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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

NPAS1 Gene

protein-coding   GIFtS: 52
GCID: GC19P047523

neuronal PAS domain protein 1
 Explore 2 diseases affiliated with
NPAS1 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for NPAS1    

Aliases
for NPAS1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Neuronal PAS Domain Protein 11 2     Member Of PAS Protein 52 3
MOP51 2 3 5     Neuronal PAS12 3
PASD51 2 3     PAS Domain-Containing Protein 52 3
BHLHe111     Member Of PAS Superfamily 52
Basic-Helix-Loop-Helix-PAS Protein MOP52 3     Neuronal PAS Domain-Containing Protein 12
Class E Basic Helix-Loop-Helix Protein 112 3     BHLHE113

External Ids:    HGNC: 78941   Entrez Gene: 48612   Ensembl: ENSG000001307517   OMIM: 6033465   UniProtKB: Q997423   

Export aliases for NPAS1 gene to outside databases

Previous GC identifers: GC19P048167 GC19P047915 GC19P052199 GC19P052214 GC19P052215 GC19P043948


Summaries
for NPAS1 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for NPAS1:
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)

UniProtKB/Swiss-Prot: NPAS1_HUMAN, Q99742
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)




Genomic Views
for NPAS1 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NC_018930.1  NT_011109.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the NPAS1 gene promoter:
         HNF-1A   CREB   POU2F1   POU2F1a   deltaCREB   FOXO4   HNF-1   Chx10   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: NPAS1 promoter sequence
   Search SABiosciences Chromatin IP Primers for NPAS1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NPAS1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.2-q13.3   Ensembl cytogenetic band:  19q13.32   HGNC cytogenetic band: 19q13.2-q13.3

NPAS1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NPAS1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P047523:  view genomic region     (about GC identifiers)

Start:
 47,524,143 bp from pter      End:
 47,549,017 bp from pter
Size:
 24,875 bases      Orientation:
 plus strand

Proteins
for NPAS1 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: NPAS1_HUMAN, Q99742 (See protein sequence)
Recommended Name: Neuronal PAS domain-containing protein 1  
Size: 590 amino acids; 62702 Da
Subunit: Efficient DNA binding requires dimerization with another bHLH protein. Interacts with ARNT (By similarity)
Subcellular location: Nucleus (Potential)
Secondary accessions: Q99632 Q9BY83

Explore the universe of human proteins at neXtProt for NPAS1: NX_Q99742

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q99742

    • NPAS1 Protein expression data from MOPED and PaxDb: --
    REFSEQ proteins: NP_002508.2  
    ENSEMBL proteins: 
     ENSP00000405290   ENSP00000398689  

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    Uscn Proteins for NPAS1

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--


    NPAS1 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for NPAS1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    NPAS1 for domains           About GeneDecksing

    5 InterPro domains/families:
     IPR001610 PAC
     IPR013767 PAS_fold
     IPR000014 PAS
     IPR011598 HLH_dom
     IPR013655 PAS_fold_3

    Graphical View of Domain Structure for InterPro Entry Q99742

    ProtoNet protein and cluster: Q99742

    3 Blocks protein families:
    IPB001092 Basic helix-loop-helix dimerization domain bHLH
    IPB001610 PAC motif
    IPB013655 PAS fold-3


    UniProtKB/Swiss-Prot: NPAS1_HUMAN, Q99742
    Similarity: Contains 1 bHLH (basic helix-loop-helix) domain
    Similarity: Contains 1 PAC (PAS-associated C-terminal) domain
    Similarity: Contains 2 PAS (PER-ARNT-SIM) domains


    Function
    for NPAS1 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: NPAS1_HUMAN, Q99742
    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 entry for NPAS1:
    neuronal PAS domain protein 1,expressed in the central nervous system

    miRNA
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    Inhib. RNA
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    Gene Editing
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    Clone
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    Search LifeMap BioReagents cell lines for NPAS1

    In Situ Assay
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    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity TAS9012850
    GO:0004871signal transducer activity IEA--
    GO:0046983protein dimerization activity IEA--


    NPAS1 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for NPAS1:
     Decreased influenza A/WSN/33 r 

    Animal Models:
         3 MGI mutant phenotypes (inferred from 1 allele) (MGI details for Npas1):
     behavior/neurological  growth/size  nervous system 

    NPAS1 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for NPAS1 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for NPAS1

    1 Interacting protein for NPAS1 (Q997423) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARNTP275403I2D: score=1 
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter ----
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent ----
    GO:0007417central nervous system development TAS9012850
    GO:0007610behavior ----


    NPAS1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for NPAS1 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for NPAS1
    Search CenterWatch for drugs/clinical trials and news about NPAS1 

    Transcripts
    for NPAS1 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for NPAS1 gene: 
    NM_002517.2  

    Unigene Cluster for NPAS1:

    Neuronal PAS domain protein 1
    Hs.79564  [show with all ESTs]
    Unigene Representative Sequence: BC039016
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000449844(uc002pfw.3 uc002pfy.3) ENST00000439365(uc010xyj.2)


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    Inhib. RNA
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    Clone
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    Additional cDNA sequence: 

    AB054002.1 AK299128.1 BC039016.1 U51628.1 U77968.1 

    6 DOTS entries:

    DT.105226  DT.95363290  DT.95363289  DT.100026000  DT.100836459  DT.91989212 

    24/49 AceView cDNA sequences (see all 49):

    AI916513 BM848100 BC039016 CR605653 BM847385 BU161211 NM_002517 BM930717 
    BX420694 U77968 BX431563 BX411336 BM845842 BM546750 BI756020 BU183718 
    BM845835 BE618116 AW406253 AB054002 BX412863 BX431562 BE895733 CA420408 

    GeneLoc Exon Structure

    5/10 Alternative Splicing Database (ASD) splice patterns (SP) for NPAS1 (see all 10)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b ^ 12
    SP1:                    -     -                       -     -     -                                                                     
    SP2:                                                                                                                                    
    SP3:                                                  -     -     -                                                                     
    SP4:                                                                          -     -     -           -                                 
    SP5:              -     -     -                       -     -     -                                                                     


    ECgene alternative splicing isoforms for NPAS1

    Expression
    for NPAS1 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    NPAS1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGGCCTGGCA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    NPAS1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    PureStem™ progenitor SK17 (Embryonic Progenitor Cell)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    Genevestigator expression for NPAS1

    SOURCE GeneReport for Unigene cluster: Hs.79564
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    In Situ
    Assay Products:     
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    Orthologs
    for NPAS1 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for NPAS1 gene from 3/16 species (see all 16)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    zebrafish
    (Danio rerio)    		 Actinopterygii npas3b6
    		 neuronal PAS domain protein 3b
    		 36(a)
    		 1 ↔ 1
    		 15(8494653-8568063)
    fruit fly
    (Drosophila melanogaster)    		 Insecta trh3 salivary gland morphogenesis transcription
    factor    		 44(a)   3 61C1   --
    worm
    (Caenorhabditis elegans)    		 Secernentea hlh-346
    		 Helix-loop-helix 34
    		 30(a)
    		 possible ortholog
    		 V(13705963-13707347)


    ENSEMBL Gene Tree for NPAS1 (if available)
    TreeFam Gene Tree for NPAS1 (if available) 

    Paralogs
    for NPAS1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for NPAS1 gene
    ARNT22  CLOCK2  NPAS22  ARNT2  EPAS12  HIF1A2  NPAS32  SIM22  
    SIM12  HIF3A2  ARNTL2  ARNTL22  
    2 SIMAP similar genes for NPAS1 using alignment to 5 protein entries:     NPAS1_HUMAN (see all proteins):
    NPAS3    SIM2

    NPAS1 for paralogs           About GeneDecksing



    Genomic Variants
    for NPAS1 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/550 NCBI SNPs in NPAS1 are shown (see all 550)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 19 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs37607641,2
    		C,F,A,--47522228(+) CCGCCC/TTGGCC 1 -- us2k18Minor allele frequency- T:0.44NA WA CSA 133
    rs1908580971,2
    		--47522478(+) TACTAC/GAACCC 1 -- us2k10--------
    rs788060881,2
    		F,--47522725(+) GGAGGG/TTCTCG 1 -- us2k11Minor allele frequency- T:0.05WA 118
    rs735648901,2
    		C,--47522729(+) GGTCTC/GGAATT 1 -- us2k12Minor allele frequency- G:0.04WA 120
    rs1465061491,2
    		--47522779(+) TCACTC/TGTACA 1 -- us2k10--------
    rs1823117321,2
    		--47523046(+) GGCAGA/CCCCCG 1 -- us2k10--------
    rs1865859581,2
    		--47523077(+) CGCGCA/GTCTCC 1 -- us2k10--------
    rs104055641,2
    		C,F,H,--47523337(+) GGGGGA/CTAGGG 1 -- us2k116Minor allele frequency- C:0.26NS EA WA CSA 2212
    rs1896127491,2
    		--47523341(+) GATAGA/C/GGGGTG 1 -- us2k10--------
    rs677798611,2
    		C,F,--47523365(+) CCGAGA/C/GCTGGG 1 -- us2k18NA WA CSA EA 366

    HapMap Linkage Disequilibrium report for NPAS1 (47524143 - 47549017 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for NPAS1
         2 CNVs: 102855 7208
         1 Indel: 26303

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    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing NPAS1
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    Disorders / Diseases
    for NPAS1 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    NPAS1 for disorders           About GeneDecksing

    OMIM gene information: 603346    OMIM disorders: --

    2 diseases for NPAS1:    About MalaCards
    neuronitis    schizophrenia


    Export disorders for NPAS1 gene to outside databases

    Publications
    for NPAS1 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for NPAS1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with NPAS1)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular characterization of two mammalian bHLH-PAS domain proteins selectively expressed in the central nervous system. (PubMed id 9012850)1, 2, 3 Zhou Y.-D.... McKnight S.L. (1997)
    2. Characterization of a subset of the basic-helix-loop-helix-PAS superfamily that interacts with components of the dioxin signaling pathway. (PubMed id 9079689)1, 2, 3 Hogenesch J.B.... Bradfield C.A. (1997)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    4. Novel function of neuronal PAS domain protein 1 in erythropoietin expression in neuronal cells. (PubMed id 15635607)1, 9 Ohsawa S....Miura M. (2005)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    6. Neuronal PAS domain protein 1 is a transcriptional repressor and requires arylhydrocarbon nuclear translocator for its nuclear localization. (PubMed id 16954219)9 Teh C.H....Lim T.M. (2006)

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    Genome Databases showing NPAS1 gene

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    Entrez Gene: 4861 HGNC: 7894 AceView: NPAS1 Ensembl:ENSG00000130751 euGenes: HUgn4861
    ECgene: NPAS1 H-InvDB: NPAS1

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    Specialized Databases showing NPAS1 gene

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    PharmGKB entry for NPAS1 Pharmacogenomics, SNPs, Pathways

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