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Aliases for SMYD1 Gene

Aliases for SMYD1 Gene

  • SET And MYND Domain Containing 1 2 3 5
  • 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

Previous GeneCards Identifiers for SMYD1 Gene

  • GC02P088252
  • GC02P088269
  • GC02P088206
  • GC02P088367
  • GC02P087289

Summaries for SMYD1 Gene

GeneCards Summary for SMYD1 Gene

SMYD1 (SET And MYND Domain Containing 1) is a Protein Coding gene. Among its related pathways are Heart Development and PKMTs methylate histone lysines. 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

Regulatory Elements for SMYD1 Gene

Enhancers for SMYD1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02F088066 1.3 Ensembl ENCODE 6.9 +0.3 335 3.8 PKNOX1 IRF2 HCFC1 E2F5 BACH1 ZBTB40 ZNF83 FOSL1 FOXK2 IRF1 FABP1 THNSL2 SMYD1 MIR4780
GH02F088070 0.9 Ensembl 5.6 +2.5 2521 0.2 FABP1 THNSL2 SMYD1 MIR4780
GH02F088074 1.2 FANTOM5 Ensembl ENCODE 4.4 +7.2 7248 1.5 HLF CEBPB CEBPG ZBTB40 ZNF7 JUND CEBPA KDM1A FABP1 THNSL2 SMYD1 MIR4780
GH02F088082 1 Ensembl 0.4 +14.7 14721 0.2 KRCC1 MIR4780 SMYD1
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SMYD1 on UCSC Golden Path with GeneCards custom track

Promoters for SMYD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001544276 720 1000 NR2F6 MAFK

Genomic Location for SMYD1 Gene

Chromosome:
2
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

Genes around SMYD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMYD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMYD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

Post-translational modifications for SMYD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SMYD1 Gene

No data available for DME Specific Peptides for SMYD1 Gene

Domains & Families for SMYD1 Gene

Protein Domains for SMYD1 Gene

Suggested Antigen Peptide Sequences for SMYD1 Gene

Graphical View of Domain Structure for InterPro Entry

Q8NB12

UniProtKB/Swiss-Prot:

SMYD1_HUMAN :
  • 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.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
  • Contains 1 MYND-type zinc finger.
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.
  • Contains 1 SET domain.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Similarity:
  • Contains 1 MYND-type zinc finger.
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:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity 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:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets 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
nucleus 4
cytosol 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 & Interactions for SMYD1 Gene

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

Pathways by source for SMYD1 Gene

1 GeneTex pathway for SMYD1 Gene
2 BioSystems pathways 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:0006355 regulation of transcription, DNA-templated IEA --
GO:0007507 heart development IEA --
GO:0010831 positive regulation of myotube differentiation IDA 19783823
genes like me logo Genes that share ontologies with SMYD1: view

No data available for SIGNOR curated interactions for SMYD1 Gene

Transcripts for SMYD1 Gene

Unigene Clusters for SMYD1 Gene

SET and MYND domain containing 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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 (x20.4), Heart - Left Ventricle (x20.2), and Heart - Atrial Appendage (x6.0).

Protein differential expression in normal tissues from HIPED for SMYD1 Gene

This gene is overexpressed in Heart (32.6), Fetal heart (18.8), and Tonsil (15.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SMYD1 Gene



Protein tissue co-expression partners for SMYD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SMYD1 Gene:

SMYD1

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 expression patterns with SMYD1: view

Primer Products

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 34 35
  • 97.49 (n)
dog
(Canis familiaris)
Mammalia SMYD1 34 35
  • 92.87 (n)
cow
(Bos Taurus)
Mammalia SMYD1 34 35
  • 92.24 (n)
rat
(Rattus norvegicus)
Mammalia Smyd1 34
  • 89.59 (n)
mouse
(Mus musculus)
Mammalia Smyd1 34 16 35
  • 89.45 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SMYD1 35
  • 88 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMYD1 35
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMYD1 34 35
  • 78.69 (n)
lizard
(Anolis carolinensis)
Reptilia SMYD1 35
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smyd1 34
  • 72.68 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1817 34
zebrafish
(Danio rerio)
Actinopterygii smyd1b 34 35
  • 67.63 (n)
CU469500.4 35
  • 61 (a)
OneToMany
smyd1a 35
  • 60 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.922 34
fruit fly
(Drosophila melanogaster)
Insecta Bzd 35
  • 22 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea set-14 35
  • 20 (a)
ManyToMany
set-18 35
  • 19 (a)
ManyToMany
set-10 35
  • 16 (a)
ManyToMany
set-30 35
  • 16 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 36 (a)
OneToOne
Species where no ortholog for SMYD1 was found in the sources mined by GeneCards:
  • 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

(3) 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
rs10168951 -- 88,104,168(+) TCACC(A/G)TGTTA intron-variant
rs10170115 -- 88,097,837(+) CATGT(A/G)CATGC intron-variant
rs10170209 -- 88,067,820(+) GACTT(A/G)GCTCA upstream-variant-2KB, utr-variant-5-prime
rs10170645 -- 88,092,499(+) GAAGC(C/T)AGACA intron-variant
rs10172567 -- 88,098,064(+) CGCTA(C/T)AGAAA intron-variant

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

Variant ID Type Subtype PubMed ID
dgv61n16 CNV deletion 17901297
dgv6947n54 CNV gain 21841781
nsv1072005 CNV deletion 25765185
nsv1130752 CNV deletion 24896259
nsv1148611 CNV deletion 26484159
nsv582383 CNV gain 21841781
nsv582384 CNV loss 21841781
nsv582386 CNV loss 21841781
nsv834289 CNV gain 17160897

Variation tolerance for SMYD1 Gene

Residual Variation Intolerance Score: 77% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.74; 78.84% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMYD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMYD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMYD1 Gene

Disorders for SMYD1 Gene

Relevant External Links for SMYD1

Genetic Association Database (GAD)
SMYD1
Human Genome Epidemiology (HuGE) Navigator
SMYD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMYD1

No disorders were found for SMYD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SMYD1 Gene

Publications for SMYD1 Gene

  1. 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 46 64
  2. 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 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. 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 64
  5. 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 64

Products for SMYD1 Gene

Sources for SMYD1 Gene

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