NPAS4 neuronal PAS domain protein 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NPAS4provided by HGNC
Official Full Name: neuronal PAS domain protein 4provided by HGNC
Primary source: HGNC:HGNC:18983
See related: Ensembl:ENSG00000174576 MIM:608554
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NXF; Le-PAS; PASD10; bHLHe79
Summary: NXF is a member of the basic helix-loop-helix-PER (MIM 602260)-ARNT (MIM 126110)-SIM (see SIM2; MIM 600892) (bHLH-PAS) class of transcriptional regulators, which are involved in a wide range of physiologic and developmental events (Ooe et al., 2004 [PubMed 14701734]).[supplied by OMIM, Mar 2008]
Expression: Broad expression in brain (RPKM 1.7), endometrium (RPKM 1.7) and 14 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 11q13.2

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
109.20200522	current	GRCh38.p13 (GCF_000001405.39)	11	NC_000011.10 (66408922..66426707)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (66188475..66194177)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

NPAS4 is expressed in endothelial cells, regulates VE-cadherin expression and regulates sprouting angiogenesis.
Title: The neuronal transcription factor NPAS4 is a strong inducer of sprouting angiogenesis and tip cell formation.
This review summarizes the current knowledge of the roles that Npas4 may play in neuroinflammation and ischemia. [review]
Title: The Role of the Neuroprotective Factor Npas4 in Cerebral Ischemia.
we provide the first evidence that Npas4 is expressed during embryonic development and that it may have a developmental role that is unrelated to its function in the adult brain
Title: A reduction in Npas4 expression results in delayed neural differentiation of mouse embryonic stem cells.
These results provide insight into the mechanisms of NPAS4/ARNT dimerisation and transcriptional activation.
Title: Human variants in the neuronal basic helix-loop-helix/Per-Arnt-Sim (bHLH/PAS) transcription factor complex NPAS4/ARNT2 disrupt function.
a novel NXF signaling system on neural gene promoter may be a molecular target of the adverse effects of Sim2 in the mental retardation of Down's syndrome
Title: Identification of a novel basic helix-loop-helix-PAS factor, NXF, reveals a Sim2 competitive, positive regulatory role in dendritic-cytoskeleton modulator drebrin gene expression.

Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

NHGRI GWAS Catalog

Description
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. NHGRI GWA Catalog NHGRI GWA CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Homology

Homologs of the NPAS4 gene: The NPAS4 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 276 organisms have orthologs with human gene NPAS4
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
RNA polymerase II proximal promoter sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein heterodimerization activity	IDA Inferred from Direct Assay more info	PubMed
protein-containing complex binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
cell differentiation	IEA Inferred from Electronic Annotation more info
cellular response to corticosterone stimulus	IEA Inferred from Electronic Annotation more info
excitatory postsynaptic potential	ISS Inferred from Sequence or Structural Similarity more info
inhibitory postsynaptic potential	ISS Inferred from Sequence or Structural Similarity more info
inhibitory synapse assembly	ISS Inferred from Sequence or Structural Similarity more info
learning	ISS Inferred from Sequence or Structural Similarity more info
long-term memory	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
regulation of synaptic plasticity	ISS Inferred from Sequence or Structural Similarity more info
regulation of synaptic transmission, GABAergic	ISS Inferred from Sequence or Structural Similarity more info
regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
short-term memory	ISS Inferred from Sequence or Structural Similarity more info
social behavior	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
nuclear chromatin	ISA Inferred from Sequence Alignment more info
nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
postsynapse	IEA Inferred from Electronic Annotation more info
transcription factor complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
transcription factor complex	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: neuronal PAS domain-containing protein 4

Names: HLH-PAS transcription factor NXF; PAS domain-containing protein 10; class E basic helix-loop-helix protein 79; neuronal PAS4

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_001318804.1 → NP_001305733.1 neuronal PAS domain-containing protein 4 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AK094025, AK096253, BC143630

UniProtKB/Swiss-Prot

Q8IUM7
NM_178864.4 → NP_849195.2 neuronal PAS domain-containing protein 4 isoform 1

See identical proteins and their annotated locations for NP_849195.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AB049469, AK096253, AP001107

Consensus CDS

CCDS8138.1

UniProtKB/Swiss-Prot

Q8IUM7

Related

ENSP00000311196.2, ENST00000311034.7

Conserved Domains (4) summary

smart00091
Location:72 → 135

PAS; PAS domain

cd00130
Location:214 → 294

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 ...

pfam08447
Location:95 → 188

PAS_3; PAS fold

pfam14598
Location:217 → 319

PAS_11; PAS domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p13 Primary Assembly

Range

66408922..66426707

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017017537.1 → XP_016873026.1 neuronal PAS domain-containing protein 4 isoform X1
XM_017017539.1 → XP_016873028.1 neuronal PAS domain-containing protein 4 isoform X3

UniProtKB/Swiss-Prot

Q8IUM7

Related

ENSP00000433135.1, ENST00000525148.1

Conserved Domains (2) summary

smart00353
Location:10 → 52

HLH; helix loop helix domain

smart00091
Location:72 → 135

PAS; PAS domain
XM_017017538.1 → XP_016873027.1 neuronal PAS domain-containing protein 4 isoform X2