Human Gene NPAS4 (ENST00000311034.7) from GENCODE V44
  Description: Homo sapiens neuronal PAS domain protein 4 (NPAS4), transcript variant 1, mRNA. (from RefSeq NM_178864)
RefSeq Summary (NM_178864): 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].
Gencode Transcript: ENST00000311034.7
Gencode Gene: ENSG00000174576.11
Transcript (Including UTRs)
   Position: hg38 chr11:66,421,035-66,426,707 Size: 5,673 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr11:66,421,180-66,425,989 Size: 4,810 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr11:66,421,035-66,426,707)mRNA (may differ from genome)Protein (802 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Neuronal PAS domain-containing protein 4; Short=Neuronal PAS4; AltName: Full=Class E basic helix-loop-helix protein 79; Short=bHLHe79; AltName: Full=HLH-PAS transcription factor NXF; AltName: Full=PAS domain-containing protein 10;
FUNCTION: Acts as a transcriptional activator in the presence of ARNT. Can activate the CME (CNS midline enhancer) element and the expression of the drebrin gene.
SUBUNIT: Efficient DNA binding requires dimerization with another bHLH protein. Forms a heterodimer with ARNT.
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
SIMILARITY: Contains 1 PAC (PAS-associated C-terminal) domain.
SIMILARITY: Contains 2 PAS (PER-ARNT-SIM) domains.
SEQUENCE CAUTION: Sequence=BAC04271.1; Type=Frameshift; Positions=681;

-  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

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.11 RPKM in Pituitary
Total median expression: 32.34 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -58.10145-0.401 Picture PostScript Text
3' UTR -315.80718-0.440 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.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011598 - HLH_dom
IPR000014 - PAS
IPR013655 - PAS_fold_3

Pfam Domains:
PF08447 - PAS fold

ModBase Predicted Comparative 3D Structure on Q8IUM7
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001012 RNA polymerase II regulatory region DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0046982 protein heterodimerization activity
GO:0046983 protein dimerization activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007399 nervous system development
GO:0007612 learning
GO:0007614 short-term memory
GO:0007616 long-term memory
GO:0030154 cell differentiation
GO:0032228 regulation of synaptic transmission, GABAergic
GO:0035176 social behavior
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048167 regulation of synaptic plasticity
GO:0060079 excitatory postsynaptic potential
GO:0060080 inhibitory postsynaptic potential
GO:0071386 cellular response to corticosterone stimulus
GO:1904862 inhibitory synapse assembly

Cellular Component:
GO:0005634 nucleus
GO:0005667 transcription factor complex
GO:0098794 postsynapse

-  Descriptions from all associated GenBank mRNAs
  JD079907 - Sequence 60931 from Patent EP1572962.
AK096253 - Homo sapiens cDNA FLJ38934 fis, clone NT2NE2014221.
JD461139 - Sequence 442163 from Patent EP1572962.
JD187211 - Sequence 168235 from Patent EP1572962.
JD104851 - Sequence 85875 from Patent EP1572962.
JD458059 - Sequence 439083 from Patent EP1572962.
JD336707 - Sequence 317731 from Patent EP1572962.
JD070854 - Sequence 51878 from Patent EP1572962.
AB049469 - Homo sapiens mRNA for HLH-PAS transcription factor NXF, complete cds.
BC105001 - Homo sapiens neuronal PAS domain protein 4, mRNA (cDNA clone MGC:132661 IMAGE:8144004), complete cds.
BC105003 - Homo sapiens neuronal PAS domain protein 4, mRNA (cDNA clone MGC:132663 IMAGE:8144006), complete cds.
BC143630 - Homo sapiens neuronal PAS domain protein 4, mRNA (cDNA clone IMAGE:9052143), complete cds.
EU446888 - Synthetic construct Homo sapiens clone IMAGE:100070090; IMAGE:100012097; FLH257553.01L neuronal PAS domain protein 4 (NPAS4) gene, encodes complete protein.
AK094025 - Homo sapiens cDNA FLJ36706 fis, clone UTERU2009483.
AX748416 - Sequence 1941 from Patent EP1308459.
JD510961 - Sequence 491985 from Patent EP1572962.
JD406087 - Sequence 387111 from Patent EP1572962.
JD113890 - Sequence 94914 from Patent EP1572962.
JD383575 - Sequence 364599 from Patent EP1572962.
JD190044 - Sequence 171068 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BHLHE79, ENST00000311034.1, ENST00000311034.2, ENST00000311034.3, ENST00000311034.4, ENST00000311034.5, ENST00000311034.6, NM_178864, NPAS4_HUMAN, NXF, PASD10, Q8IUM7, Q8N8S5, Q8N9Q9, uc001ohx.1, uc001ohx.2, uc001ohx.3
UCSC ID: ENST00000311034.7
RefSeq Accession: NM_178864
Protein: Q8IUM7 (aka NPAS4_HUMAN)
CCDS: CCDS8138.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.