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

NPAS4 Gene

protein-coding   GIFtS: 48
GCID: GC11P066188

neuronal PAS domain protein 4
 Explore 4 diseases affiliated with
NPAS4 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for NPAS4    

Aliases
for NPAS4 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 41 2     Neuronal PAS42 3
NXF1 2 3 5     HLH-PAS Transcription Factor NXF2 3
PASD101 2 3     PAS Domain-Containing Protein 102 3
BHLHe791     Neuronal PAS Domain-Containing Protein 42
Le-PAS1 2     BHLHE793
Class E Basic Helix-Loop-Helix Protein 792 3     

External Ids:    HGNC: 189831   Entrez Gene: 2667432   Ensembl: ENSG000001745767   OMIM: 6085545   UniProtKB: Q8IUM73   

Export aliases for NPAS4 gene to outside databases

Previous GC identifers: GC11P065946 GC11P062516


Summaries
for NPAS4 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 NPAS4:
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)

UniProtKB/Swiss-Prot: NPAS4_HUMAN, Q8IUM7
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




Genomic Views
for NPAS4 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_000011.9  NC_018922.1  NT_167190.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the NPAS4 gene promoter:
         Elk-1   MAZR   NRSF form 1   FOXD3   MyoD   Olf-1   MIF-1   NRSF form 2   SEF-1 (1)   STAT3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: NPAS4 promoter sequence
   Search SABiosciences Chromatin IP Primers for NPAS4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NPAS4


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

Entrez Gene cytogenetic band: 11q13   Ensembl cytogenetic band:  11q13.2   HGNC cytogenetic band: 11q13.2

NPAS4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NPAS4 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P066188:  view genomic region     (about GC identifiers)

Start:
 66,188,475 bp from pter      End:
 66,194,178 bp from pter
Size:
 5,704 bases      Orientation:
 plus strand

Proteins
for NPAS4 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: NPAS4_HUMAN, Q8IUM7 (See protein sequence)
Recommended Name: Neuronal PAS domain-containing protein 4  
Size: 802 amino acids; 87117 Da
Subunit: Efficient DNA binding requires dimerization with another bHLH protein. Forms a heterodimer with ARNT
Subcellular location: Nucleus
Sequence caution: Sequence=BAC04271.1; Type=Frameshift; Positions=681;
Secondary accessions: Q8N8S5 Q8N9Q9

Explore the universe of human proteins at neXtProt for NPAS4: NX_Q8IUM7

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8IUM7

    • NPAS4 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_849195.2  
    ENSEMBL proteins: 
     ENSP00000311196   ENSP00000433135  

    Human Recombinant Protein Products: 
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    Uscn Proteins for NPAS4

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ----
    GO:0005667transcription factor complex IEA--


    NPAS4 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for NPAS4

    Protein Domains /
    Families
    for NPAS4 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    NPAS4 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR000014 PAS
     IPR013655 PAS_fold_3

    Graphical View of Domain Structure for InterPro Entry Q8IUM7

    ProtoNet protein and cluster: Q8IUM7

    2 Blocks protein families:
    IPB000014 PAS domain
    IPB013655 PAS fold-3


    UniProtKB/Swiss-Prot: NPAS4_HUMAN, Q8IUM7
    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 NPAS4 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: NPAS4_HUMAN, Q8IUM7
    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

    miRNA
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    hsa-miR-142-5p hsa-miR-193a-3p hsa-miR-513a-5p hsa-miR-146a hsa-miR-1224-3p hsa-miR-29a hsa-miR-605 hsa-miR-1260b
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    Inhib. RNA
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    Gene Editing
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    Clone
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    In Situ Assay
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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0004871signal transducer activity IEA--
    GO:0046982protein heterodimerization activity IEA--


    NPAS4 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Npas4tm1Ooe for NPAS4
         6 MGI mutant phenotypes (inferred from 3 alleles) (MGI details for Npas4):
     behavior/neurological  cellular  homeostasis/metabolism  mortality/aging  muscle 
     nervous system 

    NPAS4 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for NPAS4 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 NPAS4

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for NPAS4 (Q8IUM73 ENSP000003111964) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARNT2Q9HBZ23, ENSP000003074794I2D: score=2 STRING: ENSP00000307479
    ARNTP275403, ENSP000003514074I2D: score=2 STRING: ENSP00000351407
    ARNTLO003273, ENSP000003743574I2D: score=2 STRING: ENSP00000374357
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent ----
    GO:0045893positive regulation of transcription, DNA-dependent ----
    GO:0045944positive regulation of transcription from RNA polymerase II promoter IEA--


    NPAS4 for ontologies           About GeneDecksing



    Drugs & Compounds
    for NPAS4 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 NPAS4
    Search CenterWatch for drugs/clinical trials and news about NPAS4 

    Transcripts
    for NPAS4 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 NPAS4 gene: 
    NM_178864.3  

    Unigene Cluster for NPAS4:

    Neuronal PAS domain protein 4
    Hs.256036  [show with all ESTs]
    Unigene Representative Sequence: NM_178864
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000311034(uc001ohx.1 uc010rpc.1) ENST00000525148 ENST00000524617


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    hsa-miR-142-5p hsa-miR-193a-3p hsa-miR-513a-5p hsa-miR-146a hsa-miR-1224-3p hsa-miR-29a hsa-miR-605 hsa-miR-1260b
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    Inhib. RNA
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    Clone
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    Primer
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    Additional cDNA sequence: 

    AB049469.1 AK094025.1 AK096253.1 BC105001.1 BC105003.1 BC143630.1 

    1 DOTS entry:

    DT.40304812 

    13 AceView cDNA sequences:

    BE669790 BE674004 AB049469 AX748416 NM_178864 AA311734 BF437907 AW340980 
    AK096253 AK094025 BM687284 AA323867 AW291648 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for NPAS4    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8
    SP1:                                                            
    SP2:                                -                           


    ECgene alternative splicing isoforms for NPAS4

    Expression
    for NPAS4 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

    NPAS4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AAGATGGAAG

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

    NPAS4 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    2 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    PancreasDorsal Pancreatic BudImmature Beta Progenitor CellsPancreas
    PancreasVentral Pancreatic BudImmature Beta Progenitor CellsPancreas
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See NPAS4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for NPAS4

    SOURCE GeneReport for Unigene cluster: Hs.256036

    UniProtKB/Swiss-Prot: NPAS4_HUMAN, Q8IUM7
    Tissue specificity: Brain

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    In Situ
    Assay Products:     
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    Orthologs
    for NPAS4 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 NPAS4 gene from 5/12 species (see all 12)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Npas41 , 5 neuronal PAS domain protein 41, 5 90.25(n)1
    93.12(a)1    		   19 (4.20 cM)5
    2258721  NM_153553.41  NP_705781.11 
     49843555 
    lizard
    (Anolis carolinensis)    		 Reptilia NPAS46
    		 --
    		 37(a)
    		 1 ↔ 1
    		 2(144666221-144679266)
    zebrafish
    (Danio rerio)    		 Actinopterygii npas4a1 neuronal PAS domain protein 4a 55.69(n)
    52.91(a)    		   724016  NM_001045321.1  NP_001038786.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta dys6
    		 dysfusion
    		 17(a)
    		 1 ↔ 1
    		 3R(21902314-21924433)
    worm
    (Caenorhabditis elegans)    		 Secernentea cky-16
    		 CKY homolog family member (cky-1)
    		 22(a)
    		 1 ↔ 1
    		 V(12736686-12741194)


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

    Paralogs
    for NPAS4 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    		  --

    Genomic Variants
    for NPAS4 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

    10/124 NCBI SNPs in NPAS4 are shown (see all 124)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 11 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1496410461,2
    		--66186523(+) TCATAC/GGGAAG 1 -- us2k10--------
    rs1843177301,2
    		--66186565(+) GAAGAC/TTGAGA 1 -- us2k10--------
    rs1442069121,2
    		--66186696(+) ATAAGC/TGGACA 1 -- us2k10--------
    rs112274811,2
    		C,F,H,--66186744(+) ATGGCC/TCCAAC 1 -- us2k116Minor allele frequency- T:0.11NS EA NA CSA WA 2162
    rs79473911,2
    		C,F,A,H,--66186882(+) AGCGGG/AGAGTT 1 -- us2k123Minor allele frequency- A:0.41NS EA NA WA CSA 2522
    rs587527601,2
    		F,--66186997(+) CCAGCC/TACTTA 1 -- us2k12Minor allele frequency- T:0.17NA EA 240
    rs1896467791,2
    		--66187005(+) TTAAGG/TGATTC 1 -- us2k10--------
    rs1923345531,2
    		--66187827(+) TTCCAA/CCCATC 1 -- us2k10--------
    rs1487297151,2
    		--66187896(+) AGCGGA/GGGCGG 1 -- us2k10--------
    rs1845533811,2
    		--66188024(+) CGTGAA/CCTTGT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for NPAS4 (66188475 - 66194178 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for NPAS4: --
    Human Gene Mutation Database (HGMD): NPAS4

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing NPAS4
    DNA2.0 Custom Variant and Variant Library Synthesis for NPAS4

    Disorders / Diseases
    for NPAS4 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
    NPAS4 for disorders           About GeneDecksing

    OMIM gene information: 608554    OMIM disorders: --

    4 diseases for NPAS4:    About MalaCards
    pelizaeus-merzbacher disease    neuronitis    intellectual disability    pharyngitis


    Export disorders for NPAS4 gene to outside databases

    Publications
    for NPAS4 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 NPAS4 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with NPAS4)    		    Utopia: connect your pdf to the dynamic
    world of online information

    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. (PubMed id 14701734)1, 2, 3 Ooe N.... Kaneko H. (2004)
    2. 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)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Large-scale genome-wide association analysis of bipol ar disorder identifies a new susceptibility locus near ODZ4. (PubMed id 21926972)1 Sklar P....Purcell S.M. (2011)
    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. Characterization of Drosophila and Caenorhabditis elegans NXF-like-factors, putative homologs of mammalian NXF. (PubMed id 17628356)9 Ooe N....Kaneko H. (2007)
    7. Characterization of functional heterodimer partners in brain for a bHLH-PAS factor NXF. (PubMed id 19284974)9 Ooe N....Kaneko H. (2009)
    8. Dynamic regulation of bHLH-PAS-type transcription factor NXF gene expression and neurotrophin dependent induction of the transcriptional control activity. (PubMed id 19083991)9 Ooe N....Kaneko H. (2009)

    External Searches for NPAS4 gene

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    Genome Databases showing NPAS4 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 266743 HGNC: 18983 AceView: NXF Ensembl:ENSG00000174576 euGenes: HUgn266743
    ECgene: NPAS4 H-InvDB: NPAS4

    Other Databases showing NPAS4 gene

    (According to HUGE)
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    Specialized Databases showing NPAS4 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for NPAS4 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
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    IP news from LifeMap Sciences, Inc.)
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    		Patent Information for NPAS4 gene:
    Search GeneIP for patents involving NPAS4

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