Aliases for SMYD4 Gene

Aliases for SMYD4 Gene

  • SET And MYND Domain Containing 4 2 3 5
  • SET And MYND Domain-Containing Protein 4 3 4
  • KIAA1936 2 4
  • ZMYND21 2 3
  • EC 2.1.1.- 4
  • SMYD4 5

External Ids for SMYD4 Gene

Previous GeneCards Identifiers for SMYD4 Gene

  • GC00U911629
  • GC17M001891
  • GC17M001630
  • GC17M001682
  • GC17M001580

Summaries for SMYD4 Gene

GeneCards Summary for SMYD4 Gene

SMYD4 (SET And MYND Domain Containing 4) is a Protein Coding gene. Among its related pathways are PKMTs methylate histone lysines. Gene Ontology (GO) annotations related to this gene include methyltransferase activity. An important paralog of this gene is SMYD2.

Gene Wiki entry for SMYD4 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SMYD4 Gene

Genomics for SMYD4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SMYD4 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMYD4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SMYD4

Top Transcription factor binding sites by QIAGEN in the SMYD4 gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • CBF-C
  • CP1A
  • CP1C
  • FAC1
  • MAZR
  • NF-Y
  • NF-YA

Genomic Locations for SMYD4 Gene

Latest Assembly
chr17:1,779,485-1,830,634
(GRCh38/hg38)
Size:
51,150 bases
Orientation:
Minus strand

Previous Assembly
chr17:1,682,779-1,733,196
(GRCh37/hg19 by Entrez Gene)
Size:
50,418 bases
Orientation:
Minus strand

chr17:1,682,779-1,733,928
(GRCh37/hg19 by Ensembl)
Size:
51,150 bases
Orientation:
Minus strand

Genomic View for SMYD4 Gene

Genes around SMYD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMYD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMYD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMYD4 Gene

Proteins for SMYD4 Gene

  • Protein details for SMYD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IYR2-SMYD4_HUMAN
    Recommended name:
    SET and MYND domain-containing protein 4
    Protein Accession:
    Q8IYR2
    Secondary Accessions:
    • Q8N1P2
    • Q8NAT0
    • Q96LV4
    • Q96PV2

    Protein attributes for SMYD4 Gene

    Size:
    804 amino acids
    Molecular mass:
    89225 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SMYD4 Gene

Post-translational modifications for SMYD4 Gene

  • Ubiquitination at Lys717
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SMYD4 Gene

Domains & Families for SMYD4 Gene

Gene Families for SMYD4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for SMYD4 Gene

InterPro:
Blocks:
  • Nuclear protein SET
  • Zn-finger, MYND type

Suggested Antigen Peptide Sequences for SMYD4 Gene

GenScript: Design optimal peptide antigens:
  • SET and MYND domain-containing protein 4 (SMYD4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IYR2

UniProtKB/Swiss-Prot:

SMYD4_HUMAN :
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with SMYD4: view

Function for SMYD4 Gene

Enzyme Numbers (IUBMB) for SMYD4 Gene

Phenotypes From GWAS Catalog for SMYD4 Gene

Gene Ontology (GO) - Molecular Function for SMYD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0008168 methyltransferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with SMYD4: view
genes like me logo Genes that share phenotypes with SMYD4: view

Animal Models for SMYD4 Gene

MGI Knock Outs for SMYD4:
  • Smyd4 Smyd4<tm1a(EUCOMM)Wtsi>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMYD4

No data available for Molecular function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SMYD4 Gene

Localization for SMYD4 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMYD4 gene
Compartment Confidence
nucleus 3
cytosol 3
golgi apparatus 2
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for SMYD4 Gene

Pathways & Interactions for SMYD4 Gene

PathCards logo

SuperPathways for SMYD4 Gene

SuperPathway Contained pathways
1 PKMTs methylate histone lysines
genes like me logo Genes that share pathways with SMYD4: view

Pathways by source for SMYD4 Gene

1 BioSystems pathway for SMYD4 Gene
1 GeneTex pathway for SMYD4 Gene

Gene Ontology (GO) - Biological Process for SMYD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with SMYD4: view

No data available for SIGNOR curated interactions for SMYD4 Gene

Drugs & Compounds for SMYD4 Gene

No Compound Related Data Available

Transcripts for SMYD4 Gene

mRNA/cDNA for SMYD4 Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMYD4

Alternative Splicing Database (ASD) splice patterns (SP) for SMYD4 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b · 12c ^ 13
SP1: - - - -
SP2: -
SP3: -
SP4: -
SP5:

Relevant External Links for SMYD4 Gene

GeneLoc Exon Structure for
SMYD4

Expression for SMYD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SMYD4 Gene

Protein differential expression in normal tissues from HIPED for SMYD4 Gene

This gene is overexpressed in Monocytes (18.6), Fetal gut (18.4), Bone (14.7), and Fetal ovary (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SMYD4 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SMYD4

SOURCE GeneReport for Unigene cluster for SMYD4 Gene:

Hs.514602

Evidence on tissue expression from TISSUES for SMYD4 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with SMYD4: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMYD4 Gene

Orthologs for SMYD4 Gene

This gene was present in the common ancestor of animals.

Orthologs for SMYD4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SMYD4 29 30
  • 98.92 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SMYD4 29 30
  • 82.07 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SMYD4 29 30
  • 81.69 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Smyd4 29 16 30
  • 79.48 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Smyd4 29
  • 79.07 (n)
Oppossum
(Monodelphis domestica)
Mammalia SMYD4 30
  • 56 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SMYD4 30
  • 55 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SMYD4 29 30
  • 58.48 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SMYD4 30
  • 50 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia smyd4 29
  • 53.21 (n)
Zebrafish
(Danio rerio)
Actinopterygii smyd4 29 30
  • 48.24 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008839 29
  • 44.08 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG7759 29 30
  • 42.87 (n)
OneToMany
CG8378 30
  • 26 (a)
OneToMany
Smyd4 30
  • 22 (a)
OneToMany
CG1868 30
  • 21 (a)
OneToMany
dao 30
  • 15 (a)
OneToMany
Species where no ortholog for SMYD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for SMYD4 Gene

ENSEMBL:
Gene Tree for SMYD4 (if available)
TreeFam:
Gene Tree for SMYD4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SMYD4: view image
Alliance of Genome Resources:
Additional Orthologs for SMYD4

Paralogs for SMYD4 Gene

Paralogs for SMYD4 Gene

(34) SIMAP similar genes for SMYD4 Gene using alignment to 5 proteins:

  • SMYD4_HUMAN
  • I3L1V4_HUMAN
  • I3L2P4_HUMAN
  • I3L428_HUMAN
  • I3L496_HUMAN
genes like me logo Genes that share paralogs with SMYD4: view

Variants for SMYD4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SMYD4 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs11549830 -- p.Arg562Trp
rs3809875 -- p.Pro382Arg
rs7224496 -- p.Arg131Ile
rs9890631 -- p.Ile374Met
rs9902398 -- p.Tyr727Cys

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SMYD4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SMYD4 Gene

Variant ID Type Subtype PubMed ID
esv33335 CNV loss 17666407
esv3639699 CNV loss 21293372
nsv1065585 CNV gain 25217958
nsv1946 CNV insertion 18451855
nsv574215 CNV gain 21841781
nsv833335 CNV gain+loss 17160897
nsv9490 CNV loss 18304495

Variation tolerance for SMYD4 Gene

Residual Variation Intolerance Score: 79% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 23.14; 99.51% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMYD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMYD4
Leiden Open Variation Database (LOVD)
SMYD4

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMYD4 Gene

Disorders for SMYD4 Gene

Additional Disease Information for SMYD4

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for SMYD4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SMYD4 Gene

Publications for SMYD4 Gene

  1. Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. (PMID: 11572484) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 2 3 4
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. (PMID: 30021884) Fasci D … Heck AJR (Molecular & cellular proteomics : MCP 2018) 3

Products for SMYD4 Gene

Sources for SMYD4 Gene