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    Npas2 neuronal PAS domain protein 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 316351, updated on 3-Apr-2024

    Summary

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    Official Symbol
    Npas2provided by RGD
    Official Full Name
    neuronal PAS domain protein 2provided by RGD
    Primary source
    RGD:1309681
    See related
    Ensembl:ENSRNOG00000013408 AllianceGenome:RGD:1309681
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    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, Feb 2014]
    Expression
    Biased expression in Brain (RPKM 40.2), Adrenal (RPKM 33.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Npas2 in Genome Data Viewer
    Location:
    9q22
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (48959225..49138036)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (41463361..41642322)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (45901262..46081880)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108352023 Neighboring gene uncharacterized LOC134480360 Neighboring gene uncharacterized LOC120094670 Neighboring gene uncharacterized LOC134480570 Neighboring gene uncharacterized LOC120094671 Neighboring gene uncharacterized LOC134480361 Neighboring gene TBC1 domain family, member 8 Neighboring gene ribosomal protein L31 Neighboring gene uncharacterized LOC134480362

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Prefrontal cortex and dorsomedial hypothalamus mediate food reward-induced effects via npas2 and egr1 expression in rat. Herichová I, et al. Physiol Res, 2017 Dec 30. PMID 29355377
    2. NPAS2 Regulation of Anxiety-Like Behavior and GABAA Receptors. Ozburn AR, et al. Front Mol Neurosci, 2017. PMID 29163035, Free PMC Article
    3. The circadian gene NPAS2, a putative tumor suppressor, is involved in DNA damage response. Hoffman AE, et al. Mol Cancer Res, 2008 Sep. PMID 18819933, Free PMC Article
    4. Effect of streptozotocin-induced diabetes on clock gene expression in tissues inside and outside the blood-brain barrier in rat. Šoltésová D, et al. Exp Clin Endocrinol Diabetes, 2013 Aug. PMID 23864491
    5. Effects of NAD(P)H and its derivatives on the DNA-binding activity of NPAS2, a mammalian circadian transcription factor. Yoshii K, et al. Biochem Biophys Res Commun, 2013 Aug 2. PMID 23831463

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. In the prefrontal cortex, food reward induced rhythm in the expression of npas2.
      Title: Prefrontal cortex and dorsomedial hypothalamus mediate food reward-induced effects via npas2 and egr1 expression in rat.
    2. Possible role of npas2 in locomotor activity regulation in diabetic animals. The most pronounced changes were observed in the frontal cortex, which displayed up-regulation of npas2 expression.
      Title: Effect of streptozotocin-induced diabetes on clock gene expression in tissues inside and outside the blood-brain barrier in rat.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables Hsp90 protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in circadian regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in circadian regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in circadian rhythm ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within circadian sleep/wake cycle ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within locomotor rhythm ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of behavioral fear response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of circadian rhythm ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to xenobiotic stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of CLOCK-BMAL transcription complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    neuronal PAS domain-containing protein 2

    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.

    mRNA and Protein(s)

    1. NM_001108214.3 → NP_001101684.2  neuronal PAS domain-containing protein 2

      See identical proteins and their annotated locations for NP_001101684.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/TrEMBL
      F1MAG2
      Related
      ENSRNOP00000056327.2, ENSRNOT00000059571.3
      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:97 → 195
      PAS_9; PAS domain
      pfam14598
      Location:249 → 352
      PAS_11; PAS domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086027.1 Reference GRCr8

      Range
      48959225..49138036
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039083584.2 → XP_038939512.1  neuronal PAS domain-containing protein 2 isoform X1

      Conserved Domains (3) summary
      cd19737
      Location:1 → 77
      bHLH-PAS_NPAS2_PASD4; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 2 (NPAS2) and similar proteins
      pfam00989
      Location:84 → 234
      PAS; PAS fold
      pfam14598
      Location:288 → 391
      PAS_11; PAS domain

    2. XM_063267162.1 → XP_063123232.1  neuronal PAS domain-containing protein 2 isoform X3

      UniProtKB/TrEMBL
      F1MAG2

    3. XM_039083582.2 → XP_038939510.1  neuronal PAS domain-containing protein 2 isoform X1

      Conserved Domains (3) summary
      cd19737
      Location:1 → 77
      bHLH-PAS_NPAS2_PASD4; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 2 (NPAS2) and similar proteins
      pfam00989
      Location:84 → 234
      PAS; PAS fold
      pfam14598
      Location:288 → 391
      PAS_11; PAS domain

    4. XM_039083586.2 → XP_038939514.1  neuronal PAS domain-containing protein 2 isoform X2

      Conserved Domains (4) summary
      PHA03247
      Location:601 → 739
      PHA03247; large tegument protein UL36; Provisional
      cd19737
      Location:1 → 77
      bHLH-PAS_NPAS2_PASD4; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 2 (NPAS2) and similar proteins
      pfam00989
      Location:84 → 234
      PAS; PAS fold
      pfam14598
      Location:288 → 391
      PAS_11; PAS domain

    5. XM_008767031.4 → XP_008765253.1  neuronal PAS domain-containing protein 2 isoform X3

      See identical proteins and their annotated locations for XP_008765253.1

      UniProtKB/TrEMBL
      F1MAG2
      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:97 → 195
      PAS_9; PAS domain
      pfam14598
      Location:249 → 352
      PAS_11; PAS domain

    6. XM_039083583.2 → XP_038939511.1  neuronal PAS domain-containing protein 2 isoform X1

      Conserved Domains (3) summary
      cd19737
      Location:1 → 77
      bHLH-PAS_NPAS2_PASD4; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 2 (NPAS2) and similar proteins
      pfam00989
      Location:84 → 234
      PAS; PAS fold
      pfam14598
      Location:288 → 391
      PAS_11; PAS domain

    7. XM_039083585.2 → XP_038939513.1  neuronal PAS domain-containing protein 2 isoform X1

      Conserved Domains (3) summary
      cd19737
      Location:1 → 77
      bHLH-PAS_NPAS2_PASD4; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 2 (NPAS2) and similar proteins
      pfam00989
      Location:84 → 234
      PAS; PAS fold
      pfam14598
      Location:288 → 391
      PAS_11; PAS domain

    8. XM_039083587.2 → XP_038939515.1  neuronal PAS domain-containing protein 2 isoform X4

      UniProtKB/TrEMBL
      B5DFA7
      Conserved Domains (1) summary
      pfam14598
      Location:9 → 112
      PAS_11; PAS domain

    RNA

    1. XR_010054596.1 RNA Sequence

    2. XR_010054597.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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