Human Gene NPAS3 (ENST00000356141.9_5) from GENCODE V47lift37

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Description: neuronal PAS domain protein 3, transcript variant 1 (from RefSeq NM_001164749.2)
Gencode Transcript: ENST00000356141.9_5
Gencode Gene: ENSG00000151322.20_20
Transcript (Including UTRs)
Position: hg19 chr14:33,408,085-34,273,379 Size: 865,295 Total Exon Count: 12 Strand: +
Coding Region
Position: hg19 chr14:33,408,523-34,270,315 Size: 861,793 Coding Exon Count: 12

Page Index	Sequence and Links	Primers	MalaCards	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Other Species	mRNA Descriptions	Other Names
Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr14:33,408,085-34,273,379)			mRNA (may differ from genome)		Protein (933 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Human Cortex Gene Expression	Malacards	MGI	OMIM	PubMed
UniProtKB	Wikipedia	BioGrid CRISPR DB

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: NPAS3 Diseases sorted by gene-association score: holoprosencephaly 8 (12), schizophrenia (11), learning disability (8)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D013749 Tetrachlorodibenzodioxin C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone D001564 Benzo(a)pyrene D002794 Choline D003375 Coumestrol D004958 Estradiol D005492 Folic Acid D006830 Hydralazine D008715 Methionine D014635 Valproic Acid more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 5.60 RPKM in Brain - Amygdala Total median expression: 56.48 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-234.60	438	-0.536	Picture	PostScript	Text
3' UTR	-733.60	3064	-0.239	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details
Gene Sorter

Descriptions from all associated GenBank mRNAs


	AY157302 - Homo sapiens neuronal PAS3 transcript variant 1 (NPAS3) mRNA, complete cds. AF164438 - Homo sapiens basic-helix-loop-helix-PAS protein (MOP6) mRNA, complete cds. AB054575 - Homo sapiens mRNA for NPAS3 (MOP6), complete cds. AB463928 - Synthetic construct DNA, clone: pF1KB9765, Homo sapiens NPAS3 gene for neuronal PAS domain protein 3, without stop codon, in Flexi system. KJ534893 - Homo sapiens clone NPAS3_iso-F_adult-A01 neuronal PAS domain protein 3 isoform F (NPAS3) mRNA, partial cds, alternatively spliced. KJ534894 - Homo sapiens clone NPAS3_iso-A_adult-A04 neuronal PAS domain protein 3 isoform A (NPAS3) mRNA, partial cds, alternatively spliced. KJ534895 - Homo sapiens clone NPAS3_iso-G_adult-A05 neuronal PAS domain protein 3 isoform G (NPAS3) mRNA, partial cds, alternatively spliced. KJ534896 - Homo sapiens clone NPAS3_iso-E_fetal-F05 neuronal PAS domain protein 3 isoform E (NPAS3) mRNA, partial cds, alternatively spliced. KJ534897 - Homo sapiens clone NPAS3_iso-C_fetal-F06 neuronal PAS domain protein 3 isoform C (NPAS3) mRNA, partial cds, alternatively spliced. KJ534898 - Homo sapiens clone NPAS3_iso-D_fetal-F12 neuronal PAS domain protein 3 isoform D (NPAS3) mRNA, partial cds, alternatively spliced. KJ535018 - Homo sapiens clone NPAS3_iso-I_adult-A07 neuronal PAS domain protein 3 isoform I (NPAS3) mRNA, complete cds, alternatively spliced. KJ535019 - Homo sapiens clone NPAS3_iso-B_fetal-F16 neuronal PAS domain protein 3 isoform B (NPAS3) mRNA, complete cds, alternatively spliced. KJ535078 - Homo sapiens clone NPAS3_iso-H_adult-A02 neuronal PAS domain protein 3 isoform H (NPAS3) mRNA, complete cds, alternatively spliced. AB054576 - Homo sapiens NPAS3v mRNA for NPAS3 variant, complete cds. AB055962 - Homo sapiens NPAS3 mRNA, complete cds. BC146317 - Synthetic construct Homo sapiens clone IMAGE:100015245, MGC:180263 neuronal PAS domain protein 3 (NPAS3) mRNA, encodes complete protein. AY157303 - Homo sapiens neuronal PAS3 transcript variant 2 (NPAS3) mRNA, complete cds. AL079281 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 809726. BC035075 - Homo sapiens cDNA clone IMAGE:5260324. JD461037 - Sequence 442061 from Patent EP1572962. JD409923 - Sequence 390947 from Patent EP1572962. JD235299 - Sequence 216323 from Patent EP1572962. JD418655 - Sequence 399679 from Patent EP1572962. JD100217 - Sequence 81241 from Patent EP1572962.

Other Names for This Gene


	Alternate Gene Symbols: ENST00000356141.1, ENST00000356141.2, ENST00000356141.3, ENST00000356141.4, ENST00000356141.5, ENST00000356141.6, ENST00000356141.7, ENST00000356141.8, NM_001164749, NPAS3 , uc317zkq.1, uc317zkq.2, X5D2Q4, X5D2Q4_HUMAN UCSC ID: ENST00000356141.9_5 RefSeq Accession: NM_001164749.2

Gene Model Information


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Methods, Credits, and Use Restrictions


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