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Aliases for NPAS1 Gene

Aliases for NPAS1 Gene

  • Neuronal PAS Domain Protein 1 2 3 5
  • Neuronal PAS1 2 3 4
  • Class E Basic Helix-Loop-Helix Protein 11 3 4
  • Basic-Helix-Loop-Helix-PAS Protein MOP5 3 4
  • PAS Domain-Containing Protein 5 3 4
  • Member Of PAS Superfamily 5 2 3
  • Member Of PAS Protein 5 3 4
  • BHLHe11 3 4
  • PASD5 3 4
  • MOP5 3 4
  • Neuronal PAS Domain-Containing Protein 1 3
  • BHLHE11 4

External Ids for NPAS1 Gene

Previous GeneCards Identifiers for NPAS1 Gene

  • GC19P048167
  • GC19P047915
  • GC19P052199
  • GC19P052214
  • GC19P052215
  • GC19P047523
  • GC19P043948

Summaries for NPAS1 Gene

Entrez Gene Summary for NPAS1 Gene

  • The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH)-PAS family of transcription factors. Studies of a related mouse gene suggest that it functions in neurons. The exact function of this gene is unclear, but it may play protective or modulatory roles during late embryogenesis and postnatal development. [provided by RefSeq, Jul 2008]

GeneCards Summary for NPAS1 Gene

NPAS1 (Neuronal PAS Domain Protein 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and protein dimerization activity. An important paralog of this gene is NPAS3.

UniProtKB/Swiss-Prot for NPAS1 Gene

  • May control regulatory pathways relevant to schizophrenia and to psychotic illness. May play a role in late central nervous system development by modulating EPO expression in response to cellular oxygen level (By similarity).

Additional gene information for NPAS1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NPAS1 Gene

Genomics for NPAS1 Gene

GeneHancer (GH) Regulatory Elements for NPAS1 Gene

Promoters and enhancers for NPAS1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J047019 Promoter/Enhancer 1.3 EPDnew Ensembl 650.7 +1.1 1139 3.5 KLF14 ZNF335 GLIS2 EGR1 ZNF143 KLF13 EGR2 SP3 ZBTB2 ZNF398 PIR57310 NPAS1 TMEM160 SAE1 ARHGAP35
GH19J047712 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 4.4 +694.0 693965 2 HDGF PKNOX1 ATF1 SIN3A ZNF48 GTF3C2 ARID2 ZNF143 ZFP91 ZNF263 EHD2 ZC3H4 BICRA CYTH2 GRWD1 NOP53-AS1 KDELR1 CCDC9 NOP53 RPL18
GH19J046974 Enhancer 1.2 Ensembl ENCODE dbSUPER 6.4 -43.1 -43130 4.9 PKNOX1 ZSCAN4 MZF1 FEZF1 RAD21 YY1 ZNF335 ZSCAN5C EGR2 RXRA ZC3H4 CCDC61 BICRA ARHGAP35 AP2S1 TMEM160 ENSG00000268810 SAE1 NPAS1 GC19P046965
GH19J047012 Enhancer 1.3 Ensembl ENCODE dbSUPER 4.7 -6.7 -6705 0.9 ARID4B SIN3A ZNF2 ZBTB7B YY1 ARID2 ZNF143 ATF7 DEK YY2 ZC3H4 BICRA ENSG00000268810 NOP53-AS1 NPAS1 PIR58641
GH19J046961 Enhancer 0.9 Ensembl ENCODE dbSUPER 6.2 -56.5 -56478 3 SCRT1 JUND FOS PRDM1 ARHGAP35 AP2S1 TMEM160 FKRP STRN4 NPAS1 GC19P046965 GC19M046915
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NPAS1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NPAS1 gene promoter:
  • Chx10
  • POU2F1a
  • POU2F1
  • Pax-4a
  • CREB
  • deltaCREB
  • FOXO4
  • HNF-1A
  • HNF-1

Genomic Locations for NPAS1 Gene

Genomic Locations for NPAS1 Gene
25,956 bases
Plus strand
25,957 bases
Plus strand

Genomic View for NPAS1 Gene

Genes around NPAS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPAS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPAS1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPAS1 Gene

Proteins for NPAS1 Gene

  • Protein details for NPAS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Neuronal PAS domain-containing protein 1
    Protein Accession:
    Secondary Accessions:
    • B4DR69
    • Q99632
    • Q9BY83

    Protein attributes for NPAS1 Gene

    590 amino acids
    Molecular mass:
    62702 Da
    Quaternary structure:
    • Efficient DNA binding requires dimerization with another bHLH protein. Interacts with ARNT (By similarity).

    Alternative splice isoforms for NPAS1 Gene


neXtProt entry for NPAS1 Gene

Post-translational modifications for NPAS1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NPAS1 Gene

Domains & Families for NPAS1 Gene

Gene Families for NPAS1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for NPAS1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with NPAS1: view

No data available for UniProtKB/Swiss-Prot for NPAS1 Gene

Function for NPAS1 Gene

Molecular function for NPAS1 Gene

UniProtKB/Swiss-Prot Function:
May control regulatory pathways relevant to schizophrenia and to psychotic illness. May play a role in late central nervous system development by modulating EPO expression in response to cellular oxygen level (By similarity).
GENATLAS Biochemistry:
neuronal PAS domain protein 1,expressed in the central nervous system

Gene Ontology (GO) - Molecular Function for NPAS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IBA,NAS 19274049
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity TAS 9012850
GO:0005515 protein binding IEA --
GO:0046983 protein dimerization activity IEA --
genes like me logo Genes that share ontologies with NPAS1: view
genes like me logo Genes that share phenotypes with NPAS1: view

Animal Models for NPAS1 Gene

MGI Knock Outs for NPAS1:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NPAS1 Gene

Localization for NPAS1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPAS1 Gene

Subcellular locations from

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 NPAS1 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for NPAS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
genes like me logo Genes that share ontologies with NPAS1: view

Pathways & Interactions for NPAS1 Gene

SuperPathways for NPAS1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for NPAS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0001964 startle response IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA --
genes like me logo Genes that share ontologies with NPAS1: view

No data available for Pathways by source and SIGNOR curated interactions for NPAS1 Gene

Drugs & Compounds for NPAS1 Gene

No Compound Related Data Available

Transcripts for NPAS1 Gene

Unigene Clusters for NPAS1 Gene

Neuronal PAS domain protein 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NPAS1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b ^ 12
SP1: - - - - -
SP3: - - -
SP4: - - - -
SP5: - - - - - -
SP6: - - -
SP7: -
SP10: - - -

Relevant External Links for NPAS1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NPAS1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NPAS1 Gene

mRNA differential expression in normal tissues according to GTEx for NPAS1 Gene

This gene is overexpressed in Brain - Cortex (x5.7), Brain - Hippocampus (x4.9), Brain - Frontal Cortex (BA9) (x4.6), and Brain - Anterior cingulate cortex (BA24) (x4.3).

NURSA nuclear receptor signaling pathways regulating expression of NPAS1 Gene:


SOURCE GeneReport for Unigene cluster for NPAS1 Gene:


Evidence on tissue expression from TISSUES for NPAS1 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with NPAS1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NPAS1 Gene

Orthologs for NPAS1 Gene

This gene was present in the common ancestor of animals.

Orthologs for NPAS1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NPAS1 34 33
  • 99.55 (n)
(Canis familiaris)
Mammalia NPAS1 34 33
  • 88.19 (n)
(Bos Taurus)
Mammalia NPAS1 34 33
  • 87.76 (n)
(Mus musculus)
Mammalia Npas1 16 34 33
  • 83.84 (n)
(Rattus norvegicus)
Mammalia Npas1 33
  • 82.54 (n)
(Monodelphis domestica)
Mammalia NPAS1 34
  • 61 (a)
(Ornithorhynchus anatinus)
Mammalia NPAS1 34
  • 46 (a)
(Danio rerio)
Actinopterygii npas3b 34 33
  • 63.08 (n)
fruit fly
(Drosophila melanogaster)
Insecta trh 34 35
  • 25 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3066 34
  • 24 (a)
Species where no ortholog for NPAS1 was found in the sources mined by GeneCards:
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • 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)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for NPAS1 Gene

Gene Tree for NPAS1 (if available)
Gene Tree for NPAS1 (if available)
Evolutionary constrained regions (ECRs) for NPAS1: view image

Paralogs for NPAS1 Gene

Paralogs for NPAS1 Gene

(2) SIMAP similar genes for NPAS1 Gene using alignment to 5 proteins:

  • B4DR69_HUMAN
  • M0QX32_HUMAN
  • M0R1R8_HUMAN
  • M0R2M8_HUMAN
genes like me logo Genes that share paralogs with NPAS1: view

Variants for NPAS1 Gene

Sequence variations from dbSNP and Humsavar for NPAS1 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000091127 -- 47,021,019(+) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant
rs1000201627 -- 47,043,298(+) T/A intron_variant
rs1000260615 -- 47,022,929(+) G/C genic_upstream_transcript_variant, intron_variant
rs1000369133 -- 47,042,192(+) C/G/T intron_variant
rs1000608007 -- 47,023,920(+) C/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NPAS1 Gene

Variant ID Type Subtype PubMed ID
dgv15e24 CNV gain 17666407
dgv649e199 CNV deletion 23128226
esv1670372 CNV deletion 17803354
esv2560518 CNV deletion 19546169
esv2718657 CNV deletion 23290073
esv2718658 CNV deletion 23290073
esv2718659 CNV deletion 23290073
esv2718660 CNV deletion 23290073
esv33386 CNV gain 17666407
esv3556486 CNV deletion 23714750
esv3644543 CNV loss 21293372
nsv2512 CNV insertion 18451855

Variation tolerance for NPAS1 Gene

Residual Variation Intolerance Score: 55.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.43; 27.98% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NPAS1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NPAS1 Gene

Disorders for NPAS1 Gene

Additional Disease Information for NPAS1

No disorders were found for NPAS1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NPAS1 Gene

Publications for NPAS1 Gene

  1. Characterization of a subset of the basic-helix-loop-helix-PAS superfamily that interacts with components of the dioxin signaling pathway. (PMID: 9079689) Hogenesch JB … Bradfield CA (The Journal of biological chemistry 1997) 2 3 4 58
  2. Molecular characterization of two mammalian bHLH-PAS domain proteins selectively expressed in the central nervous system. (PMID: 9012850) Zhou YD … McKnight SL (Proceedings of the National Academy of Sciences of the United States of America 1997) 2 3 4 58
  3. Novel function of neuronal PAS domain protein 1 in erythropoietin expression in neuronal cells. (PMID: 15635607) Ohsawa S … Miura M (Journal of neuroscience research 2005) 3 22 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for NPAS1 Gene

Sources for NPAS1 Gene

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