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    npas2 neuronal PAS domain protein 2 [ Danio rerio (zebrafish) ]

    Gene ID: 352934, updated on 9-Dec-2024

    Summary

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    Official Symbol
    npas2provided by ZNC
    Official Full Name
    neuronal PAS domain protein 2provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030408-3
    See related
    Ensembl:ENSDARG00000016536 AllianceGenome:ZFIN:ZDB-GENE-030408-3
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    clock2; zfCLOCK2
    Summary
    Contributes to double-stranded DNA binding activity. Acts upstream of or within circadian rhythm and photoperiodism. Part of transcription regulator complex. Is expressed in telencephalon. Orthologous to human NPAS2 (neuronal PAS domain protein 2). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See npas2 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 5 NC_007116.7 (22707958..22835072)
    105 previous assembly GRCz10 (GCF_000002035.5) 5 NC_007116.6 (22204117..22328456)

    Chromosome 5 - NC_007116.7Genomic Context describing neighboring genes Neighboring gene melatonin receptor 1C Neighboring gene vacuolar ATPase assembly factor VMA21 Neighboring gene uncharacterized LOC137490109 Neighboring gene RPA1 related single stranded DNA binding protein Neighboring gene apolipoprotein O-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Thyroid-stimulating hormone-thyroid hormone signaling contributes to circadian regulation through repressing clock2/npas2 in zebrafish. Ji C, et al. J Genet Genomics, 2024 Jan. PMID 37328030
    2. A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland. Alon S, et al. Bioinformatics, 2009 Mar 1. PMID 19147662, Free PMC Article
    3. Homeobox-clock protein interaction in zebrafish. A shared mechanism for pineal-specific and circadian gene expression. Appelbaum L, et al. J Biol Chem, 2005 Mar 25. PMID 15657039
    4. Temperature regulates transcription in the zebrafish circadian clock. Lahiri K, et al. PLoS Biol, 2005 Nov. PMID 16176122, Free PMC Article
    5. A blind circadian clock in cavefish reveals that opsins mediate peripheral clock photoreception. Cavallari N, et al. PLoS Biol, 2011 Sep. PMID 21909239, Free PMC Article

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Thyroid-stimulating hormone-thyroid hormone signaling contributes to circadian regulation through repressing clock2/npas2 in zebrafish.
      Title: Thyroid-stimulating hormone-thyroid hormone signaling contributes to circadian regulation through repressing clock2/npas2 in zebrafish.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    contributes_to double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		  
    enables protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in circadian regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within circadian regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within circadian rhythm IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within photoperiodism IEP
    Inferred from Expression Pattern
    more info
    		  
    acts_upstream_of_or_within regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within response to light stimulus IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within rhythmic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of CLOCK-BMAL transcription complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of transcription regulator complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of transcription regulator complex IPI
    Inferred from Physical Interaction
    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_178299.1 → NP_840084.1  neuronal PAS domain-containing protein 2

      See identical proteins and their annotated locations for NP_840084.1

      Status: PROVISIONAL

      Source sequence(s)
      AB087255
      UniProtKB/TrEMBL
      B3DIU8, F6PCM6, Q8JIG3
      Related
      ENSDARP00000016938.4, ENSDART00000014806.5
      Conserved Domains (3) summary
      cd00083
      Location:40 → 96
      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, ...
      pfam00989
      Location:119 → 203
      PAS; PAS fold
      cl25986
      Location:285 → 388
      PAS_3; PAS fold

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007116.7 Reference GRCz11 Primary Assembly

      Range
      22707958..22835072
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005165120.5 → XP_005165177.1  neuronal PAS domain-containing protein 2 isoform X1

      See identical proteins and their annotated locations for XP_005165177.1

      UniProtKB/TrEMBL
      B3DIU8, F6PCM6, Q8JIG3
      Conserved Domains (3) summary
      cd00083
      Location:40 → 96
      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, ...
      pfam00989
      Location:119 → 203
      PAS; PAS fold
      cl25986
      Location:285 → 388
      PAS_3; PAS fold

    2. XM_005165121.5 → XP_005165178.1  neuronal PAS domain-containing protein 2 isoform X1

      See identical proteins and their annotated locations for XP_005165178.1

      UniProtKB/TrEMBL
      B3DIU8, F6PCM6, Q8JIG3
      Conserved Domains (3) summary
      cd00083
      Location:40 → 96
      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, ...
      pfam00989
      Location:119 → 203
      PAS; PAS fold
      cl25986
      Location:285 → 388
      PAS_3; PAS fold

    3. XM_068221114.1 → XP_068077215.1  neuronal PAS domain-containing protein 2 isoform X1

      UniProtKB/TrEMBL
      B3DIU8, F6PCM6, Q8JIG3

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394574.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      28371..67264
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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