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Aliases for NELFA Gene

Aliases for NELFA Gene

  • Negative Elongation Factor Complex Member A 2 3 5
  • Wolf-Hirschhorn Syndrome Candidate 2 Protein 3 4
  • NELF-A 3 4
  • WHSC2 3 4
  • Wolf-Hirschhorn Syndrome Candidate 2 2
  • Negative Elongation Factor A 3
  • 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 Chromosomal Deletion Syndrome. 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 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. The NELF complex is involved in HIV-1 latency possibly involving recruitment of PCF11 to paused RNA polymerase II. In vitro, the NELFA:NELFCD subcomplex binds to ssDNA and ssRNA in a sequence- and structure-dependent manner. Probably required to interact with the RNA polymerase II complex.

Gene Wiki entry for NELFA Gene

Additional gene information for NELFA Gene

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

Genomics for NELFA Gene

GeneHancer (GH) Regulatory Elements for NELFA Gene

Promoters and enhancers for NELFA 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
GH04J002007 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 684.5 +32.7 32708 3.2 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 IRF4 NELFA HAUS3 NOP14-AS1 MFSD10 FAM193A RNF4 MAEA SCARNA22 C4orf48 SH3BP2
GH04J002041 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 666.3 -0.4 -352 1.1 SIN3A ZBTB7B POLR2B GLIS2 ZNF143 KLF7 ZNF263 RFX3 GMEB1 GLIS1 NELFA GC04P002041 C4orf48 RNF4 MFSD10 FAM193A HAUS3 ENSG00000270195 MAEA CRIPAK
GH04J001710 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 39.7 +328.5 328491 5.7 HDGF PKNOX1 CLOCK SMAD1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ENSG00000270195 SLBP RNF4 HAUS3 NELFA FAM193A FAM53A GAK CRIPAK MAEA
GH04J001867 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 29.7 +170.7 170724 7 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 SLC30A9 POLR2B NSD2 GC04M001869 RNF4 HAUS3 NELFA FAM193A GAK CRIPAK MAEA ENSG00000270195
GH04J002329 Enhancer 1.1 Ensembl ENCODE 46.3 -288.4 -288365 1.3 HDGF ARNT ZNF133 FEZF1 ZNF2 GLIS2 ZNF416 FOS SP3 YY2 NELFA RNF4 CRIPAK HAUS3 FAM193A NOP14 ENSG00000270195 MFSD10 ENSG00000254094 ENSG00000207009
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NELFA on UCSC Golden Path with GeneCards custom track

Genomic Locations for NELFA Gene

Genomic Locations for NELFA Gene
chr4:1,982,714-2,041,914
(GRCh38/hg38)
Size:
59,201 bases
Orientation:
Minus strand
chr4:1,984,441-2,043,630
(GRCh37/hg19)
Size:
59,190 bases
Orientation:
Minus strand

Genomic View for NELFA Gene

Genes around NELFA on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence 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; NELFA and NELFCD form a stable subcomplex that binds to the N-terminus of NELFB. 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};

    Three dimensional structures from OCA and Proteopedia for NELFA Gene

    Alternative splice isoforms for NELFA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NELFA Gene

Post-translational modifications for NELFA Gene

  • Ubiquitination at Lys371
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NELFA Gene

Domains & Families for NELFA Gene

Gene Families for NELFA Gene

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

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.
Family:
  • Belongs to the NELF-A family.
genes like me logo Genes that share domains with NELFA: view

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. The NELF complex is involved in HIV-1 latency possibly involving recruitment of PCF11 to paused RNA polymerase II. In vitro, the NELFA:NELFCD subcomplex binds to ssDNA and ssRNA in a sequence- and structure-dependent manner. Probably required to interact with the RNA polymerase II complex.

Phenotypes From GWAS Catalog for NELFA Gene

Gene Ontology (GO) - Molecular Function for NELFA Gene

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

Human Phenotype Ontology for NELFA Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for NELFA Gene

miRTarBase miRNAs that target NELFA

Inhibitory RNA Products

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

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

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 NELFA gene
Compartment Confidence
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (4)
  • Nucleoplasm (4)
  • Cytosol (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NELFA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS,IDA --
GO:0005829 cytosol IDA --
GO:0016604 nuclear body IDA --
GO:0032021 NELF complex IDA 12612062
genes like me logo Genes that share ontologies with NELFA: view

Pathways & Interactions for NELFA Gene

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

Gene Ontology (GO) - Biological Process for NELFA 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:0007275 multicellular organism development TAS 10409432
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

mRNA/cDNA for NELFA Gene

Unigene Clusters for NELFA Gene

Negative elongation factor complex member A:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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 and MOPED for NELFA Gene



Protein tissue co-expression partners for NELFA Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NELFA Gene:

NELFA

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.

Evidence on tissue expression from TISSUES for NELFA Gene

  • Nervous system(4.9)
  • Liver(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NELFA Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • scalp
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • diaphragm
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • intestine
  • kidney
  • large intestine
  • liver
  • small intestine
  • spleen
  • stomach
Pelvis:
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • urethra
  • uterus
  • vagina
  • vas deferens
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • bone marrow
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with NELFA: view

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
chimpanzee
(Pan troglodytes)
Mammalia NELFA 34
  • 100 (a)
OneToOne
WHSC2 33
  • 99.38 (n)
dog
(Canis familiaris)
Mammalia NELFA 34 33
  • 88.7 (n)
OneToOne
cow
(Bos Taurus)
Mammalia WHSC2 34 33
  • 88.32 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nelfa 33
  • 85.48 (n)
mouse
(Mus musculus)
Mammalia Nelfa 16 34 33
  • 85.1 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NELFA 34
  • 83 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NELFA 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves WHSC2 34 33
  • 73.61 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NELFA 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nelfa 33
  • 73.7 (n)
Str.20488 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.18947 33
zebrafish
(Danio rerio)
Actinopterygii nelfa 34 33
  • 73.12 (n)
OneToOne
wufi75f03 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.574 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002290 33
  • 57.14 (n)
fruit fly
(Drosophila melanogaster)
Insecta Nelf-A 34
  • 14 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 39 (a)
OneToOne
Species where no ortholog for NELFA was found in the sources mined by GeneCards:
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for NELFA: view image

Paralogs for NELFA Gene

(19) SIMAP similar genes for NELFA Gene using alignment to 11 proteins:

  • NELFA_HUMAN
  • B3KSP0_HUMAN
  • C9JEM7_HUMAN
  • C9JHL4_HUMAN
  • F8W954_HUMAN
  • F8WF98_HUMAN
  • H0Y3X6_HUMAN
  • H7C0W2_HUMAN
  • H7C2C7_HUMAN
  • H7C2M8_HUMAN
  • H7C3C2_HUMAN
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 Variation AA Info Type
rs1000028762 -- 2,000,581(-) C/T intron_variant
rs1000061386 -- 2,000,983(-) T/C intron_variant
rs1000092412 -- 1,993,852(-) G/C intron_variant
rs1000094265 -- 2,006,329(-) T/G intron_variant
rs1000161060 -- 2,009,586(-) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant

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

Variant ID Type Subtype PubMed ID
esv33438 CNV loss 17666407
nsv822441 CNV loss 20364138

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)

Additional Variant Information for NELFA Gene

Human Gene Mutation Database (HGMD)
NELFA
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NELFA

SNP Genotyping and Copy Number Assay Products

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

Disorders for NELFA Gene

MalaCards: The human disease database

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

- elite association - COSMIC cancer census association via MalaCards
Search NELFA in MalaCards View complete list of genes associated with diseases

Additional Disease Information for 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 TJ … Altherr MR (Genomics 1999) 2 3 4 22 58
  2. 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
  3. Stimulation of RNA polymerase II elongation by hepatitis delta antigen. (PMID: 11387440) Yamaguchi Y … Handa H (Science (New York, N.Y.) 2001) 3 4 22 58
  4. Modulation of WHSC2 expression in human endothelial cells. (PMID: 11150502) Mariotti M … Maier JA (FEBS letters 2000) 3 4 22 58
  5. Architecture and RNA binding of the human negative elongation factor. (PMID: 27282391) Vos SM … Cramer P (eLife 2016) 3 4 58

Products for NELFA Gene

Sources for NELFA Gene

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