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NPAS2 neuronal PAS domain protein 2 [ Homo sapiens (human) ]

Gene ID: 4862, updated on 21-Mar-2023

Summary

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Official Symbol
NPAS2provided by HGNC
Official Full Name
neuronal PAS domain protein 2provided by HGNC
Primary source
HGNC:HGNC:7895
See related
Ensembl:ENSG00000170485 MIM:603347; AllianceGenome:HGNC:7895
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MOP4; PASD4; bHLHe9
Summary
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]
Expression
Ubiquitous expression in esophagus (RPKM 4.7), urinary bladder (RPKM 4.5) and 22 other tissues See more
Orthologs
mouse all
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Genomic context

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See NPAS2 in Genome Data Viewer
Location:
2q11.2
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (100818723..100996829)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (101278833..101455526)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (101436601..101613291)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375310 Neighboring gene Sharpr-MPRA regulatory region 3478 Neighboring gene uncharacterized LOC105373508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:101504140-101504909 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:101518843-101520042 Neighboring gene Sharpr-MPRA regulatory region 12407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:101599407-101599908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:101599909-101600408 Neighboring gene NPAS2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:101607367-101608009 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:101611812-101612312 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:101619087-101619741 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:101621211-101621711 Neighboring gene ribosomal protein L31

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Genetic variants in NPAS2 gene and clinical outcomes of resectable non-small-cell lung cancer. He Y, et al. Future Oncol, 2021 Mar. PMID 33541123
  2. Circadian clock gene NPAS2 promotes reprogramming of glucose metabolism in hepatocellular carcinoma cells. Yuan P, et al. Cancer Lett, 2020 Jan 28. PMID 31765736
  3. Pyrosequencing analysis of methylation levels of clock genes in leukocytes from Parkinson's disease patients. Mao W, et al. Neurosci Lett, 2018 Mar 6. PMID 29353016
  4. A polymorphic GGC repeat in the NPAS2 gene and its association with melanoma. Franzoni A, et al. Exp Biol Med (Maywood), 2017 Sep. PMID 28799406, Free PMC Article
  5. Genetic association study of circadian genes with seasonal pattern in bipolar disorders. Geoffroy PA, et al. Sci Rep, 2015 May 19. PMID 25989161, Free PMC Article

See all (79) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Integrative Molecular Analyses of an Individual Transcription Factor-Based Genomic Model for Lung Cancer Prognosis.
    Title: Integrative Molecular Analyses of an Individual Transcription Factor-Based Genomic Model for Lung Cancer Prognosis.
  2. Roles of NPAS2 in circadian rhythm and disease.
    Title: Roles of NPAS2 in circadian rhythm and disease.
  3. Genetic variants in NPAS2 gene and clinical outcomes of resectable non-small-cell lung cancer.
    Title: Genetic variants in NPAS2 gene and clinical outcomes of resectable non-small-cell lung cancer.
  4. Circadian genes polymorphisms, night work and prostate cancer risk: Findings from the EPICAP study.
    Title: Circadian genes polymorphisms, night work and prostate cancer risk: Findings from the EPICAP study.
  5. Our findings demonstrate that NPAS2 plays a critical role in glucose metabolism reprogramming, suggesting that NPAS2 may serve as a potential therapeutic target in HCC.
    Title: Circadian clock gene NPAS2 promotes reprogramming of glucose metabolism in hepatocellular carcinoma cells.
  6. Study reported an association between the risk of prostate cancer and the circadian pathway where significant associations were found for the genes NPAS2 and PER1.
    Title: Circadian genes and risk of prostate cancer: Findings from the EPICAP study.
  7. NPAS2 hypomethylation occurs at the early stage of PD and is a moderate biomarker for distinguishing PD patients from healthy subjects.
    Title: Pyrosequencing analysis of methylation levels of clock genes in leukocytes from Parkinson's disease patients.
  8. NPAS2 has a critical role in HCC cell survival and tumor growth, which is mainly mediated by transcriptional upregulation of CDC25A.
    Title: NPAS2 promotes cell survival of hepatocellular carcinoma by transactivating CDC25A.
  9. Aggregate genetic variation in circadian rhythm and melatonin pathways were significantly associated with the risk of prostate cancer in data combining GAME-ON and PLCO, after Bonferroni correction (ppathway < 0.00625). The two most significant genes were NPAS2 (pgene = 0.0062) and AANAT (pgene = 0.00078); the latter being significant after Bonferroni correction.
    Title: Inherited variation in circadian rhythm genes and risks of prostate cancer and three other cancer sites in combined cancer consortia.
  10. Significantly, this study is the first to show that a variant copy number GGC repeat sequence in the NPAS2 clock gene associates with melanoma risk and which may be useful in the assessment of melanoma predisposition.
    Title: A polymorphic GGC repeat in the NPAS2 gene and its association with melanoma.
Submit: New GeneRIF Correction See all GeneRIFs (37)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
EBI GWAS Catalog
Genome-wide study links MTMR7 gene to variant Creutzfeldt-Jakob risk.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ23138, MGC71151

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables Hsp90 protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in central nervous system development TAS
Traceable Author Statement
more info
 PubMed 
involved_in circadian regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of cell death IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of DNA repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of behavioral fear response ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in response to redox state IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to xenobiotic stimulus ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of CLOCK-BMAL transcription complex IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
neuronal PAS domain-containing protein 2
Names
PAS domain-containing protein 4
basic-helix-loop-helix-PAS protein MOP4
class E basic helix-loop-helix protein 9
member of PAS protein 4
member of PAS superfamily 4
neuronal PAS2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_023259.1 RefSeqGene

    Range
    4989..181679
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002518.4 → NP_002509.2  neuronal PAS domain-containing protein 2

    See identical proteins and their annotated locations for NP_002509.2

    Status: REVIEWED

    Source sequence(s)
    AC016738, AC092168, AK095806, AK128586, BC072383, BM724652, U77970
    Consensus CDS
    CCDS2048.1
    UniProtKB/Swiss-Prot
    Q99629, Q99743
    UniProtKB/TrEMBL
    A2I2P5
    Related
    ENSP00000338283.5, ENST00000335681.10
    Conserved Domains (5) summary
    smart00091
    Location:84 → 149
    PAS; PAS domain
    cd00083
    Location:7 → 61
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    cd00130
    Location:250 → 350
    PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
    pfam13426
    Location:94 → 195
    PAS_9; PAS domain
    pfam14598
    Location:249 → 352
    PAS_11; PAS domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    100818723..100996829
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047444506.1 → XP_047300462.1  neuronal PAS domain-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q99629
    UniProtKB/TrEMBL
    A2I2P5

  2. XM_047444515.1 → XP_047300471.1  neuronal PAS domain-containing protein 2 isoform X8

  3. XM_011511242.3 → XP_011509544.1  neuronal PAS domain-containing protein 2 isoform X2

    Conserved Domains (3) summary
    cd00083
    Location:7 → 61
    HLH; Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, ...
    cd00130
    Location:220 → 320
    PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
    pfam14598
    Location:219 → 322
    PAS_11; PAS domain

  4. XM_047444510.1 → XP_047300466.1  neuronal PAS domain-containing protein 2 isoform X6

  5. XM_047444513.1 → XP_047300469.1  neuronal PAS domain-containing protein 2 isoform X7

  6. XM_047444511.1 → XP_047300467.1  neuronal PAS domain-containing protein 2 isoform X9

  7. XM_005263953.3 → XP_005264010.2  neuronal PAS domain-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q99629
    UniProtKB/TrEMBL
    A2I2P5

  8. XM_017004214.2 → XP_016859703.2  neuronal PAS domain-containing protein 2 isoform X4

  9. XM_005263960.3 → XP_005264017.2  neuronal PAS domain-containing protein 2 isoform X8

  10. XM_047444502.1 → XP_047300458.1  neuronal PAS domain-containing protein 2 isoform X2

  11. XM_005263959.3 → XP_005264016.2  neuronal PAS domain-containing protein 2 isoform X6

  12. XM_017004216.2 → XP_016859705.2  neuronal PAS domain-containing protein 2 isoform X7

  13. XM_017004217.2 → XP_016859706.2  neuronal PAS domain-containing protein 2 isoform X10

  14. XM_011511243.3 → XP_011509545.2  neuronal PAS domain-containing protein 2 isoform X12

  15. XM_047444503.1 → XP_047300459.1  neuronal PAS domain-containing protein 2 isoform X3

  16. XM_047444504.1 → XP_047300460.1  neuronal PAS domain-containing protein 2 isoform X5

  17. XM_047444512.1 → XP_047300468.1  neuronal PAS domain-containing protein 2 isoform X10

  18. XM_047444505.1 → XP_047300461.1  neuronal PAS domain-containing protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q99629
    UniProtKB/TrEMBL
    A2I2P5

  19. XM_005263961.5 → XP_005264018.1  neuronal PAS domain-containing protein 2 isoform X11

    Conserved Domains (2) summary
    cd00130
    Location:126 → 226
    PAS; PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in ...
    pfam14598
    Location:125 → 228
    PAS_11; PAS domain

RNA

  1. XR_007075420.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    101278833..101455526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342282.1 → XP_054198257.1  neuronal PAS domain-containing protein 2 isoform X6

  2. XM_054342286.1 → XP_054198261.1  neuronal PAS domain-containing protein 2 isoform X7

  3. XM_054342287.1 → XP_054198262.1  neuronal PAS domain-containing protein 2 isoform X8

  4. XM_054342279.1 → XP_054198254.1  neuronal PAS domain-containing protein 2 isoform X2

  5. XM_054342283.1 → XP_054198258.1  neuronal PAS domain-containing protein 2 isoform X9

  6. XM_054342273.1 → XP_054198248.1  neuronal PAS domain-containing protein 2 isoform X13

  7. XM_054342277.1 → XP_054198252.1  neuronal PAS domain-containing protein 2 isoform X15

  8. XM_054342275.1 → XP_054198250.1  neuronal PAS domain-containing protein 2 isoform X14

  9. XM_054342280.1 → XP_054198255.1  neuronal PAS domain-containing protein 2 isoform X16

  10. XM_054342289.1 → XP_054198264.1  neuronal PAS domain-containing protein 2 isoform X19

  11. XM_054342281.1 → XP_054198256.1  neuronal PAS domain-containing protein 2 isoform X17

  12. XM_054342284.1 → XP_054198259.1  neuronal PAS domain-containing protein 2 isoform X18

  13. XM_054342274.1 → XP_054198249.1  neuronal PAS domain-containing protein 2 isoform X3

  14. XM_054342276.1 → XP_054198251.1  neuronal PAS domain-containing protein 2 isoform X5

  15. XM_054342285.1 → XP_054198260.1  neuronal PAS domain-containing protein 2 isoform X10

  16. XM_054342278.1 → XP_054198253.1  neuronal PAS domain-containing protein 2 isoform X1

  17. XM_054342288.1 → XP_054198263.1  neuronal PAS domain-containing protein 2 isoform X11

RNA

  1. XR_008486377.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q99743.3 GenPept UniProtKB/Swiss-Prot:Q99743

Gene LinkOut

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