Human Gene MYCN (ENST00000281043.4) from GENCODE V44
  Description: Homo sapiens MYCN proto-oncogene, bHLH transcription factor (MYCN), transcript variant 2, mRNA. (from RefSeq NM_005378)
RefSeq Summary (NM_001293233): This gene is a member of the MYC family and encodes a protein with a basic helix-loop-helix (bHLH) domain. This protein is located in the nucleus and must dimerize with another bHLH protein in order to bind DNA. Amplification of this gene is associated with a variety of tumors, most notably neuroblastomas. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2014].
Gencode Transcript: ENST00000281043.4
Gencode Gene: ENSG00000134323.13
Transcript (Including UTRs)
   Position: hg38 chr2:15,940,550-15,947,004 Size: 6,455 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg38 chr2:15,942,065-15,946,097 Size: 4,033 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:15,940,550-15,947,004)mRNA (may differ from genome)Protein (464 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MYCN_HUMAN
DESCRIPTION: RecName: Full=N-myc proto-oncogene protein; AltName: Full=Class E basic helix-loop-helix protein 37; Short=bHLHe37;
FUNCTION: May function as a transcription factor.
SUBUNIT: Efficient DNA binding requires dimerization with another bHLH protein. Binds DNA as a heterodimer with MAX. Interacts with KDM5A, KDM5B and HUWE1.
INTERACTION: O14965:AURKA; NbExp=2; IntAct=EBI-878369, EBI-448680; Q13287:NMI; NbExp=3; IntAct=EBI-878369, EBI-372942; Q96EB6:SIRT1; NbExp=3; IntAct=EBI-878369, EBI-1802965;
SUBCELLULAR LOCATION: Nucleus.
DEVELOPMENTAL STAGE: Expressed during fetal development.
DISEASE: Note=Amplification of the N-MYC gene is associated with a variety of human tumors, most frequently neuroblastoma, where the level of amplification appears to increase as the tumor progresses.
DISEASE: Defects in MYCN are the cause of Feingold syndrome type 1 (FGLDS1) [MIM:164280]. A syndrome characterized by variable combinations of esophageal and duodenal atresias, microcephaly, learning disability, mental retardation, and limb malformations. Cardiac and renal malformations, vertebral anomalies, and deafness have also been described.
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
SEQUENCE CAUTION: Sequence=AAA36371.1; Type=Erroneous initiation; Sequence=CAA68678.1; Type=Erroneous initiation;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/NMYC112.html";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/MYCN";

-  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: MYCN
Diseases sorted by gene-association score: feingold syndrome 1* (1711), neuroblastoma* (43), cerebral primitive neuroectodermal tumor (23), childhood medulloblastoma (22), autonomic nervous system neoplasm (20), peripheral nervous system neoplasm (20), familial retinoblastoma* (20), non-hereditary retinoblastoma* (18), nodular ganglioneuroblastoma (16), askin's tumor (16), ganglioneuroblastoma (15), desmoplastic infantile ganglioglioma (13), bilateral retinoblastoma (12), charcot-marie-tooth disease, type 4d (12), ganglioneuroma (11), rhabdomyosarcoma 2, alveolar (11), cervical neuroblastoma (11), extracranial neuroblastoma (11), embryonal rhabdomyosarcoma (10), adrenal neuroblastoma (9), nervous system cancer (8), esophageal atresia (8), medulloblastoma (8), brain cancer (7), infratentorial cancer (7), ewing sarcoma (6), tracheoesophageal fistula (6), differentiating neuroblastoma (6), mismatch repair cancer syndrome (6), bone ewing's sarcoma (5), choriocarcinoma of the testis (5), phelan-mcdermid syndrome (4), charcot-marie-tooth disease, type 1d (4), pericardium cancer (4), rhabdomyosarcoma (4), medullomyoblastoma (4), adult medulloblastoma (3), extraosseous ewing's sarcoma (3), lung cancer (2), wilms tumor susceptibility-5 (2), neuropathy, congenital hypomyelinating (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D004997 Ethinyl Estradiol
  • D014212 Tretinoin
  • C017947 sodium arsenite
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • C085911 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one
  • C009505 4,4'-diaminodiphenylmethane
  • C558529 9-(6-aminopyridin-3-yl)-1-(3-(trifluoromethyl)phenyl)benzo(h)(1,6)naphthyridin-2(1H)-one
  • D000082 Acetaminophen
  • D000643 Ammonium Chloride
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.17 RPKM in Testis
Total median expression: 36.98 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 -144.50311-0.465 Picture PostScript Text
3' UTR -236.90907-0.261 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
IPR002418 - Tscrpt_reg_Myc
IPR012682 - Tscrpt_reg_Myc_N

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain
PF01056 - Myc amino-terminal region

ModBase Predicted Comparative 3D Structure on P04198
FrontTopSide
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 BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  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:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0019900 kinase binding
GO:0046983 protein dimerization activity

Biological Process:
GO:0001502 cartilage condensation
GO:0002053 positive regulation of mesenchymal cell proliferation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0008284 positive regulation of cell proliferation
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0010942 positive regulation of cell death
GO:0030324 lung development
GO:0042733 embryonic digit morphogenesis
GO:0045607 regulation of auditory receptor cell differentiation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048704 embryonic skeletal system morphogenesis
GO:0048712 negative regulation of astrocyte differentiation
GO:0048754 branching morphogenesis of an epithelial tube
GO:1903800 positive regulation of production of miRNAs involved in gene silencing by miRNA
GO:2000378 negative regulation of reactive oxygen species metabolic process

Cellular Component:
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  M55330 - Human RNase A-resistant RNA duplexes mRNAs.
AK298225 - Homo sapiens cDNA FLJ51262 complete cds, highly similar to N-myc proto-oncogene protein.
AF320053 - Homo sapiens N-MYC mRNA, complete cds.
AK299495 - Homo sapiens cDNA FLJ59229 complete cds, highly similar to Homo sapiens v-myc myelocytomatosis viral related oncogene, neuroblastoma derived, mRNA.
BC002712 - Homo sapiens v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian), mRNA (cDNA clone MGC:3962 IMAGE:3627330), complete cds.
JD142242 - Sequence 123266 from Patent EP1572962.
JD179906 - Sequence 160930 from Patent EP1572962.
AB464743 - Synthetic construct DNA, clone: pF1KB8396, Homo sapiens MYCN gene for v-myc myelocytomatosis viral related oncogene, neuroblastoma derived, without stop codon, in Flexi system.
BT007384 - Homo sapiens v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) mRNA, complete cds.
CQ873769 - Sequence 188 from Patent WO2004076622.
DD413606 - Regulation of Mammalian Cells.
JD348297 - Sequence 329321 from Patent EP1572962.
JD223114 - Sequence 204138 from Patent EP1572962.
JD134727 - Sequence 115751 from Patent EP1572962.
JD133238 - Sequence 114262 from Patent EP1572962.
JD239191 - Sequence 220215 from Patent EP1572962.
JD083767 - Sequence 64791 from Patent EP1572962.
JD060923 - Sequence 41947 from Patent EP1572962.
JD083560 - Sequence 64584 from Patent EP1572962.
JD563643 - Sequence 544667 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BHLHE37, ENST00000281043.1, ENST00000281043.2, ENST00000281043.3, MYCN_HUMAN, NMYC, NM_005378, P04198, Q6LDT9, uc002rci.1, uc002rci.2, uc002rci.3, uc002rci.4, uc002rci.5
UCSC ID: ENST00000281043.4
RefSeq Accession: NM_001293233
Protein: P04198 (aka MYCN_HUMAN)
CCDS: CCDS1687.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene MYCN:
feingold (Feingold Syndrome 1)

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