Aliases for SMYD5 Gene

Aliases for SMYD5 Gene

  • SMYD Family Member 5 2 3 5
  • SET And MYND Domain-Containing Protein 5 3 4
  • Retinoic Acid-Induced Protein 15 3 4
  • Retinoic Acid Induced 15 2 3
  • NN8-4AG 2 3
  • ZMYND23 2 3
  • RAI15 3 4
  • RRG1 2 3
  • Retinoic Acid Responsive 3
  • Protein NN8-4AG 4
  • EC 2.1.1.- 4
  • SMYD5 5

External Ids for SMYD5 Gene

Previous HGNC Symbols for SMYD5 Gene

  • RAI15

Previous GeneCards Identifiers for SMYD5 Gene

  • GC02P073399
  • GC02P073415
  • GC02P073353
  • GC02P073294
  • GC02P073441
  • GC02P073177

Summaries for SMYD5 Gene

GeneCards Summary for SMYD5 Gene

SMYD5 (SMYD Family Member 5) 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.

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SMYD5 Gene

Genomics for SMYD5 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SMYD5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J073213 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 260.4 +0.3 332 2.5 SP1 ZNF207 NCOR1 MYC ZNF600 ZMYM3 KLF9 POLR2A CEBPA BRCA1 SMYD5 PRADC1 ALMS1 DUSP11 CCT7 HSALNG0015951
GH02J073212 Enhancer 0.8 ENCODE 250.7 -1.4 -1364 0.7 ZNF654 CHD4 MXD4 CTCF REST TRIM22 THAP11 SMAD4 ZNF511 SAP130 SMYD5 PRADC1 CCT7 RAB11FIP5 SFXN5 SPR lnc-RAB11FIP5-3 NOTO
GH02J073175 Promoter/Enhancer 1.6 FANTOM5 ENCODE CraniofacialAtlas 21 -37.3 -37324 2.4 EZH2 ZNF654 MYC ZNF600 IKZF1 ZNF580 ZNF592 KLF9 CEBPA BRCA1 ALMS1 SMYD5 SFXN5 ENSG00000273245 RAB11FIP5 PRADC1 NOTO SPR EMX1 CCT7
GH02J074196 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 14 +985.2 985186 5.2 BCLAF1 SP1 ZNF207 MYC ZNF600 SSRP1 ZNF580 ZNF592 POLR2A CEBPA ENSG00000279070 MTHFD2 INO80B WBP1 PCGF1 ENSG00000273245 CCDC142 DUSP11 ALMS1 SEMA4F
GH02J073069 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 11.5 -143.3 -143321 3.8 BCLAF1 SP1 ZNF207 NCOR1 MYC IKZF1 ZNF600 SIX5 ZNF592 ZNF10 SFXN5 CCT7 TPRKB SMYD5 ALMS1 RAB11FIP5 piR-32770 lnc-SFXN5-1 piR-50443-215 EMX1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SMYD5 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SMYD5

Top Transcription factor binding sites by QIAGEN in the SMYD5 gene promoter:
  • CREB
  • deltaCREB
  • GATA-2
  • HOXA9
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-AT3
  • NF-AT4

Genomic Locations for SMYD5 Gene

Latest Assembly
chr2:73,214,222-73,227,221
(GRCh38/hg38)
Size:
13,000 bases
Orientation:
Plus strand

Previous Assembly
chr2:73,441,373-73,454,349
(GRCh37/hg19 by Entrez Gene)
Size:
12,977 bases
Orientation:
Plus strand

chr2:73,441,350-73,454,365
(GRCh37/hg19 by Ensembl)
Size:
13,016 bases
Orientation:
Plus strand

Genomic View for SMYD5 Gene

Genes around SMYD5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMYD5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMYD5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMYD5 Gene

Proteins for SMYD5 Gene

  • Protein details for SMYD5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6GMV2-SMYD5_HUMAN
    Recommended name:
    SET and MYND domain-containing protein 5
    Protein Accession:
    Q6GMV2
    Secondary Accessions:
    • D6W5H3
    • Q13558

    Protein attributes for SMYD5 Gene

    Size:
    418 amino acids
    Molecular mass:
    47341 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH73806.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for SMYD5 Gene

Post-translational modifications for SMYD5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SMYD5 Gene

No data available for DME Specific Peptides for SMYD5 Gene

Domains & Families for SMYD5 Gene

Gene Families for SMYD5 Gene

Protein Domains for SMYD5 Gene

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

Suggested Antigen Peptide Sequences for SMYD5 Gene

GenScript: Design optimal peptide antigens:
  • Retinoic acid-induced protein 15 (SMYD5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6GMV2

UniProtKB/Swiss-Prot:

SMYD5_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 SMYD5: view

Function for SMYD5 Gene

Enzyme Numbers (IUBMB) for SMYD5 Gene

Phenotypes From GWAS Catalog for SMYD5 Gene

Gene Ontology (GO) - Molecular Function for SMYD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005515 protein binding IPI 32296183
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 SMYD5: view
genes like me logo Genes that share phenotypes with SMYD5: view

Animal Models for SMYD5 Gene

MGI Knock Outs for SMYD5:
  • Smyd5 Smyd5<tm1a(EUCOMM)Wtsi>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SMYD5

No data available for Molecular function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SMYD5 Gene

Localization for SMYD5 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 SMYD5 gene
Compartment Confidence
extracellular 2
mitochondrion 2
nucleus 2
cytoskeleton 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SMYD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
genes like me logo Genes that share ontologies with SMYD5: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SMYD5 Gene

Pathways & Interactions for SMYD5 Gene

PathCards logo

SuperPathways for SMYD5 Gene

SuperPathway Contained pathways
1 PKMTs methylate histone lysines
genes like me logo Genes that share pathways with SMYD5: view

Pathways by source for SMYD5 Gene

1 BioSystems pathway for SMYD5 Gene
1 GeneTex pathway for SMYD5 Gene

Gene Ontology (GO) - Biological Process for SMYD5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008150 biological_process ND --
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with SMYD5: view

No data available for SIGNOR curated interactions for SMYD5 Gene

Drugs & Compounds for SMYD5 Gene

No Compound Related Data Available

Transcripts for SMYD5 Gene

mRNA/cDNA for SMYD5 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
9 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 SMYD5

Alternative Splicing Database (ASD) splice patterns (SP) for SMYD5 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c · 4d ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14
SP1: - - - - - -
SP2: - - - - -
SP3: - -
SP4: - - -
SP5:
SP6:
SP7:
SP8:

Relevant External Links for SMYD5 Gene

GeneLoc Exon Structure for
SMYD5

Expression for SMYD5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SMYD5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SMYD5 Gene

This gene is overexpressed in Adrenal (18.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SMYD5 Gene



Protein tissue co-expression partners for SMYD5 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SMYD5

SOURCE GeneReport for Unigene cluster for SMYD5 Gene:

Hs.631882

Evidence on tissue expression from TISSUES for SMYD5 Gene

  • Nervous system(4.9)
genes like me logo Genes that share expression patterns with SMYD5: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMYD5 Gene

Orthologs for SMYD5 Gene

This gene was present in the common ancestor of animals.

Orthologs for SMYD5 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SMYD5 29 30
  • 99.44 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SMYD5 29 30
  • 92.98 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SMYD5 29 30
  • 91.95 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Smyd5 29
  • 89.21 (n)
Mouse
(Mus musculus)
Mammalia Smyd5 29 16 30
  • 87.18 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SMYD5 30
  • 51 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SMYD5 29 30
  • 77.45 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SMYD5 30
  • 84 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia smyd5 29
  • 75.46 (n)
Str.8196 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.8640 29
Zebrafish
(Danio rerio)
Actinopterygii smyd5 29 30
  • 69.64 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG3353 29 30
  • 54.24 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003552 29
  • 53.39 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.3716 30
  • 46 (a)
OneToOne
Species where no ortholog for SMYD5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Oppossum (Monodelphis domestica)
  • 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 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 SMYD5 Gene

ENSEMBL:
Gene Tree for SMYD5 (if available)
TreeFam:
Gene Tree for SMYD5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SMYD5: view image
Alliance of Genome Resources:
Additional Orthologs for SMYD5

Paralogs for SMYD5 Gene

Paralogs for SMYD5 Gene

genes like me logo Genes that share paralogs with SMYD5: view

Variants for SMYD5 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SMYD5 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs115495075 Benign: not provided 73,220,775(+) G/A
NM_006062.3(SMYD5):c.460G>A (p.Ala154Thr)
MISSENSE
rs61736525 Benign: not provided 73,221,873(+) C/T
NM_006062.3(SMYD5):c.585C>T (p.Asn195=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SMYD5 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 SMYD5 Gene

Variant ID Type Subtype PubMed ID
nsv2776 CNV deletion 18451855

Variation tolerance for SMYD5 Gene

Residual Variation Intolerance Score: 40.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.91; 35.57% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SMYD5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMYD5
Leiden Open Variation Database (LOVD)
SMYD5

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMYD5 Gene

Disorders for SMYD5 Gene

Additional Disease Information for SMYD5

No disorders were found for SMYD5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SMYD5 Gene

Publications for SMYD5 Gene

  1. Isolation of a novel retinoic acid-responsive gene by selection of genomic fragments derived from CpG-island-enriched DNA. (PMID: 8754834) Shago M … Giguére V (Molecular and cellular biology 1996) 2 3 4
  2. 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
  3. Synthetic Lethal and Resistance Interactions with BET Bromodomain Inhibitors in Triple-Negative Breast Cancer. (PMID: 32416067) Shu S … Polyak K (Molecular cell 2020) 3
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  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 SMYD5 Gene

Sources for SMYD5 Gene