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NPAS2 Gene

protein-coding   GIFtS: 61
GCID: GC02P101436

Neuronal PAS Domain Protein 2

  See NPAS2-related disease
at  

(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 21 2     PASD42 3
MOP42 3 5     bHLHe92 3
Basic-Helix-Loop-Helix-PAS Protein MOP42 3     PAS Domain-Containing Protein 42 3
Class E Basic Helix-Loop-Helix Protein 92 3     Member Of PAS Superfamily 42
Member Of PAS Protein 42 3     Neuronal PAS Domain-Containing Protein 22
Neuronal PAS22 3     BHLHE93

External Ids:    HGNC: 78951   Entrez Gene: 48622   Ensembl: ENSG000001704857   OMIM: 6033475   UniProtKB: Q997433   

Export aliases for NPAS2 gene to outside databases

Previous GC identifers: GC02P099300 GC02P099889 GC02P101041 GC02P101058 GC02P100895 GC02P100803 GC02P095284


(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 NPAS2 Gene:
The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH)-PAS family of transcription
factors. A similar mouse protein may play a regulatory role in the acquisition of specific types of memory. It
also may function as a part of a molecular clock operative in the mammalian forebrain. (provided by RefSeq, Jul
2008)

GeneCards Summary for NPAS2 Gene:
NPAS2 (neuronal PAS domain protein 2) is a protein-coding gene. Diseases associated with NPAS2 include seasonal affective disorder. 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: NPAS2_HUMAN, Q99743
Function: BMAL1-NPAS2 heterodimers activate E-box element (5'-CACGTG-3') transcription of a number of proteins of
the circadian clock. This transcription is inhibited in a feedback loop by PER, and also by CRY proteins (By
similarity)

Gene Wiki entry for NPAS2 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NT_005403.18  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the NPAS2 gene promoter:
         AML1a   C/EBPalpha   Evi-1   HNF-1A   CP2   HNF-1   POU2F1a   RSRFC4   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNPAS2 promoter sequence
   Search Chromatin IP Primers for NPAS2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NPAS2


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

Entrez Gene cytogenetic band: 2q11.2   Ensembl cytogenetic band:  2q11.2   HGNC cytogenetic band: 2q11.2

NPAS2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NPAS2 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P101436:  view genomic region     (about GC identifiers)

Start:
101,436,613 bp from pter      End:
101,613,291 bp from pter
Size:
176,679 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: NPAS2_HUMAN, Q99743 (See protein sequence)
Recommended Name: Neuronal PAS domain-containing protein 2  
Size: 824 amino acids; 91791 Da
Subunit: Component of the circadian clock oscillator which includes the CRY proteins, CLOCK or NPAS2, BMAL1 or
BMAL2, CSNK1D and/or CSNK1E, TIMELESS and the PER proteins. Efficient DNA binding requires dimerization with
another bHLH protein. Heterodimerization with CLOCK or NPAS2 is required for E-box-dependent transactivation
Secondary accessions: Q4ZFV9 Q53SQ3 Q86V96 Q99629

Explore the universe of human proteins at neXtProt for NPAS2: NX_Q99743

Explore proteomics data for NPAS2 at MOPED


See NPAS2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_002509.2  
ENSEMBL proteins: 
 ENSP00000338283   ENSP00000397595   ENSP00000388528   ENSP00000395265   ENSP00000392125  
 ENSP00000393396   ENSP00000438428  
Reactome Protein details: Q99743

NPAS2 Human Recombinant Protein Products:

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Novus Biologicals NPAS2 Proteins
Novus Biologicals NPAS2 Lysate
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Browse Sino Biological Cell Lysates
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Cloud-Clone Corp. Proteins for NPAS2

 
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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
 IPR001067 Nuc_translocat

Graphical View of Domain Structure for InterPro Entry Q99743

ProtoNet protein and cluster: Q99743

5 Blocks protein domains:
IPB000014 PAS domain
IPB001067 Nuclear translocator signature
IPB001092 Basic helix-loop-helix dimerization domain bHLH
IPB001610 PAC motif
IPB013655 PAS fold-3


UniProtKB/Swiss-Prot: NPAS2_HUMAN, Q99743
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 NPAS2           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: NPAS2_HUMAN, Q99743
Function: BMAL1-NPAS2 heterodimers activate E-box element (5'-CACGTG-3') transcription of a number of proteins of
the circadian clock. This transcription is inhibited in a feedback loop by PER, and also by CRY proteins (By
similarity)

     Genatlas biochemistry entry for NPAS2:
neuronal PAS domain protein 2,expressed in the central nervous system

     Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding IPI9576906
GO:0003700sequence-specific DNA binding transcription factor activity IEA--
GO:0004871signal transducer activity IEA--
GO:0005515protein binding ----
GO:0046983protein dimerization activity IEA--
     
Find genes that share ontologies with NPAS2           About GenesLikeMe


Phenotypes:
     4 MGI mutant phenotypes (inferred from 1 allele(MGI details for Npas2):
 behavior/neurological  cardiovascular system  homeostasis/metabolism  nervous system 

Find genes that share phenotypes with NPAS2           About GenesLikeMe

Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for NPAS2
   inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for NPAS2

   genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for NPAS2
   genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for NPAS2

Transcription Factor Targeting: 
Targeting motifs: HOMER Transcription Factor Regulatory Elements motif viewer 
                                      Consensus sequence:  KCCACGTGAC 

miRNA
Products:
    
miRTarBase miRNAs that target NPAS2:
hsa-mir-335-5p (MIRT018156), hsa-mir-17-5p (MIRT050815), hsa-mir-484 (MIRT042271)

Block miRNA regulation of human, mouse, rat NPAS2 using miScript Target Protectors
Selected qRT-PCR Assays for microRNAs that regulate NPAS2 (see all 58):
hsa-miR-106a hsa-miR-374a hsa-miR-219-5p hsa-miR-30d hsa-miR-519a hsa-miR-218 hsa-miR-508-3p hsa-miR-30a
SwitchGear 3'UTR luciferase reporter plasmidNPAS2 3' UTR sequence
Inhib. RNA
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OriGene RNAi products in human, mouse, rat for NPAS2
Predesigned siRNA for gene silencing in human, mouse, rat NPAS2

Gene Editing
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DNA2.0 Custom Protein Engineering Service for NPAS2

Clone
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OriGene clones in human, mouse for NPAS2 (see all 7)
OriGene ORF clones in mouse, rat for NPAS2
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GenScript: all cDNA clones in your preferred vector: NPAS2 (NM_002518)
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DNA2.0 Custom Codon Optimized Gene Synthesis Service for NPAS2
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat NPAS2

Cell Line
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Browse ESI BIO Cell Lines and PureStem Progenitors for NPAS2 
In Situ Assay
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NPAS2


(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
NPAS2_HUMAN, Q99743: Nucleus (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol4
nucleus4
plasma membrane1

Gene Ontology (GO): 4 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--
GO:0005667transcription factor complex IPI9576906
GO:0005737cytoplasm ----
GO:0005829cytosol TAS--

Find genes that share ontologies with NPAS2           About GenesLikeMe


(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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SuperPaths for NPAS2 About   (see all 7)  
See pathways by source

SuperPathContained pathways About
1Fatty acid, triacylglycerol, and ketone body metabolism
Fatty acid, triacylglycerol, and ketone body metabolism0.65
PPARA Activates Gene Expression0.63
Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)0.65
2Circadian Repression of Expression by REV-ERBA
Circadian Repression of Expression by REV-ERBA0.88
RORA Activates Circadian Expression0.88
3Circadian Clock
Circadian Clock0.66
BMAL1-CLOCK/NPAS2 Activates Circadian Expression0.66
4Metabolism
Metabolism0.38
Metabolism of lipids and lipoproteins0.37
5Circadian rhythm
Circadian rhythm0.31


Find genes that share SuperPaths with NPAS2           About GenesLikeMe

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways

1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for NPAS2
    Metabolic States and Circadian Oscillators

1 BioSystems Pathway for NPAS2
    Circadian rhythm pathway

5 Reactome Pathways for NPAS2
    Circadian Clock
PPARA activates gene expression
REV-ERBA represses gene expression
BMAL1:CLOCK,NPAS2 activates circadian gene expression
RORA activates circadian gene expression


1 Kegg Pathway  (Kegg details for NPAS2):
    Circadian rhythm

    Pathway & Disease-focused RT2 Profiler PCR Array including NPAS2: 
          Circadian Rhythms in human mouse rat

Interactions:

    GeneGlobe Interaction Network for NPAS2

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for NPAS2 (Q997433 ENSP000003382834) via UniProtKB, MINT, STRING, and/or I2D (see all 52)
InteractantInteraction Details
GeneCardExternal ID(s)
CREBBPQ927933, ENSP000002623674I2D: score=2 STRING: ENSP00000262367
RARAP102763, ENSP000002540664I2D: score=2 STRING: ENSP00000254066
TRAF4Q9BUZ43, ENSP000002623954I2D: score=1 STRING: ENSP00000262395
ZSCAN1Q8NBB43, ENSP000002823264I2D: score=1 STRING: ENSP00000282326
ARNTLO003273, ENSP000003743574I2D: score=2 STRING: ENSP00000374357
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Gene Ontology (GO): Selected biological process terms (see all 9):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006351transcription, DNA-templated IEA--
GO:0006355regulation of transcription, DNA-templated ----
GO:0007165signal transduction ----
GO:0007417central nervous system development TAS9012850
GO:0042745circadian sleep/wake cycle IEA--

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(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 NPAS2



(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 NPAS2 gene: 
NM_002518.3  

Unigene Cluster for NPAS2:

Neuronal PAS domain protein 2
Hs.156832  [show with all ESTs]
Unigene Representative Sequence: NM_002518
13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000335681(uc002tap.1 uc010yvt.1 uc010fit.1) ENST00000427413
ENST00000486017 ENST00000448812 ENST00000451740 ENST00000492373 ENST00000474550
ENST00000471974 ENST00000450763 ENST00000433408 ENST00000495559 ENST00000490052
ENST00000542504
miRNA
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Block miRNA regulation of human, mouse, rat NPAS2 using miScript Target Protectors
Selected qRT-PCR Assays for microRNAs that regulate NPAS2 (see all 58):
hsa-miR-106a hsa-miR-374a hsa-miR-219-5p hsa-miR-30d hsa-miR-519a hsa-miR-218 hsa-miR-508-3p hsa-miR-30a
SwitchGear 3'UTR luciferase reporter plasmidNPAS2 3' UTR sequence
Inhib. RNA
Products:
     
OriGene RNAi products in human, mouse, rat for NPAS2
Predesigned siRNA for gene silencing in human, mouse, rat NPAS2
Clone
Products:
     
OriGene clones in human, mouse for NPAS2 (see all 7)
OriGene ORF clones in mouse, rat for NPAS2
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
GenScript: all cDNA clones in your preferred vector: NPAS2 (NM_002518)
DNA2.0 Custom Codon Optimized Gene Synthesis Service for NPAS2
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat NPAS2
Primer
Products:
    
OriGene qSTAR qPCR primer pairs in human, mouse for NPAS2
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat NPAS2
  QuantiTect SYBR Green Assays in human, mouse, rat NPAS2
  QuantiFast Probe-based Assays in human, mouse, rat NPAS2

Additional mRNA sequence: 

AK091939.1 AK095806.1 AK128586.1 AK226093.1 AK294733.1 BC028107.1 BC051351.1 BC072383.1 
U51625.1 U77970.1 

14 DOTS entries:

DT.436335  DT.100026680  DT.85102881  DT.100786389  DT.40214010  DT.92431921  DT.121029483  DT.92431922 
DT.95277739  DT.121029381  DT.65285512  DT.95221441  DT.121029652  DT.95277736 

1 AceView cDNA sequence:

BC035412 

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for NPAS2 (see all 6)    About this scheme

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b · 18c ^ 19 ^
SP1:                                -                                               -                                                     -                     
SP2:                                                                                                                                -     -     -     -     -   
SP3:                                                                                                                                                            
SP4:                                                                                                                                                            
SP5:                                                                                                                                                            

ExUns: 20 ^ 21a · 21b
SP1:                  
SP2:                  
SP3:                  
SP4:                  
SP5:        -         


ECgene alternative splicing isoforms for NPAS2

(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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NPAS2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AGAATACTGA
NPAS2 Expression
About this image


NPAS2 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Blood (Hematopoietic System)    fully expand to see all 2 entries
         T-Cytotoxic Cells Peripheral Blood
 
 Endothelium (Cardiovascular System)
         Human umbilical vein endothelial cells (HUVEC)
NPAS2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

NPAS2 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.156832
    Pathway & Disease-focused RT2 Profiler PCR Array including NPAS2: 
          Circadian Rhythms in human mouse rat

Primer
Products:
OriGene qSTAR qPCR primer pairs in human, mouse for NPAS2
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat NPAS2
QuantiTect SYBR Green Assays in human, mouse, rat NPAS2
QuantiFast Probe-based Assays in human, mouse, rat NPAS2
In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NPAS2

(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 NPAS2 gene from Selected species (see all 12)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Npas21 , 5 neuronal PAS domain protein 21, 5 86.9(n)1
88.55(a)1
  1 (17.98 cM)5
181431  NM_008719.21  NP_032745.21 
 391937315 
chicken
(Gallus gallus)
Aves NPAS21 neuronal PAS domain protein 2 75.56(n)
75.19(a)
  395433  NM_001030542.1  NP_001025713.1 
lizard
(Anolis carolinensis)
Reptilia NPAS26
neuronal PAS domain protein 2
63(a)
1 ↔ 1
GL343542.1(244589-337732)
tropical clawed frog
(Xenopus tropicalis)
Amphibia npas21 neuronal PAS domain protein 2 64.85(n)
61.72(a)
  101731519  XM_004911781.1  XP_004911838.1 
zebrafish
(Danio rerio)
Actinopterygii AB087255.12   -- 74.59(n)   352934  AB087255.1 
fruit fly
(Drosophila melanogaster)
Insecta Clk3 positive regulation of transcription,
DNA-dependent more
50(a)   3 66A12   --


ENSEMBL Gene Tree for NPAS2 (if available)
TreeFam Gene Tree for NPAS2 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for NPAS2 gene
ARNT22  CLOCK2  AHR2  ARNT2  EPAS12  NPAS32  HIF1A2  SIM22  
SIM12  HIF3A2  ARNTL2  NPAS12  ARNTL22  AHRR2  
8 SIMAP similar genes for NPAS2 using alignment to 10 protein entries:     NPAS2_HUMAN (see all proteins):
clock    CLOCK    ARNTL2    ARNTL    ARNT    HIF3A
NCOA2    AHRR

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(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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Polymorphic Variants from UniProtKB/Swiss-Prot
NPAS2_HUMAN, Q99743: Variants in NPAS2 show a susceptibility to seasonal affective disorder (SAD) [MIM:608516]. SAD is a
depressive condition resulting from seasonal changes, and with diurnal preference


Selected SNPs for NPAS2 (see all 3891)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1389481671,2
C--95292420(+) TTATT-/A/    
   TATTA
ATTAT
1 -- int10--------
rs342763811,2
C--95295361(+) GAACC-/CT/TC 
        
TCTCT
1 -- int10--------
rs345733291,2
C,F--95304890(+) GGCCA-/CCCCGT 1 -- int13Minor allele frequency- C:0.33NA CSA 6
rs67054661,2
C,F,A,H--95333929(+) AAAAAA/CAAAAA 1 -- int13Minor allele frequency- C:0.40NA 10
rs1388291941,2
C--95333929(+) AAAAA-/CAAAAA 1 -- int10--------
rs118903711,2
C,H--95339639(+) AAAAAA/CACAAA 1 -- int1 trp30--------
rs2017055351,2
--95360009(+) ATAAC-/TATATAT 1 -- int10--------
rs134326241,2
C--95360029(+) TATATA/TTTTTT 1 -- int10--------
rs75588581,2
C--95360031(+) TATATA/TTTTTT 1 -- int1 trp30--------
rs772122221,2
C--95361517(+) GTCGTGAA/-GAAGC 1 -- cds11Minor allele frequency- -:0.50CSA 2

HapMap Linkage Disequilibrium report for NPAS2 (101436613 - 101613291 bp)

Structural Variations
     Database of Genomic Variants (DGV) 5 variations for NPAS2:    About this table    
Variant IDTypeSubtypePubMed ID
esv2720445CNV Deletion23290073
esv2667827CNV Deletion23128226
nsv834315CNV Gain17160897
nsv834316CNV Gain17160897
nsv829584CNV Gain20364138

Human Gene Mutation Database (HGMD): NPAS2
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing NPAS2
DNA2.0 Custom Variant and Variant Library Synthesis for NPAS2

(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: 603347    OMIM disorders: --

1 disease for NPAS2:    
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seasonal affective disorder


Find genes that share disorders with NPAS2           About GenesLikeMe

Genetic Association Database (GAD): NPAS2
Human Genome Epidemiology (HuGE) Navigator: NPAS2 (22 documents)

Export disorders for NPAS2 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 NPAS2 gene, integrated from 10 sources (see all 52):
(articles sorted by number of sources associating them with NPAS2)
    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 circadian gene NPAS2 is a novel prognostic biomarker for breast cancer. (PubMed id 19649706)1, 4, 9 Yi C....Katsaro D. (Breast Cancer Res. Treat. 2010)
  4. Non-synonymous polymorphisms in the circadian gene NPAS2 and breast cancer risk. (PubMed id 17453337)1, 4, 9 Zhu Y....Zheng T. (Breast Cancer Res. Treat. 2008)
  5. Ala394Thr polymorphism in the clock gene NPAS2: a circadian modifier for the risk of non-Hodgkin's lymphoma. (PubMed id 17096334)1, 4, 9 Zhu Y....Zheng T. (Int. J. Cancer 2007)
  6. Novel breast cancer risk alleles and interaction with ionizing radiation among U.S. radiologic technologists. (PubMed id 20095854)1, 4 Bhatti P....Sigurdson A.J. (Radiat. Res. 2010)
  7. Systematic analysis of circadian genes in a population-based sample reveals association of TIMELESS with depression and sleep disturbance. (PubMed id 20174623)1, 4 Utge S.J....Paunio T. (PLoS ONE 2010)
  8. PER2 variantion is associated with depression vulnerability. (PubMed id 19693801)1, 4 Lavebratt C....Forsell Y. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2010)
  9. Circadian clock gene polymorphisms in alcohol use disorders and alcohol consumption. (PubMed id 20554694)1, 4 Kovanen L....Partonen T. (Alcohol Alcohol. 2010)
  10. Differential association of circadian genes with mood disorders: CRY1 and NPAS2 are associated with unipolar major depression and CLOCK and VIP with bipolar disorder. (PubMed id 20072116)1, 4 Soria V....Urretavizcaya M. (Neuropsychopharmacology 2010)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 4862 HGNC: 7895 AceView: NPAS2.1 Ensembl:ENSG00000170485 euGenes: HUgn4862
ECgene: NPAS2 Kegg: 4862 H-InvDB: NPAS2

(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 NPAS2 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 NPAS2 gene:
Search GeneIP for patents involving NPAS2

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



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