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
HGNCHPRDLynxMGIneXtProtOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NPAS4_HUMAN
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.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Brain.
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
 

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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
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-  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     
MGIRGDEnsemblEnsemblWormBase 
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 
AlignmentAlignmentAlignmentAlignmentAlignment 

-  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.