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

Gene ID: 4862, updated on 27-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
  • 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)

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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