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Aliases for NPAS4 Gene

Aliases for NPAS4 Gene

  • Neuronal PAS Domain Protein 4 2 3 5
  • Class E Basic Helix-Loop-Helix Protein 79 3 4
  • HLH-PAS Transcription Factor NXF 3 4
  • PAS Domain-Containing Protein 10 3 4
  • Neuronal PAS4 3 4
  • BHLHe79 3 4
  • PASD10 3 4
  • NXF 3 4
  • Le-PAS 3

External Ids for NPAS4 Gene

Previous GeneCards Identifiers for NPAS4 Gene

  • GC11P065946
  • GC11P066188
  • GC11P062516

Summaries for NPAS4 Gene

Entrez Gene Summary for NPAS4 Gene

  • NXF is a member of the basic helix-loop-helix-PER (MIM 602260)-ARNT (MIM 126110)-SIM (see SIM2; MIM 600892) (bHLH-PAS) class of transcriptional regulators, which are involved in a wide range of physiologic and developmental events (Ooe et al., 2004 [PubMed 14701734]).[supplied by OMIM, Mar 2008]

GeneCards Summary for NPAS4 Gene

NPAS4 (Neuronal PAS Domain Protein 4) is a Protein Coding gene. GO annotations related to this gene include protein heterodimerization activity and RNA polymerase II core promoter proximal region sequence-specific DNA binding.

UniProtKB/Swiss-Prot for NPAS4 Gene

  • Acts as a transcriptional activator in the presence of ARNT. Can activate the CME (CNS midline enhancer) element and the expression of the drebrin gene.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NPAS4 Gene

Genomics for NPAS4 Gene

Regulatory Elements for NPAS4 Gene

Enhancers for NPAS4 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around NPAS4 on UCSC Golden Path with GeneCards custom track

Genomic Location for NPAS4 Gene

66,421,004 bp from pter
66,426,707 bp from pter
5,704 bases
Plus strand

Genomic View for NPAS4 Gene

Genes around NPAS4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPAS4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPAS4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPAS4 Gene

Proteins for NPAS4 Gene

  • Protein details for NPAS4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Neuronal PAS domain-containing protein 4
    Protein Accession:
    Secondary Accessions:
    • B7ZL81
    • Q8N8S5
    • Q8N9Q9

    Protein attributes for NPAS4 Gene

    802 amino acids
    Molecular mass:
    87117 Da
    Quaternary structure:
    • Efficient DNA binding requires dimerization with another bHLH protein. Forms a heterodimer with ARNT.
    • Sequence=BAC04271.1; Type=Frameshift; Positions=681; Evidence={ECO:0000305};

    Alternative splice isoforms for NPAS4 Gene


neXtProt entry for NPAS4 Gene

Proteomics data for NPAS4 Gene at MOPED

Post-translational modifications for NPAS4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NPAS4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NPAS4 Gene

Domains & Families for NPAS4 Gene

Gene Families for NPAS4 Gene

Protein Domains for NPAS4 Gene


Suggested Antigen Peptide Sequences for NPAS4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 bHLH (basic helix-loop-helix) domain.
  • Contains 1 bHLH (basic helix-loop-helix) domain.
  • Contains 1 PAC (PAS-associated C-terminal) domain.
  • Contains 2 PAS (PER-ARNT-SIM) domains.
genes like me logo Genes that share domains with NPAS4: view

Function for NPAS4 Gene

Molecular function for NPAS4 Gene

UniProtKB/Swiss-Prot Function:
Acts as a transcriptional activator in the presence of ARNT. Can activate the CME (CNS midline enhancer) element and the expression of the drebrin gene.

Gene Ontology (GO) - Molecular Function for NPAS4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IDA 14701734
GO:0046983 protein dimerization activity IEA --
genes like me logo Genes that share ontologies with NPAS4: view
genes like me logo Genes that share phenotypes with NPAS4: view

Animal Models for NPAS4 Gene

MGI Knock Outs for NPAS4:

Animal Model Products

miRNA for NPAS4 Gene

miRTarBase miRNAs that target NPAS4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NPAS4 Gene

Localization for NPAS4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPAS4 Gene

Subcellular locations from

Jensen Localization Image for NPAS4 Gene COMPARTMENTS Subcellular localization image for NPAS4 gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 1

No data available for Gene Ontology (GO) - Cellular Components for NPAS4 Gene

Pathways & Interactions for NPAS4 Gene

SuperPathways for NPAS4 Gene

No Data Available

Interacting Proteins for NPAS4 Gene

Gene Ontology (GO) - Biological Process for NPAS4 Gene


No data available for Pathways by source and SIGNOR curated interactions for NPAS4 Gene

Drugs & Compounds for NPAS4 Gene

No Compound Related Data Available

Transcripts for NPAS4 Gene

mRNA/cDNA for NPAS4 Gene

(3) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(13) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for NPAS4 Gene

Neuronal PAS domain protein 4:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for NPAS4 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8
SP2: -

Relevant External Links for NPAS4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NPAS4 Gene

mRNA expression in normal human tissues for NPAS4 Gene

mRNA differential expression in normal tissues according to GTEx for NPAS4 Gene

This gene is overexpressed in Brain - Cerebellum (x13.1), Brain - Cerebellar Hemisphere (x10.9), and Pituitary (x6.5).

Protein differential expression in normal tissues from HIPED for NPAS4 Gene

This gene is overexpressed in Brain (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for NPAS4 Gene

SOURCE GeneReport for Unigene cluster for NPAS4 Gene Hs.256036

mRNA Expression by UniProt/SwissProt for NPAS4 Gene

Tissue specificity: Brain.
genes like me logo Genes that share expression patterns with NPAS4: view

Protein tissue co-expression partners for NPAS4 Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for NPAS4 Gene

Orthologs for NPAS4 Gene

This gene was present in the common ancestor of animals.

Orthologs for NPAS4 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia NPAS4 35
  • 91.71 (n)
  • 93.47 (a)
NPAS4 36
  • 93 (a)
(Canis familiaris)
Mammalia NPAS4 35
  • 92.46 (n)
  • 95.75 (a)
NPAS4 36
  • 96 (a)
(Mus musculus)
Mammalia Npas4 35
  • 90.25 (n)
  • 93.12 (a)
Npas4 16
Npas4 36
  • 93 (a)
(Pan troglodytes)
Mammalia NPAS4 35
  • 99.88 (n)
  • 99.88 (a)
NPAS4 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Npas4 35
  • 90.21 (n)
  • 93.37 (a)
(Monodelphis domestica)
Mammalia NPAS4 36
  • 79 (a)
(Gallus gallus)
Aves LOC101750093 35
  • 53.43 (n)
  • 44.25 (a)
(Anolis carolinensis)
Reptilia NPAS4 36
  • 34 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia npas4 35
  • 55.71 (n)
  • 52.19 (a)
(Danio rerio)
Actinopterygii npas4a 35
  • 59.53 (n)
  • 61.58 (a)
NPAS4 (2 of 3) 36
  • 46 (a)
npas4a 36
  • 39 (a)
npas4b 36
  • 38 (a)
fruit fly
(Drosophila melanogaster)
Insecta dys 36
  • 19 (a)
(Caenorhabditis elegans)
Secernentea cky-1 36
  • 24 (a)
Species with no ortholog for NPAS4:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)

Evolution for NPAS4 Gene

Gene Tree for NPAS4 (if available)
Gene Tree for NPAS4 (if available)

Paralogs for NPAS4 Gene

(1) SIMAP similar genes for NPAS4 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with NPAS4: view

No data available for Paralogs for NPAS4 Gene

Variants for NPAS4 Gene

Sequence variations from dbSNP and Humsavar for NPAS4 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs905768 -- 66,422,865(+) GCCCT(G/T)GCCCT nc-transcript-variant, reference, missense, utr-variant-5-prime
rs61890361 -- 66,423,335(+) GATAA(C/T)AGAGG intron-variant
rs112480072 -- 66,426,658(+) GCTGC(C/G)GTGAC utr-variant-3-prime
rs112594222 -- 66,426,333(+) CCAAG(A/C)CACCC downstream-variant-500B, utr-variant-3-prime
rs71457718 -- 66,424,388(+) AAGAC(A/C)AGTTG nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for NPAS4 Gene

Variant ID Type Subtype PubMed ID
dgv1187n71 CNV Loss 21882294
nsv897772 CNV Loss 21882294
nsv832193 CNV Loss 17160897

Variation tolerance for NPAS4 Gene

Residual Variation Intolerance Score: 5.28% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.67; 31.95% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NPAS4 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NPAS4 Gene

Disorders for NPAS4 Gene

Relevant External Links for NPAS4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for NPAS4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NPAS4 Gene

Publications for NPAS4 Gene

  1. Identification of a novel basic helix-loop-helix-PAS factor, NXF, reveals a Sim2 competitive, positive regulatory role in dendritic- cytoskeleton modulator drebrin gene expression. (PMID: 14701734) Ooe N. … Kaneko H. (Mol. Cell. Biol. 2004) 2 3 4 67
  2. Human variants in the neuronal basic helix-loop-helix/Per-Arnt-Sim (bHLH/PAS) transcription factor complex NPAS4/ARNT2 disrupt function. (PMID: 24465693) Bersten D.C. … Whitelaw M.L. (PLoS ONE 2014) 3
  3. A reduction in Npas4 expression results in delayed neural differentiation of mouse embryonic stem cells. (PMID: 24887558) Klaric T.S. … Lewis M.D. (Stem Cell Res Ther 2014) 3
  4. Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. (PMID: 21926972) (Nat. Genet. 2011) 3
  5. Dynamic regulation of bHLH-PAS-type transcription factor NXF gene expression and neurotrophin dependent induction of the transcriptional control activity. (PMID: 19083991) Ooe N. … Kaneko H. (Biochem. Biophys. Res. Commun. 2009) 23

Products for NPAS4 Gene

Sources for NPAS4 Gene