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Aliases for NELFA Gene

Aliases for NELFA Gene

  • Negative Elongation Factor Complex Member A 2 3
  • Wolf-Hirschhorn Syndrome Candidate 2 Protein 3 4
  • NELF-A 3 4
  • WHSC2 3 4
  • Wolf-Hirschhorn Syndrome Candidate 2 2
  • P/OKcl.15 3

External Ids for NELFA Gene

Previous HGNC Symbols for NELFA Gene

  • WHSC2

Summaries for NELFA Gene

Entrez Gene Summary for NELFA Gene

  • This gene is expressed ubiquitously with higher levels in fetal than in adult tissues. It encodes a protein sharing 93% sequence identity with the mouse protein. Wolf-Hirschhorn syndrome (WHS) is a malformation syndrome associated with a hemizygous deletion of the distal short arm of chromosome 4. This gene is mapped to the 165 kb WHS critical region, and may play a role in the phenotype of the WHS or Pitt-Rogers-Danks syndrome. The encoded protein is found to be capable of reacting with HLA-A2-restricted and tumor-specific cytotoxic T lymphocytes, suggesting a target for use in specific immunotherapy for a large number of cancer patients. This protein has also been shown to be a member of the NELF (negative elongation factor) protein complex that participates in the regulation of RNA polymerase II transcription elongation. [provided by RefSeq, Jul 2008]

GeneCards Summary for NELFA Gene

NELFA (Negative Elongation Factor Complex Member A) is a Protein Coding gene. Diseases associated with NELFA include wolf-hirschhorn syndrome and hepatitis d. Among its related pathways are Infectious disease and Gene Expression. GO annotations related to this gene include chromatin binding and translation elongation factor activity.

UniProtKB/Swiss-Prot for NELFA 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. Probably required to interact with the RNA polymerase II complex.

Gene Wiki entry for NELFA Gene

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

Genomics for NELFA Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for NELFA Gene

Chromosome:
4
Start:
1,982,714 bp from pter
End:
2,041,914 bp from pter
Size:
59,201 bases
Orientation:
Minus strand

Genomic View for NELFA Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for NELFA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NELFA Gene

No data available for Regulatory Elements for NELFA Gene

Proteins for NELFA Gene

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

    Protein Symbol:
    Q9H3P2-NELFA_HUMAN
    Recommended name:
    Negative elongation factor A
    Protein Accession:
    Q9H3P2
    Secondary Accessions:
    • A2A2T1
    • O95392

    Protein attributes for NELFA Gene

    Size:
    528 amino acids
    Molecular mass:
    57277 Da
    Quaternary structure:
    • The NELF complex is composed of NELFA, NELFB, NELFCD (isoform NELF-C or isoform NELF-D) and NELFE. Interacts with the RNA polymerase II complex when it is not phosphorylated by P-TEFb.
    SequenceCaution:
    • Sequence=AAC72982.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAG54283.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=CAM15219.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=EAW82546.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for NELFA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NELFA Gene

Proteomics data for NELFA Gene at MOPED

Post-translational modifications for NELFA Gene

  • Ubiquitination at Lys 371
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NELFA Gene

Domains & Families for NELFA Gene

Protein Domains for NELFA Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q9H3P2

UniProtKB/Swiss-Prot:

NELFA_HUMAN :
  • The HDAg-like domain is essential for transcriptional repression, and mediates the interaction with the RNA polymerase II complex.
  • Belongs to the NELF-A family.
Domain:
  • The HDAg-like domain is essential for transcriptional repression, and mediates the interaction with the RNA polymerase II complex.
  • Contains 1 HDAg-like domain.
Family:
  • Belongs to the NELF-A family.
genes like me logo Genes that share domains with NELFA: view

No data available for Gene Families for NELFA Gene

Function for NELFA Gene

Molecular function for NELFA 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. Probably required to interact with the RNA polymerase II complex.

Gene Ontology (GO) - Molecular Function for NELFA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding --
GO:0005515 protein binding IPI 12612062
genes like me logo Genes that share ontologies with NELFA: view

Phenotypes for NELFA Gene

genes like me logo Genes that share phenotypes with NELFA: view

Animal Model Products

miRNA for NELFA Gene

miRTarBase miRNAs that target NELFA

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for NELFA

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for NELFA Gene

Localization for NELFA Gene

Subcellular locations from UniProtKB/Swiss-Prot for NELFA Gene

Gene Ontology (GO) - Cellular Components for NELFA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IDA --
GO:0032021 NELF complex IDA 12612062
genes like me logo Genes that share ontologies with NELFA: view

No data available for Subcellular locations from COMPARTMENTS for NELFA Gene

Pathways & Interactions for NELFA Gene

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

Pathways by source for NELFA Gene

Gene Ontology (GO) - Biological Process for NELFA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006366 transcription from RNA polymerase II promoter TAS --
GO:0006368 transcription elongation from RNA polymerase II promoter TAS --
GO:0007275 multicellular organismal development TAS 10409432
GO:0010467 gene expression TAS --
GO:0016032 viral process TAS --
genes like me logo Genes that share ontologies with NELFA: view

No data available for SIGNOR curated interactions for NELFA Gene

Drugs & Compounds for NELFA Gene

No Compound Related Data Available

Transcripts for NELFA Gene

Unigene Clusters for NELFA Gene

Negative elongation factor complex member A:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for NELFA

Flow Cytometry Products

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

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b · 8c ^ 9a · 9b ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b ^
SP1: - - - - - - - - -
SP2: - -
SP3: - -
SP4: - - - - - - - - - - - -
SP5:
SP6: - - - - - - - - - - - - - -
SP7: - - - - - -
SP8: - - - - - - -
SP9: -
SP10: - - - - - - - - - -
SP11: - - -
SP12: -
SP13: - - - - - -
SP14: - - - - - - -
SP15: -

ExUns: 13 ^ 14 ^ 15 ^ 16a · 16b · 16c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for NELFA Gene

GeneLoc Exon Structure for
NELFA
ECgene alternative splicing isoforms for
NELFA

Expression for NELFA Gene

mRNA expression in normal human tissues for NELFA Gene

Protein differential expression in normal tissues from HIPED for NELFA Gene

This gene is overexpressed in Peripheral blood mononuclear cells (15.8) and Testis (10.8).

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



SOURCE GeneReport for Unigene cluster for NELFA Gene Hs.21771

mRNA Expression by UniProt/SwissProt for NELFA Gene

Q9H3P2-NELFA_HUMAN
Tissue specificity: Ubiquitous. Expressed in heart, brain, placenta, liver, skeletal muscle, kidney and pancreas. Expressed at lower level in adult lung. Expressed in fetal brain, lung, liver and kidney.
genes like me logo Genes that share expression patterns with NELFA: view

Protein tissue co-expression partners for NELFA Gene

- Elite partner

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for NELFA Gene

Orthologs for NELFA Gene

This gene was present in the common ancestor of animals.

Orthologs for NELFA Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia WHSC2 35
  • 88.32 (n)
  • 93.56 (a)
WHSC2 36
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NELFA 35
  • 88.7 (n)
  • 95.64 (a)
NELFA 36
  • 95 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Nelfa 35
  • 85.1 (n)
  • 95.83 (a)
Nelfa 16
Nelfa 36
  • 95 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia WHSC2 35
  • 99.38 (n)
  • 100 (a)
NELFA 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nelfa 35
  • 85.48 (n)
  • 95.83 (a)
oppossum
(Monodelphis domestica)
Mammalia NELFA 36
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NELFA 36
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves WHSC2 35
  • 73.61 (n)
  • 85.85 (a)
WHSC2 36
  • 85 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NELFA 36
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nelfa 35
  • 73.7 (n)
  • 83.69 (a)
Str.20488 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.18947 35
zebrafish
(Danio rerio)
Actinopterygii nelfa 35
  • 73.12 (n)
  • 81.02 (a)
wufi75f03 35
nelfa 36
  • 79 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.574 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002290 35
  • 57.14 (n)
  • 50.36 (a)
fruit fly
(Drosophila melanogaster)
Insecta Nelf-A 36
  • 14 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 39 (a)
OneToOne
Species with no ortholog for NELFA:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 NELFA Gene

ENSEMBL:
Gene Tree for NELFA (if available)
TreeFam:
Gene Tree for NELFA (if available)

Paralogs for NELFA Gene

genes like me logo Genes that share paralogs with NELFA: view

No data available for Paralogs for NELFA Gene

Variants for NELFA Gene

Sequence variations from dbSNP and Humsavar for NELFA Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type MAF
VAR_059459 -

Variation tolerance for NELFA Gene

Residual Variation Intolerance Score: 3.42% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.09; 38.14% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NELFA Gene

HapMap Linkage Disequilibrium report
NELFA
Human Gene Mutation Database (HGMD)
NELFA

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for NELFA Gene

Disorders for NELFA Gene

MalaCards: The human disease database

(2) MalaCards diseases for NELFA Gene - From: DISEASES, NovoSeek, and GeneCards

Disorder Aliases PubMed IDs
wolf-hirschhorn syndrome
  • pitt syndrome
hepatitis d
  • delta hepatitis
- elite association
Search NELFA in MalaCards View complete list of genes associated with diseases

Relevant External Links for NELFA

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NELFA
genes like me logo Genes that share disorders with NELFA: view

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

Publications for NELFA Gene

  1. Comparative analysis of a novel gene from the Wolf-Hirschhorn/Pitt- Rogers-Danks syndrome critical region. (PMID: 10409432) Wright T.J. … Altherr M.R. (Genomics 1999) 2 23 67
  2. Repression of RNA polymerase II elongation in vivo is critically dependent on the C-terminus of Spt5. (PMID: 19742326) Chen H. … Guo S. (PLoS ONE 2009) 23 67
  3. 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) 23 67
  4. Mild Wolf-Hirschhorn phenotype and partial GH deficiency in a patient with a 4p terminal deletion. (PMID: 15108211) Titomanlio L. … Del Giudice E. (Am. J. Med. Genet. A 2004) 23 67
  5. 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) 23 67

Products for NELFA Gene

Sources for NELFA Gene

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