene. Diseases associated with NELFE include Wolf-Hirschhorn Syndrome. Among its related pathways are Formation of HIV-1 elongation complex containing HIV-1 Tat and HIV Life Cycle. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding.

UniProtKB/Swiss-Prot Summary for NELFE Gene

  • Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II (PubMed:10199401). The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex (PubMed:11940650, PubMed:12612062). Provides the strongest RNA binding activity of the NELF complex and may initially recruit the NELF complex to RNA (PubMed:18303858, PubMed:27282391).
  • (Microbial infection) The NELF complex is involved in HIV-1 latency possibly involving recruitment of PCF11 to paused RNA polymerase II.

Gene Wiki entry for NELFE Gene

Additional gene information for NELFE Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NELFE Gene

Genomics for NELFE Gene

GeneHancer (GH) Regulatory Elements for NELFE Gene

Promoters and enhancers for NELFE Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NELFE on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NELFE

Genomic Locations for NELFE Gene

Genomic Locations for NELFE Gene
chr6:31,952,087-31,959,087
(GRCh38/hg38)
Size:
7,001 bases
Orientation:
Minus strand
chr6:31,919,864-31,926,887
(GRCh37/hg19)
Size:
7,024 bases
Orientation:
Minus strand

Genomic View for NELFE Gene

Genes around NELFE on UCSC Golden Path with GeneCards custom track

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

Proteins for NELFE Gene

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

    Protein Symbol:
    P18615-NELFE_HUMAN
    Recommended name:
    Negative elongation factor E
    Protein Accession:
    P18615
    Secondary Accessions:
    • A2BE08
    • B4DUN1
    • B4DYX9
    • Q5JP74
    • Q5JP75
    • Q96F56
    • Q9NPK2

    Protein attributes for NELFE Gene

    Size:
    380 amino acids
    Molecular mass:
    43240 Da
    Quaternary structure:
    • The NELF complex is composed of NELFA, NELFB, NELFCD (isoform NELF-C or isoform NELF-D) and NELFE (PubMed:10199401, PubMed:27282391). Interacts with NELFB (By similarity).
    • (Microbial infection) Binds to the HIV-1 TAR RNA which is located in the long terminal repeat (LTR) of HIV-1.

    Three dimensional structures from OCA and Proteopedia for NELFE Gene

    Alternative splice isoforms for NELFE Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NELFE Gene

Post-translational modifications for NELFE Gene

No data available for DME Specific Peptides for NELFE Gene

Domains & Families for NELFE Gene

Protein Domains for NELFE Gene

Blocks:
  • RNA-binding region RNP-1 (RNA recognition motif)
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NELFE Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ52247, highly similar to Negative elongation factor E (B4DUN1_HUMAN)
  • cDNA FLJ56180, highly similar to Negative elongation factor E (B4DYX9_HUMAN)
  • cDNA FLJ56553, highly similar to Negative elongation factor E (B7Z6T4_HUMAN)
  • RNA-binding protein RD (NELFE_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P18615

UniProtKB/Swiss-Prot:

NELFE_HUMAN :
  • The RRM domain interacts with RNA, and is essential for NELF complex function. It is however not required for the NELF complex formation.
  • Belongs to the RRM NELF-E family.
Domain:
  • The RRM domain interacts with RNA, and is essential for NELF complex function. It is however not required for the NELF complex formation.
Family:
  • Belongs to the RRM NELF-E family.
genes like me logo Genes that share domains with NELFE: view

Function for NELFE Gene

Molecular function for NELFE Gene

UniProtKB/Swiss-Prot Function:
Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II (PubMed:10199401). The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex (PubMed:11940650, PubMed:12612062). Provides the strongest RNA binding activity of the NELF complex and may initially recruit the NELF complex to RNA (PubMed:18303858, PubMed:27282391).
UniProtKB/Swiss-Prot Function:
(Microbial infection) The NELF complex is involved in HIV-1 latency possibly involving recruitment of PCF11 to paused RNA polymerase II.

Phenotypes From GWAS Catalog for NELFE Gene

Gene Ontology (GO) - Molecular Function for NELFE Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003682 chromatin binding IEA --
GO:0003723 RNA binding NAS,IEA 2119325
GO:0005515 protein binding IPI 12612062
genes like me logo Genes that share ontologies with NELFE: view
genes like me logo Genes that share phenotypes with NELFE: view

Animal Models for NELFE Gene

MGI Knock Outs for NELFE:
  • Nelfe Nelfe<tm1a(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NELFE Gene

Localization for NELFE Gene

Subcellular locations from UniProtKB/Swiss-Prot for NELFE Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NELFE gene
Compartment Confidence
nucleus 5
plasma membrane 4
cytosol 2
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (4)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NELFE Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus NAS 2119325
GO:0005654 nucleoplasm IDA,TAS --
GO:0005886 plasma membrane IDA --
GO:0016604 nuclear body IDA --
GO:0032021 NELF complex IEA,IDA 12612062
genes like me logo Genes that share ontologies with NELFE: view

Pathways & Interactions for NELFE Gene

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

Gene Ontology (GO) - Biological Process for NELFE Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II TAS --
GO:0006368 transcription elongation from RNA polymerase II promoter TAS --
GO:0034244 negative regulation of transcription elongation from RNA polymerase II promoter IBA 21873635
GO:0045944 positive regulation of transcription by RNA polymerase II IEA --
genes like me logo Genes that share ontologies with NELFE: view

No data available for SIGNOR curated interactions for NELFE Gene

Drugs & Compounds for NELFE Gene

No Compound Related Data Available

Transcripts for NELFE Gene

mRNA/cDNA for NELFE Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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

No ASD Table

Relevant External Links for NELFE Gene

GeneLoc Exon Structure for
NELFE

Expression for NELFE Gene

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

Protein differential expression in normal tissues from HIPED for NELFE Gene

This gene is overexpressed in Breast (10.9), Liver (10.5), and Adrenal (7.4).

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



Protein tissue co-expression partners for NELFE Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NELFE

SOURCE GeneReport for Unigene cluster for NELFE Gene:

Hs.423935

mRNA Expression by UniProt/SwissProt for NELFE Gene:

P18615-NELFE_HUMAN
Tissue specificity: Widely expressed. Expressed in heart, brain, lung, placenta, liver, skeletal muscle, kidney and pancreas.

Evidence on tissue expression from TISSUES for NELFE Gene

  • Liver(4.4)
  • Blood(4.3)
  • Eye(4.1)
  • Skin(4.1)
  • Nervous system(2.8)
genes like me logo Genes that share expression patterns with NELFE: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NELFE Gene

Orthologs for NELFE Gene

This gene was present in the common ancestor of animals.

Orthologs for NELFE Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RDBP 31
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NELFE 31
  • 93 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NELFE 31 30
  • 92.95 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NELFE 31
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NELFE 31 30
  • 91 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nelfe 17 31 30
  • 87.47 (n)
chicken
(Gallus gallus)
Aves NELFE 31
  • 65 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NELFE 31
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nelfe 30
  • 69.03 (n)
Str.7146 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.8914 30
zebrafish
(Danio rerio)
Actinopterygii nelfe 31
  • 70 (a)
OneToOne
Dr.25733 30
fruit fly
(Drosophila melanogaster)
Insecta Nelf-E 31
  • 36 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.554 31
  • 31 (a)
OneToOne
Species where no ortholog for NELFE was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for NELFE Gene

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

Paralogs for NELFE Gene

(3) SIMAP similar genes for NELFE Gene using alignment to 9 proteins:

  • NELFE_HUMAN
  • A2ABK1_HUMAN
  • A2ABK2_HUMAN
  • A2ABK4_HUMAN
  • B4DUN1_HUMAN
  • B4DYX9_HUMAN
  • E7ENC7_HUMAN
  • E7EWR7_HUMAN
  • E9PD43_HUMAN
genes like me logo Genes that share paralogs with NELFE: view

No data available for Paralogs for NELFE Gene

Variants for NELFE Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NELFE Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
711313 Likely Benign: not provided 31,957,016(-) A/T INTRON_VARIANT
716866 Likely Benign: not provided 31,954,637(-) C/T SYNONYMOUS_VARIANT
770727 Benign: not provided 31,954,663(-) TGTCTCGATCCCG/T INFRAME_DELETION
784497 Benign: not provided 31,954,568(-) CTCTCGG/C INFRAME_DELETION
rs17201466 Likely Benign: Trichohepatoenteric syndrome 31,958,823(-) C/T INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for NELFE Gene

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

Variant ID Type Subtype PubMed ID
dgv10403n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
dgv10463n54 CNV loss 21841781
esv2759415 CNV gain+loss 17122850
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1126749 CNV deletion 24896259
nsv284 CNV deletion 15895083
nsv428141 CNV gain+loss 18775914
nsv5247 CNV deletion 18451855
nsv830628 CNV loss 17160897

Variation tolerance for NELFE Gene

Residual Variation Intolerance Score: 31.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.83; 47.82% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NELFE Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NELFE

SNP Genotyping and Copy Number Assay Products

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

Disorders for NELFE Gene

MalaCards: The human disease database

(1) MalaCards diseases for NELFE Gene - From: DISEASES

Disorder Aliases PubMed IDs
wolf-hirschhorn syndrome
  • whs
- elite association - COSMIC cancer census association via MalaCards
Search NELFE in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NELFE

genes like me logo Genes that share disorders with NELFE: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NELFE Gene

Publications for NELFE Gene

  1. Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. (PMID: 12612062) Narita T … Handa H (Molecular and cellular biology 2003) 3 4 23 54
  2. The human RD protein is closely related to nuclear RNA-binding proteins and has been highly conserved. (PMID: 2119325) Surowy CS … Spritz RA (Gene 1990) 3 4 23 54
  3. Architecture and RNA binding of the human negative elongation factor. (PMID: 27282391) Vos SM … Cramer P (eLife 2016) 3 4 54
  4. Role of RDBP and SKIV2L variants in the major histocompatibility complex class III region in polypoidal choroidal vasculopathy etiology. (PMID: 19556007) Kondo N … Negi A (Ophthalmology 2009) 3 23 54
  5. NELF-E RRM undergoes major structural changes in flexible protein regions on target RNA binding. (PMID: 18303858) Rao JN … Rösch P (Biochemistry 2008) 3 4 54

Products for NELFE Gene