Mouse Gene Smyd1 (ENSMUST00000074301.9) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus SET and MYND domain containing 1 (Smyd1), transcript variant 1, mRNA. (from RefSeq NM_001160127)
Gencode Transcript: ENSMUST00000074301.9
Gencode Gene: ENSMUSG00000055027.17
Transcript (Including UTRs)
   Position: mm10 chr6:71,213,940-71,262,281 Size: 48,342 Total Exon Count: 10 Strand: -
Coding Region
   Position: mm10 chr6:71,215,751-71,262,204 Size: 46,454 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:71,213,940-71,262,281)mRNA (may differ from genome)Protein (490 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedSOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SMYD1_MOUSE
DESCRIPTION: RecName: Full=SET and MYND domain-containing protein 1; AltName: Full=CD8b-opposite; AltName: Full=Zinc finger protein BOP; Short=m-BOP;
FUNCTION: Acts as a transcriptional repressor. Essential for cardiomyocyte differentiation and cardiac morphogenesis.
SUBUNIT: Interacts with HDAC1, HDAC2 and HDAC3.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Expressed in cardiac and skeletal muscle, lymphocytes and thymus.
SIMILARITY: Contains 1 MYND-type zinc finger.
SIMILARITY: Contains 1 SET domain.
SEQUENCE CAUTION: Sequence=AAC53021.2; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAC53022.2; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -21.0077-0.273 Picture PostScript Text
3' UTR -541.801811-0.299 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
IPR001214 - SET_dom
IPR002893 - Znf_MYND

Pfam Domains:
PF00856 - SET domain
PF01753 - MYND finger

SCOP Domains:
48452 - TPR-like
82199 - SET domain
144232 - HIT/MYND zinc finger-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3N71 - X-ray


ModBase Predicted Comparative 3D Structure on P97443
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsembl   
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0016740 transferase activity
GO:0018024 histone-lysine N-methyltransferase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007507 heart development
GO:0010831 positive regulation of myotube differentiation
GO:0032259 methylation
GO:0034968 histone lysine methylation
GO:0035914 skeletal muscle cell differentiation
GO:0045663 positive regulation of myoblast differentiation
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  U76371 - Mus musculus t-BOP (Bop) mRNA, complete cds.
BC076601 - Mus musculus SET and MYND domain containing 1, mRNA (cDNA clone MGC:100109 IMAGE:30609878), complete cds.
AK142252 - Mus musculus 13 days embryo heart cDNA, RIKEN full-length enriched library, clone:D330022G08 product:SET and MYND domain containing 1, full insert sequence.
AK142153 - Mus musculus 13 days embryo heart cDNA, RIKEN full-length enriched library, clone:D330002H11 product:SET and MYND domain containing 1, full insert sequence.
AK076266 - Mus musculus 0 day neonate skin cDNA, RIKEN full-length enriched library, clone:4632404M21 product:ZINC-FINGER PROTEIN BOP, full insert sequence.
U76373 - Mus musculus skm-BOP1 (Bop) mRNA, complete cds.
U76374 - Mus musculus skm-BOP2 (Bop) mRNA, complete cds.
AK027936 - Mus musculus 18-day embryo whole body cDNA, RIKEN full-length enriched library, clone:1110025H03 product:hypothetical protein, full insert sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: Bop, NM_001160127, P97442, P97443, P97444, Q6DFW7, SMYD1_MOUSE, uc009cgj.1, uc009cgj.2
UCSC ID: uc009cgj.2
RefSeq Accession: NM_001160127
Protein: P97443 (aka SMYD1_MOUSE or SMY1_MOUSE)
CCDS: CCDS20227.2, CCDS51805.1

-  Gene Model Information
  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.