NPAS2 neuronal PAS domain protein 2 [Homo sapiens] - Gene

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Summary

Official Symbol: NPAS2provided by HGNC
Official Full Name: neuronal PAS domain protein 2provided by HGNC
Primary source: HGNC:7895
See related: Ensembl:ENSG00000170485; HPRD:09137; MIM:603347; Vega:OTTHUMG00000130675
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MOP4; PASD4; bHLHe9; FLJ23138; MGC71151
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, Jul 2008]

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Genomic context

Location :: 2q11.2

Sequence :: Chromosome: 2; NC_000002.11 (101436613..101613287)

See NPAS2 in Epigenomics, MapViewer

Chromosome 2 - NC_000002.11 Genomic Context describing neighboring genes

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Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

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Bibliography

GeneRIFs: Gene References Into Functions What's a GeneRIF?

Convergent functional genomics allowed the identification of novel candidate genes, GRIK2 and NPAS2, involved in glutamatergic neurotransmission and the circadian rhythm, respectively, that are potentially associated with CFS.
Title: Convergent genomic studies identify association of GRIK2 and NPAS2 with chronic fatigue syndrome.
found a novel functional SNP (rs3739008) located at 3'UTR of NPAS2 and the C to T changing of the SNP may disrupt the binding of microRNA- (miR-) 17-5p and miR-519e to the 3'UTR of NPAS2
Title: A variant affecting miRNAs binding in the circadian gene Neuronal PAS domain protein 2 (NPAS2) is not associated with breast cancer risk.
ARNTL and NPAS2 SNPs were associated with reproduction and with seasonal variation.
Title: ARNTL (BMAL1) and NPAS2 gene variants contribute to fertility and seasonality.
Data demonstrate that NPAS2 is also a RORalpha and REV-ERBalpha target gene.
Title: Characterization of the core mammalian clock component, NPAS2, as a REV-ERBalpha/RORalpha target gene.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
A high level of NPAS2 expression was strongly associated with improved disease free survival & overall survival. The Ala/Ala, Ala/Thr, & Thr/Thr genotypes were also differentially distributed by tumor severity, as measured by TNM classification.
Title: The circadian gene NPAS2 is a novel prognostic biomarker for breast cancer.
Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Novel breast cancer risk alleles and interaction with ionizing radiation among U.S. radiologic technologists.
The 1st list of direct transcriptional targets of NPAS2 comprises 26 genes that contain potential NPAS2 binding regions, 9 of which are involved in tumorigenesis.
Title: Cancer-related transcriptional targets of the circadian gene NPAS2 identified by genome-wide ChIP-on-chip analysis.
Variations in circadian genes are associated with serum levels of androgens and IGF markers, particularly NPAS2 rs2305160:G>A(Ala394Thr).
Title: Correlation between circadian gene variants and serum levels of sex steroids and insulin-like growth factor-I.
knockdown of NPAS2 significantly represses the expression of several cell cycle and DNA repair genes in breast and colorectal neoplasms.
Title: The circadian gene NPAS2, a putative tumor suppressor, is involved in DNA damage response.

Submit: New GeneRIF Correction See all (17)

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Phenotypes

Review eQTL and phenotype association data in this region using PheGenI

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Products	Interactant	Other Gene	Source	Pubs	Description
Q99743	O00327	ARNTL	HPRD	PubMed
Q99743	Q92793	CREBBP	HPRD	PubMed
Q99743	Q09472	EP300	HPRD	PubMed
Q99743	P07900	HSP90AA1	HPRD	PubMed
Q99743	Q92831	KAT2B	HPRD	PubMed
Q99743	Q9Y6Q9	NCOA3	HPRD	PubMed
Q99743	P10276	RARA	HPRD	PubMed
Q99743	P19793	RXRA	HPRD	PubMed
BioGRID:110923	BioGRID:106899	ARNTL	BioGRID	PubMed	Reconstituted Complex; Two-hybrid
BioGRID:110923	BioGRID:107777	CREBBP	BioGRID	PubMed	Reconstituted Complex
BioGRID:110923	BioGRID:108347	EP300	BioGRID	PubMed	Reconstituted Complex
BioGRID:110923	BioGRID:114347	HESX1	BioGRID	PubMed	Two-hybrid
BioGRID:110923	BioGRID:109552	HSP90AA1	BioGRID	PubMed	Reconstituted Complex
BioGRID:110923	BioGRID:114375	KAT2B	BioGRID	PubMed	Reconstituted Complex
BioGRID:110923	BioGRID:113841	NCOA3	BioGRID	PubMed	Reconstituted Complex
BioGRID:110923	BioGRID:111849	RARA	BioGRID	PubMed	Reconstituted Complex; Two-hybrid
BioGRID:110923	BioGRID:127708	RHOXF1	BioGRID	PubMed	Two-hybrid
BioGRID:110923	BioGRID:112168	RXRA	BioGRID	PubMed	Reconstituted Complex; Two-hybrid
BioGRID:110923	BioGRID:129825	ZSCAN1	BioGRID	PubMed	Two-hybrid

Function	Evidence Code	Pubs
DNA binding	IPI Inferred from Physical Interaction more info	PubMed
Hsp90 protein binding	IDA Inferred from Direct Assay more info	PubMed
sequence-specific DNA binding transcription factor activity	IEA Inferred from Electronic Annotation more info
signal transducer activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
cellular lipid metabolic process	TAS Traceable Author Statement more info
central nervous system development	TAS Traceable Author Statement more info	PubMed
positive regulation of transcription from RNA polymerase II promoter	IGI Inferred from Genetic Interaction more info	PubMed
regulation of transcription, DNA-dependent	TAS Traceable Author Statement more info	PubMed
rhythmic process	IEA Inferred from Electronic Annotation more info
small molecule metabolic process	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
cytosol	TAS Traceable Author Statement more info
nucleus	IEA Inferred from Electronic Annotation more info
transcription factor complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

Preferred Names: neuronal PAS domain-containing protein 2

Names: neuronal PAS domain-containing protein 2; neuronal PAS2; member of PAS protein 4; member of PAS superfamily 4; PAS domain-containing protein 4; basic-helix-loop-helix-PAS protein MOP4; class E basic helix-loop-helix protein 9

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NCBI Reference Sequences (RefSeq)

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.

Genomic

NG_023259.1 RefSeqGene

Range

5001..181675

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_002518.3 → NP_002509.2 neuronal PAS domain-containing protein 2

Status: REVIEWED

Source sequence(s)

AK095806, AK128586, BC072383, BM724652, U77970

Consensus CDS

CCDS2048.1

UniProtKB/TrEMBL

A2I2P5

UniProtKB/Swiss-Prot

Q99743

Related

ENSP00000338283, OTTHUMP00000161260, ENST00000335681, OTTHUMT00000253168

Conserved Domains (4) summary

cd00083
Location:7 – 61
Blast Score: 121

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
Blast Score: 166

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 ...

pfam00989
Location:84 – 195
Blast Score: 150

PAS; PAS fold

pfam08447
Location:261 – 348
Blast Score: 160

PAS_3; PAS fold

RefSeqs of Annotated Genomes: Build 37.3

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

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000002.11 Reference GRCh37.p5 Primary Assembly

Range

101436613..101613287

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000134.1 Alternate HuRef

Range

95284890..95377330

Download

GenBank, FASTA, Sequence Viewer (Graphics)

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Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AC016738.6	AAY14822.1
genomic	AC092168.4 (145145..199870)	None
genomic	AC106891.3	AAX88966.1
genomic	CH471127.2	EAX01830.1
		EAX01831.1
		EAX01832.1
		EAX01833.1
		EAX01834.1
		EAX01835.1
genomic	EF015903.1	ABM64214.1
mRNA	AK026791.1	BAB15554.1
mRNA	AK091939.1	None
mRNA	AK095806.1	None
mRNA	AK128586.1	None
mRNA	AK226093.1	None
mRNA	AK294733.1	BAH11862.1
mRNA	BC028107.1	AAH28107.1
mRNA	BC035412.1	None
mRNA	BC051351.1	AAH51351.2
mRNA	BC072383.1	AAH72383.1
mRNA	BM724652.1	None
mRNA	BX640699.1	None
mRNA	U51625.1	AAC51211.1
mRNA	U77970.1	AAB47250.1