Npas4 neuronal PAS domain protein 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Npas4provided by RGD
Official Full Name: neuronal PAS domain protein 4provided by RGD
Primary source: RGD:628866
See related: EnsemblRapid:ENSRNOG00000020009 AllianceGenome:RGD:628866
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
Also known as: Nxf
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein heterodimerization activity. Predicted to be involved in several processes, including chemical synaptic transmission; learning or memory; and modulation of chemical synaptic transmission. Predicted to act upstream of or within cellular response to corticosterone stimulus. Predicted to be located in nucleus. Predicted to be part of transcription regulator complex. Orthologous to human NPAS4 (neuronal PAS domain protein 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 9.6), Uterus (RPKM 6.9) and 2 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q43

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (211710640..211728038, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (202281260..202298681, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (220260310..220278177, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

In healthy cerebellar granule neurons HDAC3 associates weakly with the Npas4 promoter, however, this association is robustly increased in neurons primed to die. Study found that HDAC3 also associates differentially with the Bdnfr gene promoter, with higher association in dying neurons. Overexpression of HDAC3 leads to a suppression of Npas4 and Bdnf expression in cortical neurons.
Title: The Bdnf and Npas4 genes are targets of HDAC3-mediated transcriptional repression.
preoperative anxiety led to GABAergic system impairment in spinal cord and thus caused hyperalgesia due to glucocorticoid-induced downregulation of neuronal PAS domain protein 4.
Title: Preoperative anxiety-induced glucocorticoid signaling reduces GABAergic markers in spinal cord and promotes postoperative hyperalgesia by affecting neuronal PAS domain protein 4.
The presence of multiple localization signals and the differentiated localization of NPAS4 suggest a precise, multifactor-dependent regulation of NPAS4 trafficking, potentially crucial for its ability to act as a cellular stress sensor and transcription factor.
Title: Multiple sequences orchestrate subcellular trafficking of neuronal PAS domain-containing protein 4 (NPAS4).
The main discovery of this study is that the spontaneously expressed hippocampus Npas4 mRNA level under stressful conditions is associated with differences in hippocampus activation and behavior
Title: Stress-induced hippocampus Npas4 mRNA expression relates to specific psychophysiological patterns of stress response.
nuclear histone deacetylase 5 (HDAC5) in the nucleus accumbens (NAc) reduced cocaine reward-context associations and relapse-like behaviors in a cocaine self-administration model. We also discovered that HDAC5 associates with an activity-sensitive enhancer of the Npas4 gene and negatively regulates NPAS4 expression.
Title: HDAC5 and Its Target Gene, Npas4, Function in the Nucleus Accumbens to Regulate Cocaine-Conditioned Behaviors.
Overexpression of NPAS4 induced autophagy and effectively facilitated the clearance of endogenous total and phosphorylated tau in rat primary cortical neurons.
Title: NPAS4 Facilitates the Autophagic Clearance of Endogenous Tau in Rat Cortical Neurons.
The Npas4 protein levels increased in the acute phase of seizures (between 6 h and 72 h) and decreased in the chronic phases (between 7 d and 60 d) in the rat model.
Title: The inhibitory effects of Npas4 on seizures in pilocarpine-induced epileptic rats.
Relative hippocampal NPAS4 expression was significantly lower in depression model rats compared to controls but there was no significant difference in hippocampal ARNT2 expression between groups
Title: Hippocampal expression of aryl hydrocarbon receptor nuclear translocator 2 and neuronal PAS domain protein 4 in a rat model of depression.
The findings suggest that stroke-induced Npas4 upregulation may be involved in a transcriptional regulatory program within the corticolimbic circuitry following an ischemic insult.
Title: Upregulation of the neuronal Per-Arnt-Sim domain protein 4 (Npas4) in the rat corticolimbic system following focal cerebral ischemia.
NPAS4 overexpression restores ocular dominance plasticity in the visual cortex of adult naive animals whereas NPAS4 down-regulation prevents the plastic outcome caused by fluoxetine in adulthood
Title: Experience-dependent expression of NPAS4 regulates plasticity in adult visual cortex.

Submit: New GeneRIF Correction See all GeneRIFs (13)

General gene information

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Markers

MARC_12329-12330:1005768102:1 (e-PCR)
- UniSTS:267415

MARC_12329-12330:1017158939:3 (e-PCR)
- UniSTS:267415

Npas4 (e-PCR), detects polymorphism
- UniSTS:545972

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	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 DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to corticosterone stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to stress	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to stress	ISO Inferred from Sequence Orthology more info
involved_in excitatory postsynaptic potential	ISO Inferred from Sequence Orthology more info
involved_in excitatory postsynaptic potential	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within inhibitory postsynaptic potential	ISO Inferred from Sequence Orthology more info
involved_in inhibitory postsynaptic potential	ISO Inferred from Sequence Orthology more info
involved_in inhibitory postsynaptic potential	ISS Inferred from Sequence or Structural Similarity more info
involved_in inhibitory synapse assembly	ISO Inferred from Sequence Orthology more info
involved_in inhibitory synapse assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in learning	ISO Inferred from Sequence Orthology more info
involved_in learning	ISS Inferred from Sequence or Structural Similarity more info
involved_in long-term memory	ISO Inferred from Sequence Orthology more info
involved_in long-term memory	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	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 DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synaptic plasticity	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic plasticity	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synaptic transmission, GABAergic	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic transmission, GABAergic	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 short-term memory	ISO Inferred from Sequence Orthology more info
involved_in short-term memory	ISS Inferred from Sequence or Structural Similarity more info
involved_in social behavior	ISO Inferred from Sequence Orthology more info
involved_in social behavior	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytosol	TAS Traceable Author Statement more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in postsynapse	IEA Inferred from Electronic Annotation more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: neuronal PAS domain-containing protein 4

Names: HLH-PAS transcription factor NXF; bHLH-PAS type transcription factor NXF; neuronal PAS4

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)

NM_153626.1 → NP_705890.1 neuronal PAS domain-containing protein 4

See identical proteins and their annotated locations for NP_705890.1

Status: PROVISIONAL

Source sequence(s)

AB050103

UniProtKB/Swiss-Prot

Q8CJH6

UniProtKB/TrEMBL

A6HZ11

Related

ENSRNOP00000027119.2, ENSRNOT00000027119.4

Conserved Domains (3) summary

smart00091
Location:72 → 135

PAS; PAS domain

pfam08447
Location:230 → 298

PAS_3; PAS fold

cd19697
Location:2 → 57

bHLH-PAS_NPAS4_PASD10; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 4 (NPAS4) 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

NC_086019.1 Reference GRCr8

Range

211710640..211728038 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039102501.2 → XP_038958429.1 neuronal PAS domain-containing protein 4 isoform X1

UniProtKB/Swiss-Prot

Q8CJH6

UniProtKB/TrEMBL

A6HZ11

Conserved Domains (3) summary

smart00091
Location:72 → 135

PAS; PAS domain

pfam08447
Location:230 → 298

PAS_3; PAS fold

cd19697
Location:2 → 57

bHLH-PAS_NPAS4_PASD10; basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 4 (NPAS4) and similar proteins