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

    Gene ID: 4862, updated on 2-Nov-2024

    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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (100818723..100996829)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (101278833..101455526)
    RS_2024_09 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 ATAC-STARR-seq lymphoblastoid active region 16295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:101599407-101599908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:101599909-101600408 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:101601340-101601535 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 ATAC-STARR-seq lymphoblastoid active region 16296 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:101619087-101619741 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:101621211-101621711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16297 Neighboring gene ubiquitin specific peptidase 15 pseudogene Neighboring gene uncharacterized LOC105373510 Neighboring gene TBC1 domain family member 8 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 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. Ala394Thr polymorphism in the clock gene NPAS2: a circadian modifier for the risk of non-Hodgkin's lymphoma. Zhu Y, et al. Int J Cancer, 2007 Jan 15. PMID 17096334, Free PMC Article
    2. 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
    3. Whole-exome sequencing identifies novel homozygous mutation in NPAS2 in family with nonobstructive azoospermia. Ramasamy R, et al. Fertil Steril, 2015 Aug. PMID 25956372, Free PMC Article
    4. Lack of association of the NPAS2 gene Ala394Thr polymorphism (rs2305160:G>A) with risk of chronic lymphocytic leukemia. Rana S, et al. Asian Pac J Cancer Prev, 2014. PMID 25227809
    5. Silencing NPAS2 promotes cell growth and invasion in DLD-1 cells and correlated with poor prognosis of colorectal cancer. Xue X, et al. Biochem Biophys Res Commun, 2014 Jul 25. PMID 24978311

    See all (84) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association between glucose metabolism, the circadian cycle and hypoxia: Evaluation of the NPAS2 and Rev-Erb-alpha protein serum levels in obstructive sleep apnea patients - a pilot study.
      Title: Association between glucose metabolism, the circadian cycle and hypoxia: Evaluation of the NPAS2 and Rev-Erb-α protein serum levels in obstructive sleep apnea patients - a pilot study.
    2. High expression of the circadian clock gene NPAS2 is associated with progression and poor prognosis of gastric cancer: A single-center study.
      Title: High expression of the circadian clock gene NPAS2 is associated with progression and poor prognosis of gastric cancer: A single-center study.
    3. Characterization of molecular subtypes based on chromatin regulators and identification of the role of NPAS2 in lung adenocarcinoma.
      Title: Characterization of molecular subtypes based on chromatin regulators and identification of the role of NPAS2 in lung adenocarcinoma.
    4. NPAS2 promotes aerobic glycolysis and tumor growth in prostate cancer through HIF-1A signaling.
      Title: NPAS2 promotes aerobic glycolysis and tumor growth in prostate cancer through HIF-1A signaling.
    5. 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.
    6. Roles of NPAS2 in circadian rhythm and disease.
      Title: Roles of NPAS2 in circadian rhythm and disease.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (41)

    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
    		  
    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
    		  
    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
    		  
    involved_in circadian regulation of gene expression ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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
    		  
    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
    		  
    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
      Q4ZFV9, Q53SQ3, Q86V96, Q99629, Q99743
      UniProtKB/TrEMBL
      A2I2P5, X5DR62
      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_2024_08

    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
      Q4ZFV9, Q53SQ3, Q86V96, Q99629, Q99743
      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

      UniProtKB/TrEMBL
      X5DR62
      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
      Q4ZFV9, Q53SQ3, Q86V96, Q99629, Q99743
      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
      Q4ZFV9, Q53SQ3, Q86V96, Q99629, Q99743
      UniProtKB/TrEMBL
      A2I2P5

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

      UniProtKB/TrEMBL
      X5DR62
      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

      UniProtKB/Swiss-Prot
      Q4ZFV9, Q53SQ3, Q86V96, Q99629, Q99743
      UniProtKB/TrEMBL
      A2I2P5

    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

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