Free for academic non-profit institutions. Other users need a Commercial license

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. Diseases associated with NELFE include Macular Degeneration, Age-Related, 1. Among its related pathways are HIV Life Cycle and Formation of HIV elongation complex in the absence of HIV Tat. 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 activty 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

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

Genomics for NELFE Gene

Regulatory Elements for NELFE Gene

Enhancers for NELFE Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G031567 2.1 FANTOM5 Ensembl ENCODE dbSUPER 9.7 +380.7 380692 22.2 CREB3L1 MLX AGO1 ZFP64 DMAP1 FEZF1 YBX1 YY1 SLC30A9 ZNF143 DDX39B TNF LY6G5B LSM2 DHX16 ATF6B TCF19 PPP1R10 VARS CSNK2B
GH06G031538 1.4 ENCODE dbSUPER 9.7 +418.0 417972 4.9 MLX CREB3L1 ZFP64 FEZF1 DMAP1 YY1 ZNF143 ZNF263 SP3 MCM3 LSM2 DDX39B ATF6B LY6G5B PPP1R10 DHX16 RPL3P2 SKIV2L ATP6V1G2 MICB
GH06G032893 1.3 Ensembl ENCODE 9.7 -935.8 -935791 3.0 PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZBTB7B YY1 SLC30A9 ZNF207 ZNF263 PSMB9 HLA-DMA ATF6B BRD2 ITPR3 LEMD2 DAXX RGL2 WDR46 PBX2
GH06G032521 1 Ensembl dbSUPER 9.7 -562.8 -562791 0.2 ZNF777 ZSCAN4 GLI4 ZNF2 ZNF324 CTBP1 ZNF302 ZNF366 ZNF547 ZNF169 HLA-DRB1 HLA-DRB6 HLA-DQA2 HLA-DRB5 LSM2 BRD2 DDX39B ATF6B DAXX RGL2
GH06G031957 1.2 ENCODE 0.7 -0.1 -64 2.7 CREB3L1 MLX DMAP1 YY1 ZNF143 ZNF263 SP3 MEF2D SSRP1 RCOR2 SKIV2L HLA-C PRRC2A ZBTB12 EHMT2 STK19B HLA-DRB5 HLA-DQB2 LY6G5B NELFE
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NELFE on UCSC Golden Path with GeneCards custom track

Promoters for NELFE Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000195627 110 1201 CREB3L1 MLX DMAP1 YY1 ZNF143 ZNF263 SP3 MEF2D SSRP1 RCOR2

Genomic Location for NELFE Gene

Chromosome:
6
Start:
31,952,087 bp from pter
End:
31,959,110 bp from pter
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

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 activty 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 Ontology (GO) - Molecular Function for NELFE Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003682 chromatin binding IEA --
GO:0003723 RNA binding NAS 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

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

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 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 from RNA polymerase II promoter TAS --
GO:0006368 transcription elongation from RNA polymerase II promoter TAS --
GO:0008150 biological_process ND --
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

Unigene Clusters for NELFE Gene

Negative elongation factor complex member E:
Representative Sequences:

CRISPR Products

Inhibitory RNA 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
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, PaxDb, 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

Primer Products

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 35
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NELFE 35
  • 93 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NELFE 34 35
  • 92.95 (n)
dog
(Canis familiaris)
Mammalia NELFE 34 35
  • 91 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NELFE 35
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nelfe 34 16 35
  • 87.47 (n)
chicken
(Gallus gallus)
Aves NELFE 35
  • 65 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NELFE 35
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nelfe 34
  • 69.03 (n)
Str.7146 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.8914 34
zebrafish
(Danio rerio)
Actinopterygii nelfe 35
  • 70 (a)
OneToOne
Dr.25733 34
fruit fly
(Drosophila melanogaster)
Insecta Nelf-E 35
  • 36 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.554 35
  • 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)

Paralogs for NELFE Gene

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

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 Sequence Context AA Info Type
rs17201466 Likely benign 31,958,823(+) AGCAA(C/T)GCAAA intron-variant, upstream-variant-2KB, utr-variant-5-prime
rs375895797 Likely benign 31,952,077(+) AGCTG(C/T)GACAA downstream-variant-500B, utr-variant-3-prime
rs4151672 Likely benign 31,952,053(+) AGGGG(C/T)GTGGG downstream-variant-500B, utr-variant-3-prime
rs438999 Likely benign 31,960,529(-) GATAC(C/T)GAGTT nc-transcript-variant, upstream-variant-2KB, reference, missense
rs11541400 Uncertain significance 31,960,262(+) GCTGT(C/G)CTGGG nc-transcript-variant, upstream-variant-2KB, reference, synonymous-codon

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)

Relevant External Links for NELFE Gene

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

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 and GeneCards

Disorder Aliases PubMed IDs
macular degeneration, age-related, 1
  • macular degeneration, age-related, reduced risk of
- elite association - COSMIC cancer census association via MalaCards
Search NELFE in MalaCards View complete list of genes associated with diseases

Relevant External Links for NELFE

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. (Mol. Cell. Biol. 2003) 3 4 22 64
  2. The human RD protein is closely related to nuclear RNA-binding proteins and has been highly conserved. (PMID: 2119325) Surowy C.S. … Spritz R.A. (Gene 1990) 3 4 22 64
  3. 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 64
  4. NELF-E RRM undergoes major structural changes in flexible protein regions on target RNA binding. (PMID: 18303858) Rao J.N. … RAPsch P. (Biochemistry 2008) 3 4 64
  5. Structural studies on the RNA-recognition motif of NELF E, a cellular negative transcription elongation factor involved in the regulation of HIV transcription. (PMID: 16898873) Rao J.N. … Wohrl B.M. (Biochem. J. 2006) 3 4 64

Products for NELFE Gene

Sources for NELFE Gene

Content
Loading form....