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NPAS1 Gene

protein-coding   GIFtS: 51
GCID: GC19P047523

Neuronal PAS Domain Protein 1

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Neuronal PAS Domain Protein 11 2     Member Of PAS Protein 52 3
Neuronal PAS11 2 3     PASD52 3
MOP52 3 5     bHLHe112 3
Member Of PAS Superfamily 51 2     PAS Domain-Containing Protein 52 3
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


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. GO annotations related to this gene include protein dimerization activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is ARNT2.

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)




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000019.9  NT_011109.17  NC_018930.2  
Regulatory elements:
   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 plasmidNPAS1 promoter sequence
   Search Chromatin IP Primers for NPAS1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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:
47,523,077 bp from pter      End:
47,549,033 bp from pter
Size:
25,957 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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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)
Secondary accessions: Q99632 Q9BY83

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

Explore proteomics data for NPAS1 at MOPED


See NPAS1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_002508.2  
ENSEMBL proteins: 
 ENSP00000469142   ENSP00000472679   ENSP00000405290   ENSP00000398689   ENSP00000472075  
 ENSP00000468871  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
bHLH: Basic helix-loop-helix proteins

5 InterPro protein domains:
 IPR001610 PAC
 IPR013767 PAS_fold
 IPR000014 PAS
 IPR011598 bHLH_dom
 IPR013655 PAS_fold_3

Graphical View of Domain Structure for InterPro Entry Q99742

ProtoNet protein and cluster: Q99742

3 Blocks protein domains:
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


Find genes that share domains with NPAS1           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: 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

     Gene Ontology (GO): 5 molecular function terms:    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:0005515protein binding ----
GO:0046983protein dimerization activity IEA--
     
Find genes that share ontologies with NPAS1           About GenesLikeMe


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

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

Find genes that share phenotypes with NPAS1           About GenesLikeMe

Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NPAS1
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miRNA
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hsa-mir-335-5p (MIRT017075)

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
NPAS1_HUMAN, Q99742: Nucleus (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus3
cytosol2

Gene Ontology (GO): 1 cellular component term:    About this table

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

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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for NPAS1
Interactions:

    Search GeneGlobe Interaction Network for NPAS1

1 Interacting protein for NPAS1 (Q997423) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
ARNTP275403I2D: score=1 
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Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000122negative regulation of transcription from RNA polymerase II promoter IEA--
GO:0001964startle response IEA--
GO:0006351transcription, DNA-templated IEA--
GO:0006355regulation of transcription, DNA-templated ----
GO:0007165signal transduction ----

Find genes that share ontologies with NPAS1           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for NPAS1



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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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
8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000602212 ENST00000602189 ENST00000449844(uc002pfw.3 uc002pfy.3)
ENST00000439365(uc010xyj.2) ENST00000601169 ENST00000594670 ENST00000594257
ENST00000600352
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Pre-validated RT2 qPCR Primer Assay in human, mouse, rat NPAS1
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  QuantiFast Probe-based Assays in human, mouse, rat NPAS1

Additional mRNA 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 

Selected AceView cDNA sequences (see all 49):

AI916513 BM848100 BX420694 BC039016 NM_002517 CR605653 BM847385 BU161211 
BM930717 BX431563 U77968 BI756020 BU621495 BX431562 BX411336 CA420408 
AB054002 BM546750 BE618116 BU183718 BE895733 AW406253 BM845842 BX412863 

GeneLoc Exon Structure

Selected 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

(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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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NPAS1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGGCCTGGCA
NPAS1 Expression
About this image

NPAS1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

NPAS1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.79564
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(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)
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This gene was present in the common ancestor of animals.

Orthologs for NPAS1 gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Npas11 , 5 neuronal PAS domain protein 11, 5 83.84(n)1
86.78(a)1
  7 (9.14 cM)5
181421  NM_008718.21  NP_032744.11 
 164557215 
zebrafish
(Danio rerio)
Actinopterygii npas3b1 neuronal PAS domain protein 3b 63.08(n)
62.1(a)
  559419  XM_005157478.1  XP_005157535.1 
fruit fly
(Drosophila melanogaster)
Insecta trh3 salivary gland morphogenesis
transcription factor
44(a)   3 61C1   --


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

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for NPAS1 gene
ARNT22  CLOCK2  NPAS22  AHR2  ARNT2  EPAS12  NPAS32  HIF1A2  
SIM22  SIM12  HIF3A2  ARNTL2  ARNTL22  AHRR2  
2 SIMAP similar genes for NPAS1 using alignment to 5 protein entries:     NPAS1_HUMAN (see all proteins):
NPAS3    SIM2

Find genes that share paralogs with NPAS1           About GenesLikeMe



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for NPAS1 (see all 686)    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
C,F--47522725(+) GGAGGG/TTCTCG 1 -- us2k11Minor allele frequency- T:0.05WA 118
rs735648901,2
C,F--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 (47523077 - 47549033 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for NPAS1 (see all 13):    About this table    
Variant IDTypeSubtypePubMed ID
esv2718657CNV Deletion23290073
esv1670372CNV Deletion17803354
dgv649e199CNV Deletion23128226
esv2718658CNV Deletion23290073
esv2560518CNV Deletion19546169
esv2718660CNV Deletion23290073
esv2718659CNV Deletion23290073
nsv2512CNV Insertion18451855
dgv3962n71CNV Loss21882294
nsv912193CNV Loss21882294

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(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.)
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OMIM gene information: 603346    OMIM disorders: --


Find genes that share disorders with NPAS1           About GenesLikeMe


Export disorders for NPAS1 gene to outside databases

(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)
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PubMed articles for NPAS1 gene integrated from 10 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. (Proc. Natl. Acad. Sci. U.S.A. 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. (J. Biol. Chem. 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. (Genome Res. 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. (J. Neurosci. Res. 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. (Proc. Natl. Acad. Sci. U.S.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. (J. Biol. Chem. 2006)

(in PubMed, OMIM, and NCBI Bookshelf)
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OMIM
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 4861 HGNC: 7894 AceView: NPAS1 Ensembl:ENSG00000130751 euGenes: HUgn4861
ECgene: NPAS1 H-InvDB: NPAS1

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for NPAS1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for NPAS1 gene:
Search GeneIP for patents involving NPAS1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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