Human Gene MYOD1 (uc001mni.3) Description and Page Index
  Description: Homo sapiens myogenic differentiation 1 (MYOD1), mRNA.
RefSeq Summary (NM_002478): This gene encodes a nuclear protein that belongs to the basic helix-loop-helix family of transcription factors and the myogenic factors subfamily. It regulates muscle cell differentiation by inducing cell cycle arrest, a prerequisite for myogenic initiation. The protein is also involved in muscle regeneration. It activates its own transcription which may stabilize commitment to myogenesis. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: X56677.1, X17650.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA2153307, SAMEA2162946 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000250003.4/ ENSP00000250003.3 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr11:17,741,110-17,743,678 Size: 2,569 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr11:17,741,330-17,743,055 Size: 1,726 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:17,741,110-17,743,678)mRNA (may differ from genome)Protein (320 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: MYOD1_HUMAN
DESCRIPTION: RecName: Full=Myoblast determination protein 1; AltName: Full=Class C basic helix-loop-helix protein 1; Short=bHLHc1; AltName: Full=Myogenic factor 3; Short=Myf-3;
FUNCTION: Involved in muscle differentiation (myogenic factor). Induces fibroblasts to differentiate into myoblasts. Activates muscle-specific promoters. Interacts with and is inhibited by the twist protein. This interaction probably involves the basic domains of both proteins (By similarity).
SUBUNIT: Efficient DNA binding requires dimerization with another bHLH protein. Seems to form active heterodimers with ITF-2. Interacts with SUV39H1 and CDK9. Interacts with DDX5 (By similarity).
INTERACTION: P15923-1:TCF3; NbExp=2; IntAct=EBI-488878, EBI-769645;
SUBCELLULAR LOCATION: Nucleus.
PTM: Phosphorylated by CDK9. This phosphorylation promotes its function in muscle differentiation.
PTM: Acetylated by a complex containing EP300 and PCAF. The acetylation is essential to activate target genes. Conversely, its deacetylation by SIRT1 inhibits its function (By similarity).
PTM: Ubiquitinated on the N-terminus; which is required for proteasomal degradation.
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
WEB RESOURCE: Name=Wikipedia; Note=MyoD entry; URL="http://en.wikipedia.org/wiki/MyoD";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): MYOD1
CDC HuGE Published Literature: MYOD1

-  MalaCards Disease Associations
  MalaCards Gene Search: MYOD1
Diseases sorted by gene-association score: pleomorphic rhabdomyosarcoma (32), skeletal muscle regeneration (27), spindle cell rhabdomyosarcoma (25), skeletal muscle cancer (25), botryoid rhabdomyosarcoma (25), gallbladder sarcoma (23), horner's syndrome (22), malignant fibrous histiocytoma of bone (21), embryonal rhabdomyosarcoma (20), alveolar soft-part sarcoma (16), rhabdomyosarcoma 2, alveolar (12), rhabdomyosarcoma (12), rhabdoid cancer (11), adult fibrosarcoma (10), extraosseous ewing's sarcoma (10), breast rhabdomyosarcoma (10), malignant mesenchymoma (9), hemophagocytic lymphohistiocytosis, familial, 1 (9), central nervous system mesenchymal non-meningothelial tumor (9), oculopharyngeal muscular dystrophy (9), undifferentiated embryonal sarcoma of the liver (9), spindle cell liposarcoma (8), prostate embryonal rhabdomyosarcoma (8), mesenchymoma (8), embryonal sarcoma (8), muscle cancer (8), conventional leiomyosarcoma (7), malignant triton tumor (7), inflammatory leiomyosarcoma (7), nephrogenic adenofibroma (6), cervical polyp (6), desmoplastic small round cell tumor (6), histiocytoma (6), muscle hypertrophy (6), malignant fibroxanthoma (5), prostate rhabdomyosarcoma (5), congenital muscular dystrophy due to lmna mutation (5), gas gangrene (5), mesenchymal cell neoplasm (5), medullomyoblastoma (4), myositis (3), myopathy (3), beckwith-wiedemann syndrome (2), wilms tumor susceptibility-5 (1), muscle tissue disease (1), facioscapulohumeral muscular dystrophy 1 (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.97 RPKM in Muscle - Skeletal
Total median expression: 10.65 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 -92.30220-0.420 Picture PostScript Text
3' UTR -242.52623-0.389 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
IPR002546 - Basic
IPR011598 - HLH_dom
IPR022032 - Myf5

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain
PF01586 - Myogenic Basic domain
PF12232 - Myogenic determination factor 5

SCOP Domains:
47459 - HLH, helix-loop-helix DNA-binding domain

ModBase Predicted Comparative 3D Structure on P15172
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
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
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:0001047 core promoter binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding
GO:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0008134 transcription factor binding
GO:0019899 enzyme binding
GO:0031490 chromatin DNA binding
GO:0031625 ubiquitin protein ligase binding
GO:0035257 nuclear hormone receptor binding
GO:0043565 sequence-specific DNA binding
GO:0046982 protein heterodimerization activity
GO:0046983 protein dimerization activity
GO:0070888 E-box binding
GO:1990841 promoter-specific chromatin binding

Biological Process:
GO:0000381 regulation of alternative mRNA splicing, via spliceosome
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:0006468 protein phosphorylation
GO:0007275 multicellular organism development
GO:0007517 muscle organ development
GO:0007518 myoblast fate determination
GO:0007519 skeletal muscle tissue development
GO:0007520 myoblast fusion
GO:0009267 cellular response to starvation
GO:0010468 regulation of gene expression
GO:0014902 myotube differentiation
GO:0014904 myotube cell development
GO:0014908 myotube differentiation involved in skeletal muscle regeneration
GO:0030154 cell differentiation
GO:0035914 skeletal muscle cell differentiation
GO:0042693 muscle cell fate commitment
GO:0043415 positive regulation of skeletal muscle tissue regeneration
GO:0043484 regulation of RNA splicing
GO:0043503 skeletal muscle fiber adaptation
GO:0043966 histone H3 acetylation
GO:0043967 histone H4 acetylation
GO:0045445 myoblast differentiation
GO:0045663 positive regulation of myoblast differentiation
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048741 skeletal muscle fiber development
GO:0048743 positive regulation of skeletal muscle fiber development
GO:0051146 striated muscle cell differentiation
GO:0051149 positive regulation of muscle cell differentiation
GO:0071356 cellular response to tumor necrosis factor
GO:0071385 cellular response to glucocorticoid stimulus
GO:0071392 cellular response to estradiol stimulus
GO:0071453 cellular response to oxygen levels
GO:1901741 positive regulation of myoblast fusion
GO:1905382 positive regulation of snRNA transcription from RNA polymerase II promoter
GO:2000818 negative regulation of myoblast proliferation

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016604 nuclear body
GO:0030016 myofibril


-  Descriptions from all associated GenBank mRNAs
  LP895802 - Sequence 666 from Patent EP3253886.
AK314968 - Homo sapiens cDNA, FLJ95884, highly similar to Homo sapiens myogenic factor 3 (MYOD1), mRNA.
BC000353 - Homo sapiens cDNA clone IMAGE:2961494, **** WARNING: chimeric clone ****.
DD153960 - New method.
JD096789 - Sequence 77813 from Patent EP1572962.
JD084715 - Sequence 65739 from Patent EP1572962.
JD075892 - Sequence 56916 from Patent EP1572962.
DD153961 - New method.
JD470083 - Sequence 451107 from Patent EP1572962.
JD317914 - Sequence 298938 from Patent EP1572962.
JD445557 - Sequence 426581 from Patent EP1572962.
X56677 - Human MyoD mRNA.
JD174507 - Sequence 155531 from Patent EP1572962.
BC064493 - Homo sapiens myogenic differentiation 1, mRNA (cDNA clone MGC:71135 IMAGE:5022419), complete cds.
JD459143 - Sequence 440167 from Patent EP1572962.
JD500355 - Sequence 481379 from Patent EP1572962.
AB463907 - Synthetic construct DNA, clone: pF1KB7631, Homo sapiens MYOD1 gene for myogenic differentiation 1, without stop codon, in Flexi system.
BT007157 - Homo sapiens myogenic factor 3 mRNA, complete cds.
KJ891665 - Synthetic construct Homo sapiens clone ccsbBroadEn_01059 MYOD1 gene, encodes complete protein.
JB759091 - Sequence 16 from Patent WO2013102203.
X17650 - Human Myf-3 mRNA for myogenic determining factor 3'-fragment.
JD380190 - Sequence 361214 from Patent EP1572962.
JD146320 - Sequence 127344 from Patent EP1572962.
JD139469 - Sequence 120493 from Patent EP1572962.
JD466990 - Sequence 448014 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_MITRPathway - Signal Dependent Regulation of Myogenesis by Corepressor MITR
h_hdacPathway - Control of skeletal myogenesis by HDAC & calcium/calmodulin-dependent kinase (CaMK)

Reactome (by CSHL, EBI, and GO)

Protein P15172 (Reactome details) participates in the following event(s):

R-HSA-448962 Heterodimerization of E proteins with Myod
R-HSA-448963 Interaction of MyoD:E protein with MEF2
R-HSA-375170 CDO in myogenesis
R-HSA-525793 Myogenesis
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: BHLHC1, MYF3, MYOD, MYOD1_HUMAN, NM_002478, NP_002469, O75321, P15172
UCSC ID: uc001mni.3
RefSeq Accession: NM_002478
Protein: P15172 (aka MYOD1_HUMAN)
CCDS: CCDS7826.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002478.4
exon count: 3CDS single in 3' UTR: no RNA size: 1823
ORF size: 963CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2123.00frame shift in genome: no % Coverage: 99.07
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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