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Aliases for SMYD1 Gene

Aliases for SMYD1 Gene

  • SET And MYND Domain Containing 1 2 3
  • SET And MYND Domain-Containing Protein 1 3 4
  • Histone-Lysine N-Methyltransferase SMYD1 3
  • Zinc Finger, MYND Domain Containing 18 3
  • CD8 Beta Opposite 3
  • EC 2.1.1.43 4
  • ZMYND18 3
  • ZMYND22 3
  • KMT3D 3
  • BOP 3

External Ids for SMYD1 Gene

Summaries for SMYD1 Gene

GeneCards Summary for SMYD1 Gene

SMYD1 (SET And MYND Domain Containing 1) is a Protein Coding gene. Diseases associated with SMYD1 include hypoplastic left heart syndrome. Among its related pathways are Heart Development. GO annotations related to this gene include transcription corepressor activity and histone-lysine N-methyltransferase activity. An important paralog of this gene is SMYD2.

UniProtKB/Swiss-Prot for SMYD1 Gene

  • Methylates histone H3 at Lys-4 (H3K4me), seems able to perform both mono-, di-, and trimethylation. Acts as a transcriptional repressor. Essential for cardiomyocyte differentiation and cardiac morphogenesis

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMYD1 Gene

Genomics for SMYD1 Gene

Genomic Location for SMYD1 Gene

Start:
88,067,780 bp from pter
End:
88,113,387 bp from pter
Size:
45,608 bases
Orientation:
Plus strand

Genomic View for SMYD1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SMYD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMYD1 Gene

Regulatory Elements for SMYD1 Gene

Proteins for SMYD1 Gene

  • Protein details for SMYD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NB12-SMYD1_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase SMYD1
    Protein Accession:
    Q8NB12
    Secondary Accessions:
    • A0AV30
    • A6NE13

    Protein attributes for SMYD1 Gene

    Size:
    490 amino acids
    Molecular mass:
    56617 Da
    Quaternary structure:
    • Interacts with HDAC1, HDAC2 and HDAC3. Interacts (via MYND-type zinc finger) with NACA isoform skNAC (By similarity).

neXtProt entry for SMYD1 Gene

Proteomics data for SMYD1 Gene at MOPED

Post-translational modifications for SMYD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SMYD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SMYD1 Gene

Domains for SMYD1 Gene

Gene Families for SMYD1 Gene

HGNC:
  • ZMYND :Zinc fingers, MYND-type
  • KMT :Chromatin-modifying enzymes / K-methyltransferases

Protein Domains for SMYD1 Gene

UniProtKB/Swiss-Prot:

SMYD1_HUMAN
Domain:
  • The SET domain is split between the S-sequence (residues 1-49) and the core SET domain (residues 181-258), however the two segments still come together to form a conserved SET domain fold.:
    • Q8NB12
  • Contains 1 SET domain.:
    • Q8NB12
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.:
    • Q8NB12
Similarity:
  • Contains 1 MYND-type zinc finger.:
    • Q8NB12
genes like me logo Genes that share domains with SMYD1: view

Function for SMYD1 Gene

Molecular function for SMYD1 Gene

UniProtKB/Swiss-Prot CatalyticActivity: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]
UniProtKB/Swiss-Prot Function: Methylates histone H3 at Lys-4 (H3K4me), seems able to perform both mono-, di-, and trimethylation. Acts as a transcriptional repressor. Essential for cardiomyocyte differentiation and cardiac morphogenesis
UniProtKB/Swiss-Prot Induction: By serum response factor SRF and myogenin. SRF binds to the CArG site and MYOG binds to the E-box element on SMYD1 promoter.

Enzyme Numbers (IUBMB) for SMYD1 Gene

Gene Ontology (GO) - Molecular Function for SMYD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003714 transcription corepressor activity IEA --
GO:0005515 protein binding IPI 23455924
GO:0018024 histone-lysine N-methyltransferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SMYD1: view
genes like me logo Genes that share phenotypes with SMYD1: view

Animal Models for SMYD1 Gene

MGI Knock Outs for SMYD1:

miRNA for SMYD1 Gene

miRTarBase miRNAs that target SMYD1

No data available for Transcription Factor Targeting and HOMER Transcription for SMYD1 Gene

Localization for SMYD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMYD1 Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SMYD1 Gene COMPARTMENTS Subcellular localization image for SMYD1 gene
Compartment Confidence
cytosol 2
nucleus 2
extracellular 1

Gene Ontology (GO) - Cellular Components for SMYD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with SMYD1: view

Pathways for SMYD1 Gene

SuperPathways for SMYD1 Gene

Superpath Contained pathways
1 Heart Development
genes like me logo Genes that share pathways with SMYD1: view

Pathways by source for SMYD1 Gene

1 BioSystems pathway for SMYD1 Gene

Gene Ontology (GO) - Biological Process for SMYD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006338 chromatin remodeling IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0007507 heart development IEA --
GO:0010831 positive regulation of myotube differentiation IDA 19783823
GO:0034968 histone lysine methylation IEA --
genes like me logo Genes that share ontologies with SMYD1: view

Transcripts for SMYD1 Gene

Unigene Clusters for SMYD1 Gene

SET and MYND domain containing 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SMYD1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12
SP1: -
SP2: -
SP3:
SP4: - - - - - - - - - - - -

Relevant External Links for SMYD1 Gene

GeneLoc Exon Structure for
SMYD1
ECgene alternative splicing isoforms for
SMYD1

Expression for SMYD1 Gene

mRNA expression in normal human tissues for SMYD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMYD1 Gene

This gene is overexpressed in Muscle - Skeletal (20.4), Heart - Left Ventricle (20.2), and Heart - Atrial Appendage (6.0).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for SMYD1 Gene

SOURCE GeneReport for Unigene cluster for SMYD1 Gene Hs.516176

mRNA Expression by UniProt/SwissProt for SMYD1 Gene

Q8NB12-SMYD1_HUMAN
Tissue specificity: Expression seems mostly restricted to heart and skeletal muscle.
genes like me logo Genes that share expressions with SMYD1: view

Orthologs for SMYD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SMYD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMYD1 36
  • 97.49 (n)
  • 97.1 (a)
SMYD1 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SMYD1 36
  • 92.24 (n)
  • 95.71 (a)
SMYD1 37
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMYD1 36
  • 92.87 (n)
  • 95.81 (a)
SMYD1 37
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smyd1 36
  • 89.45 (n)
  • 94.13 (a)
Smyd1 16
Smyd1 37
  • 94 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMYD1 37
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMYD1 37
  • 88 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smyd1 36
  • 89.59 (n)
  • 94.69 (a)
chicken
(Gallus gallus)
Aves SMYD1 36
  • 78.69 (n)
  • 82.06 (a)
SMYD1 37
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMYD1 37
  • 81 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.1817 36
tropical clawed frog
(Silurana tropicalis)
Amphibia smyd1 36
  • 72.68 (n)
  • 77.49 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.922 36
zebrafish
(Danio rerio)
Actinopterygii CU469500.4 37
  • 61 (a)
OneToMany
smyd1a 37
  • 60 (a)
OneToMany
smyd1b 36
  • 67.63 (n)
  • 64.46 (a)
smyd1b 37
  • 66 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Bzd 37
  • 22 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-10 37
  • 16 (a)
ManyToMany
set-14 37
  • 20 (a)
ManyToMany
set-18 37
  • 19 (a)
ManyToMany
set-30 37
  • 16 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 36 (a)
OneToOne
Species with no ortholog for SMYD1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMYD1 Gene

ENSEMBL:
Gene Tree for SMYD1 (if available)
TreeFam:
Gene Tree for SMYD1 (if available)

Paralogs for SMYD1 Gene

Paralogs for SMYD1 Gene

Selected SIMAP similar genes for SMYD1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with SMYD1: view

Variants for SMYD1 Gene

Sequence variations from dbSNP and Humsavar for SMYD1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type MAF
rs735679 -- 88,098,287(-) AAAAA(A/G)TCTAA intron-variant
rs745293 -- 88,098,180(-) TGAAA(A/C)AAATA intron-variant
rs748226 -- 88,103,229(-) GTTCT(C/T)ACGCC intron-variant
rs750853 -- 88,102,776(+) GTCAG(C/G)TTCTG intron-variant
rs894197 -- 88,103,041(-) AGACA(C/T)ATTGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SMYD1 Gene

Variant ID Type Subtype PubMed ID
dgv61n16 CNV Deletion 17901297
nsv874581 CNV Gain 21882294
nsv834289 CNV Gain 17160897

Relevant External Links for SMYD1 Gene

HapMap Linkage Disequilibrium report
SMYD1

Disorders for SMYD1 Gene

(2) University of Copenhagen DISEASES for SMYD1 Gene

Relevant External Links for SMYD1

Genetic Association Database (GAD)
SMYD1
Human Genome Epidemiology (HuGE) Navigator
SMYD1
genes like me logo Genes that share disorders with SMYD1: view

No data available for UniProtKB/Swiss-Prot for SMYD1 Gene

Publications for SMYD1 Gene

  1. Bop encodes a muscle-restricted protein containing MYND and SET domains and is essential for cardiac differentiation and morphogenesis. (PMID: 11923873) Gottlieb P.D. … Srivastava D. (Nat. Genet. 2002) 2 3
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  4. SMYD1, the myogenic activator, is a direct target of serum response factor and myogenin. (PMID: 19783823) Li D. … Liu M. (Nucleic Acids Res. 2009) 3 4
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 49

Products for SMYD1 Gene

Sources for SMYD1 Gene

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