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Npas1 neuronal PAS domain protein 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 308387, updated on 2-Nov-2024

Summary

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Official Symbol
Npas1provided by RGD
Official Full Name
neuronal PAS domain protein 1provided by RGD
Primary source
RGD:1310040
See related
EnsemblRapid:ENSRNOG00000015376 AllianceGenome:RGD:1310040
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and protein heterodimerization activity. Predicted to be involved in negative regulation of DNA-templated transcription and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within maternal behavior; negative regulation of transcription by RNA polymerase II; and startle response. Predicted to be located in nucleus. Orthologous to human NPAS1 (neuronal PAS domain protein 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Brain (RPKM 25.7), Kidney (RPKM 3.8) and 7 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Npas1 in Genome Data Viewer
Location:
1q21
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (86295509..86316018, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (77167375..77187887, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (78420646..78441841, complement)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene zinc finger CCCH-type containing 4 Neighboring gene transmembrane protein 160 Neighboring gene Rho GTPase activating protein 35 Neighboring gene G protein subunit gamma 5, pseudogene 3 Neighboring gene CEA cell adhesion molecule 15 like 1

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 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. Behavioral and regulatory abnormalities in mice deficient in the NPAS1 and NPAS3 transcription factors. Erbel-Sieler C, et al. Proc Natl Acad Sci U S A, 2004 Sep 14. PMID 15347806, Free PMC Article
  2. Novel function of neuronal PAS domain protein 1 in erythropoietin expression in neuronal cells. Ohsawa S, et al. J Neurosci Res, 2005 Feb 15. PMID 15635607
  3. NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors. Wu D, et al. Elife, 2016 Oct 26. PMID 27782878, Free PMC Article
  4. The progenitor zone of the ventral medial ganglionic eminence requires Nkx2-1 to generate most of the globus pallidus but few neocortical interneurons. Flandin P, et al. J Neurosci, 2010 Feb 24. PMID 20181579, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein heterodimerization activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within maternal behavior ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II 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
  
acts_upstream_of_or_within startle response ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
neuronal PAS domain-containing protein 1

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_001107479.1 → NP_001100949.1  neuronal PAS domain-containing protein 1

    See identical proteins and their annotated locations for NP_001100949.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473979
    UniProtKB/TrEMBL
    A6J8B4, D3ZJ66
    Related
    ENSRNOP00000020855.3, ENSRNOT00000020855.6
    Conserved Domains (3) summary
    smart00091
    Location:141 → 198
    PAS; PAS domain
    pfam08447
    Location:317 → 388
    PAS_3; PAS fold
    cd19731
    Location:43 → 116
    bHLH-PAS_NPAS1_PASD5; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 1 (NPAS1) and similar proteins

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_086019.1 Reference GRCr8

    Range
    86295509..86316018 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006228413.3 → XP_006228475.1  neuronal PAS domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006228475.1

    UniProtKB/TrEMBL
    A6J8B4, D3ZJ66
    Conserved Domains (3) summary
    smart00091
    Location:141 → 198
    PAS; PAS domain
    pfam08447
    Location:317 → 388
    PAS_3; PAS fold
    cd19731
    Location:43 → 116
    bHLH-PAS_NPAS1_PASD5; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 1 (NPAS1) and similar proteins
Nucleotide Protein Strain
Heading Accession and Version

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