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Aliases for NELFE Gene

Aliases for NELFE Gene

  • Negative Elongation Factor Complex Member E 2 3 5
  • 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
  • Negative Elongation Factor 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. Among its related pathways are Gene Expression and Formation of HIV-1 elongation complex containing HIV-1 Tat. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding.

UniProtKB/Swiss-Prot for NELFE Gene

  • Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II. The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex. The NELF complex is involved in HIV-1 latency possibly involving recruitment of PCF11 to paused RNA polymerase II. Provides the strongest RNA binding activity of the NELF complex and may initially recruit the NELF complex to RNA. Binds to the HIV-1 TAR RNA which is located in the long terminal repeat (LTR) of HIV-1.

Gene Wiki entry for NELFE Gene

Additional gene information for NELFE Gene

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

Genomics for NELFE Gene

GeneHancer (GH) Regulatory Elements for NELFE Gene

Promoters and enhancers for NELFE 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
GH06J031957 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 -0.1 -64 2.7 CLOCK MLX DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 MEF2D RCOR2 SKIV2L NELFE LY6G5B HLA-C ATF6B MSH5 LSM2 DXO CCHCR1 STK19B
GH06J031733 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 30.9 +221.7 221655 8.5 CLOCK MLX ZFP64 YBX1 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 MSH5 CLIC1 MSH5-SAPCD1 DDX39B LY6G5B ATF6B LSM2 SKIV2L CSNK2B GPANK1
GH06J031538 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 29.8 +418.0 417971 4.9 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 ZNF263 DDX39B GC06M031573 SNORD84 GC06M031543 GC06M031542 PIR59933 PIR32498 GC06M032015 GC06M032013 GC06M032007
GH06J031813 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 20.7 +133.2 133234 25.6 CLOCK ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 C6orf48 HSPA1B HSPA1A HSPA1L GC06P032216 ATF6B DDX39B LY6G5B BAG6 LSM2
GH06J031861 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 21.9 +95.0 94994 4.5 MLX ZFP64 YBX1 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 NEU1 LY6G5B DDX39B ATF6B LSM2 GPANK1 SKIV2L MSH5 TCF19 CSNK2B
- 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

Genomic Locations for NELFE Gene

Genomic Locations for NELFE Gene
chr6:31,952,087-31,959,110
(GRCh38/hg38)
Size:
7,024 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.

    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

Gene Families for NELFE Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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. The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex. The NELF complex is involved in HIV-1 latency possibly involving recruitment of PCF11 to paused RNA polymerase II. Provides the strongest RNA binding activity of the NELF complex and may initially recruit the NELF complex to RNA. Binds to the HIV-1 TAR RNA which is located in the long terminal repeat (LTR) of HIV-1.

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 Model Products

CRISPR Products

Inhibitory RNA Products

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

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , 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

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 TAS,IDA --
GO:0005886 plasma membrane IDA --
GO:0016604 nuclear body IDA --
GO:0032021 NELF complex IDA,IEA 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:0006351 transcription, DNA-templated IEA --
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 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

Unigene Clusters for NELFE Gene

Negative elongation factor complex member E:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

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

No ASD Table

Relevant External Links for NELFE Gene

GeneLoc Exon Structure for
NELFE
ECgene alternative splicing isoforms for
NELFE

Expression for NELFE Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of NELFE Gene:

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 34
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NELFE 34
  • 93 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NELFE 34 33
  • 92.95 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NELFE 34 33
  • 91 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NELFE 34
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nelfe 16 34 33
  • 87.47 (n)
chicken
(Gallus gallus)
Aves NELFE 34
  • 65 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NELFE 34
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nelfe 33
  • 69.03 (n)
Str.7146 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.8914 33
zebrafish
(Danio rerio)
Actinopterygii nelfe 34
  • 70 (a)
OneToOne
Dr.25733 33
fruit fly
(Drosophila melanogaster)
Insecta Nelf-E 34
  • 36 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.554 34
  • 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 from dbSNP and Humsavar for NELFE Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1050394803 uncertain-significance, Trichohepatoenteric syndrome 31,959,150(-) T/C/G upstream_transcript_variant
rs1050729511 uncertain-significance, Trichohepatoenteric syndrome 31,958,920(-) G/A 5_prime_UTR_variant
rs11541400 uncertain-significance, Trichohepatoenteric syndrome 31,960,262(-) C/G upstream_transcript_variant
rs145042380 uncertain-significance, Trichohepatoenteric syndrome 31,961,081(-) C/T upstream_transcript_variant
rs146543642 uncertain-significance, Trichohepatoenteric syndrome 31,960,499(-) C/T upstream_transcript_variant

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

Additional Disease Information for NELFE

No disorders were found for NELFE Gene.

No data available for MalaCards , 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 22 58
  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 22 58
  3. Architecture and RNA binding of the human negative elongation factor. (PMID: 27282391) Vos SM … Cramer P (eLife 2016) 3 4 58
  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 22 58
  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 58

Products for NELFE Gene

Sources for NELFE Gene