Human Gene NPAS2 (uc010yvt.1)
  Description: Homo sapiens neuronal PAS domain protein 2 (NPAS2), mRNA.
RefSeq Summary (NM_002518): 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].
Transcript (Including UTRs)
   Position: hg19 chr2:101,437,487-101,613,287 Size: 175,801 Total Exon Count: 21 Strand: +
Coding Region
   Position: hg19 chr2:101,437,489-101,612,044 Size: 174,556 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:101,437,487-101,613,287)mRNA (may differ from genome)Protein (889 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F5H027_HUMAN
DESCRIPTION: SubName: Full=Neuronal PAS domain-containing protein 2;
SIMILARITY: Contains 1 PAC (PAS-associated C-terminal) domain.
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
SIMILARITY: Contains 1 basic helix-loop-helix (bHLH) domain.
SIMILARITY: Contains 2 PAS (PER-ARNT-SIM) domains.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NPAS2
CDC HuGE Published Literature: NPAS2
Positive Disease Associations: autism , Cholesterol , Erythrocyte Count , Sodium
Related Studies:
  1. autism
    Nicholas, B. et al. 2007, Association of Per1 and Npas2 with autistic disorder, Mol Psychiatry 2007. [PubMed 17264841]
  2. Cholesterol
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  3. Erythrocyte Count
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: NPAS2
Diseases sorted by gene-association score: major depressive disorder and accelerated response to antidepressant drug treatment (5), autistic disorder (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • C006780 bisphenol A
  • C029141 2,2,5,7,8-pentamethyl-1-hydroxychroman
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D000111 Acetylcysteine
  • D001564 Benzo(a)pyrene
  • D002251 Carbon Tetrachloride
  • D002330 Carmustine
  • D020111 Chlorodiphenyl (54% Chlorine)
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.77 RPKM in Esophagus - Mucosa
Total median expression: 455.83 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -366.101243-0.295 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011598 - HLH_dom
IPR001067 - Nuc_translocat
IPR001610 - PAC
IPR000014 - PAS
IPR013767 - PAS_fold
IPR013655 - PAS_fold_3

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain
PF00989 - PAS fold
PF08447 - PAS fold
PF13426 - PAS domain
PF14598 - PAS domain

SCOP Domains:
47459 - HLH, helix-loop-helix DNA-binding domain
55785 - PYP-like sensor domain (PAS domain)

ModBase Predicted Comparative 3D Structure on F5H027
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGD FlyBase  
 Protein Sequence Protein Sequence  
 Alignment Alignment  

-  Descriptions from all associated GenBank mRNAs
  KJ897259 - Synthetic construct Homo sapiens clone ccsbBroadEn_06653 NPAS2 gene, encodes complete protein.
U77970 - Human neuronal PAS2 (NPAS2) mRNA, complete cds.
BC072383 - Homo sapiens neuronal PAS domain protein 2, mRNA (cDNA clone MGC:71151 IMAGE:6371187), complete cds.
BC051351 - Homo sapiens neuronal PAS domain protein 2, mRNA (cDNA clone MGC:59643 IMAGE:6538324), complete cds.
AK294733 - Homo sapiens cDNA FLJ59682 complete cds, highly similar to Neuronal PAS domain-containing protein 2 (Neuronal PAS2) (Member of PAS protein 4) (MOP4).
BC028107 - Homo sapiens neuronal PAS domain protein 2, mRNA (cDNA clone IMAGE:5248433), partial cds.
U51625 - Human MOP4 mRNA, partial cds.
KJ534892 - Homo sapiens clone NPAS2_iso-A_adult-A01 neuronal PAS domain protein 2 isoform A (NPAS2) mRNA, partial cds, alternatively spliced.
AK226093 - Homo sapiens mRNA for neuronal PAS domain protein 2 variant, clone: ef04754.
BX640699 - Homo sapiens mRNA; cDNA DKFZp686F0725 (from clone DKFZp686F0725).
AK095806 - Homo sapiens cDNA FLJ38487 fis, clone FEBRA2023377, highly similar to NEURONAL PAS DOMAIN PROTEIN 2.
JD035213 - Sequence 16237 from Patent EP1572962.
AK128586 - Homo sapiens cDNA FLJ46745 fis, clone TRACH3021883, moderately similar to Neuronal PAS domain protein 2.
AK091939 - Homo sapiens cDNA FLJ34620 fis, clone KIDNE2014789, highly similar to NEURONAL PAS DOMAIN PROTEIN 2.
AK091665 - Homo sapiens cDNA FLJ34346 fis, clone FEBRA2010768.
AK026791 - Homo sapiens cDNA: FLJ23138 fis, clone LNG08913.
JD132305 - Sequence 113329 from Patent EP1572962.
JD408026 - Sequence 389050 from Patent EP1572962.
JD050197 - Sequence 31221 from Patent EP1572962.
JD435213 - Sequence 416237 from Patent EP1572962.
JD036892 - Sequence 17916 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04710 - Circadian rhythm - mammal

-  Other Names for This Gene
  Alternate Gene Symbols: AK294733, F5H027, F5H027_HUMAN, NM_002518, NP_002509
UCSC ID: uc010yvt.1
RefSeq Accession: NM_002518
Protein: F5H027

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK294733.1
exon count: 21CDS single in 3' UTR: no RNA size: 2725
ORF size: 2670CDS single in intron: no Alignment % ID: 99.89
txCdsPredict score: 5440.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.