Aliases for SETD3 Gene

Aliases for SETD3 Gene

  • SET Domain Containing 3, Actin Histidine Methyltransferase 2 3 5
  • Actin-Histidine N-Methyltransferase 3 4
  • SET Domain-Containing Protein 3 3 4
  • SET Domain Containing 3 2 3
  • C14orf154 3 4
  • HSETD3 3 4
  • Histone-Lysine N-Methyltransferase Setd3 3
  • Chromosome 14 Open Reading Frame 154 2
  • EC 2.1.1.85 4
  • FLJ23027 2
  • SETD3 5

External Ids for SETD3 Gene

Previous HGNC Symbols for SETD3 Gene

  • C14orf154

Previous GeneCards Identifiers for SETD3 Gene

  • GC14M098934
  • GC14M099864
  • GC14M080047

Summaries for SETD3 Gene

GeneCards Summary for SETD3 Gene

SETD3 (SET Domain Containing 3, Actin Histidine Methyltransferase) is a Protein Coding gene. Diseases associated with SETD3 include Meier-Gorlin Syndrome 1. Among its related pathways are PKMTs methylate histone lysines and Chromatin organization. Gene Ontology (GO) annotations related to this gene include transcription coactivator activity and histone methyltransferase activity (H3-K4 specific). An important paralog of this gene is SETD6.

UniProtKB/Swiss-Prot Summary for SETD3 Gene

  • Protein-histidine N-methyltransferase that specifically mediates methylation of actin at 'His-73' (PubMed:30526847, PubMed:30626964, PubMed:30785395). Histidine methylation of actin is required for smooth muscle contraction of the laboring uterus during delivery (PubMed:30626964). Does not have protein-lysine N-methyltransferase activity and probably only catalyzes histidine methylation of actin (PubMed:30626964, PubMed:30785395).

Additional gene information for SETD3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SETD3 Gene

Genomics for SETD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SETD3 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
GH14J099479 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 606.6 +5.8 5756 5.4 CEBPG SP1 CREB1 GATAD2A TEAD4 PRDM10 REST ZNF629 SOX13 IKZF1 CCNK SETD3 lnc-CCDC85C-3 BCL11B
GH14J099411 Enhancer 0.9 Ensembl ENCODE 15.7 +73.7 73682 6.7 CREB1 CTCF TEAD4 PRDM1 ZIC2 RAD21 TRIM22 ZNF341 CEBPB SMARCA5 CCNK SETD3 AB372642 lnc-CCDC85C-4 BCL11B
GH14J099459 Enhancer 0.8 Ensembl ENCODE 16 +25.0 25039 3.2 CBX3 HMBOX1 EGR1 FOXA2 AFF1 ZKSCAN1 ZFHX2 SIX4 CREM HDAC2 SETD3 RF00017-1672 lnc-CCDC85C-3 CCNK BCL11B
GH14J099225 Promoter/Enhancer 2.5 UCNEbase FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 4.4 +248.5 248478 25.4 CREB1 PRDM10 ZNF629 KDM1A ZNF692 PRDM1 ZIC2 PATZ1 POLR2A EZH2 BCL11B CCNK ENSG00000235785 ENSG00000234648 RPL3P4 DEGS2 SETD3 piR-38051-098
GH14J099424 Enhancer 0.7 Ensembl ENCODE 16.4 +60.2 60159 4.2 CEBPB JUND USF1 BHLHE40 GLIS1 SMARCA4 ZNF24 SETD3 CCNK AB372642 piR-52294-052 BCL11B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SETD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SETD3

Top Transcription factor binding sites by QIAGEN in the SETD3 gene promoter:
  • AML1a
  • ER-alpha
  • FAC1
  • FOXO4
  • MAZR
  • Meis-1b
  • p53
  • Pax-4a
  • POU6F1 (c2)

Genomic Locations for SETD3 Gene

Genomic Locations for SETD3 Gene
chr14:99,397,746-99,486,458
(GRCh38/hg38)
Size:
88,713 bases
Orientation:
Minus strand
chr14:99,864,083-99,947,226
(GRCh37/hg19)
Size:
83,144 bases
Orientation:
Minus strand

Genomic View for SETD3 Gene

Genes around SETD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETD3 Gene

Proteins for SETD3 Gene

  • Protein details for SETD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86TU7-SETD3_HUMAN
    Recommended name:
    Actin-histidine N-methyltransferase
    Protein Accession:
    Q86TU7
    Secondary Accessions:
    • A0PJU3
    • A5PLP0
    • B4DZE8
    • Q0VAQ2
    • Q659C0
    • Q86TU8
    • Q96GY9
    • Q9H5U5

    Protein attributes for SETD3 Gene

    Size:
    594 amino acids
    Molecular mass:
    67257 Da
    Quaternary structure:
    • Interacts with MYOD1.
    SequenceCaution:
    • Sequence=BAB15525.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SETD3 Gene

    Alternative splice isoforms for SETD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SETD3 Gene

Post-translational modifications for SETD3 Gene

  • Phosphorylated by GSK3B, which is required for recognition by the SCF(FBXW7) complex and subsequent degradation.
  • Ubiquitinated by the SCF(FBXW7) complex following phosphorylation by GSK3B, leading to its degradation by the proteasome.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SETD3 Gene

Domains & Families for SETD3 Gene

Gene Families for SETD3 Gene

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

Protein Domains for SETD3 Gene

InterPro:
Blocks:
  • Nuclear protein SET
ProtoNet:

Suggested Antigen Peptide Sequences for SETD3 Gene

GenScript: Design optimal peptide antigens:
  • SET domain containing 3, isoform CRA_b (A0PJU3_HUMAN)
  • SET domain-containing protein 3 (SETD3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q86TU7

UniProtKB/Swiss-Prot:

SETD3_HUMAN :
  • The SET domain specifically recognizes and binds actin, suggesting that it does not accommodate substrates diverging from actin.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. SETD3 actin-histidine methyltransferase family.
Domain:
  • The SET domain specifically recognizes and binds actin, suggesting that it does not accommodate substrates diverging from actin.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily. SETD3 actin-histidine methyltransferase family.
genes like me logo Genes that share domains with SETD3: view

Function for SETD3 Gene

Molecular function for SETD3 Gene

UniProtKB/Swiss-Prot Function:
Protein-histidine N-methyltransferase that specifically mediates methylation of actin at 'His-73' (PubMed:30526847, PubMed:30626964, PubMed:30785395). Histidine methylation of actin is required for smooth muscle contraction of the laboring uterus during delivery (PubMed:30626964). Does not have protein-lysine N-methyltransferase activity and probably only catalyzes histidine methylation of actin (PubMed:30626964, PubMed:30785395).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-histidyl-[protein] + S-adenosyl-L-methionine = H(+) + N(tele)-methyl-L-histidyl-[protein] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:19369, Rhea:RHEA-COMP:9745, Rhea:RHEA-COMP:11600, ChEBI:CHEBI:15378, ChEBI:CHEBI:16367, ChEBI:CHEBI:29979, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789; EC=2.1.1.85; Evidence={ECO:0000269|PubMed:30526847, ECO:0000269|PubMed:30626964, ECO:0000269|PubMed:30785395};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.752 uM for beta-actin {ECO:0000269|PubMed:30526847}; KM=0.502 uM for beta-actin {ECO:0000269|PubMed:30785395}; KM=0.116 uM for S-adenosyl-L-methionine {ECO:0000269|PubMed:30526847}; KM=0.111 uM for S-adenosyl-L-methionine {ECO:0000269|PubMed:30785395}; Vmax=9.091 nmol/min/mg enzyme with beta-actin as substrate {ECO:0000269|PubMed:30526847}; Vmax=13.550 nmol/min/mg enzyme with beta-actin as substrate {ECO:0000269|PubMed:30785395}; Vmax=8.649 nmol/min/mg enzyme with S-adenosyl-L-methionine as substrate {ECO:0000269|PubMed:30526847}; Vmax=11.260 nmol/min/mg enzyme with S-adenosyl-L-methionine as substrate {ECO:0000269|PubMed:30785395}; Note=Kcat is 0.65 min(-1) with beta-actin as substrate (PubMed:30526847). Kcat is 0.809 min(-1) with beta-actin as substrate (PubMed:30785395). Kcat is 0.61 min(-1) with S-adenosyl-L-methionine as substrate (PubMed:30526847). Kcat is 0.673 min(-1) with S-adenosyl-L-methionine as substrate (PubMed:30785395). {ECO:0000269|PubMed:30526847, ECO:0000269|PubMed:30785395};

Enzyme Numbers (IUBMB) for SETD3 Gene

Phenotypes From GWAS Catalog for SETD3 Gene

Gene Ontology (GO) - Molecular Function for SETD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001102 RNA polymerase II activating transcription factor binding IEA --
GO:0003713 transcription coactivator activity IBA,ISS --
GO:0003779 actin binding IEA --
GO:0005515 protein binding IEA,IPI 26030842
GO:0008168 methyltransferase activity IEA --
genes like me logo Genes that share ontologies with SETD3: view
genes like me logo Genes that share phenotypes with SETD3: view

Animal Models for SETD3 Gene

MGI Knock Outs for SETD3:
  • Setd3 Setd3<tm1.1(NCOM)Mfgc>

Animal Model Products

  • Taconic Biosciences Mouse Models for SETD3

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SETD3

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SETD3 Gene

Localization for SETD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SETD3 Gene

Cytoplasm. Nucleus. Note=Localizes mainly in the cytoplasm. {ECO:0000269 PubMed:28442573}.

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 SETD3 gene
Compartment Confidence
nucleus 4
mitochondrion 3
cytosol 2
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SETD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IBA 21873635
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA,IDA 30626964
genes like me logo Genes that share ontologies with SETD3: view

Pathways & Interactions for SETD3 Gene

genes like me logo Genes that share pathways with SETD3: view

Pathways by source for SETD3 Gene

1 BioSystems pathway for SETD3 Gene

Gene Ontology (GO) - Biological Process for SETD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010452 histone H3-K36 methylation ISS --
GO:0018021 peptidyl-histidine methylation IEA,IDA 30526847
GO:0018023 peptidyl-lysine trimethylation ISS --
GO:0018026 peptidyl-lysine monomethylation IBA,ISS --
GO:0018027 peptidyl-lysine dimethylation IBA,ISS --
genes like me logo Genes that share ontologies with SETD3: view

No data available for SIGNOR curated interactions for SETD3 Gene

Drugs & Compounds for SETD3 Gene

(1) Drugs for SETD3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma 0

(1) Additional Compounds for SETD3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with SETD3: view

Transcripts for SETD3 Gene

mRNA/cDNA for SETD3 Gene

2 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SETD3

Alternative Splicing Database (ASD) splice patterns (SP) for SETD3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15a · 15b · 15c
SP1: - - - - -
SP2: - - -
SP3: - - - -
SP4: -
SP5: - - -
SP6:
SP7: - - - - -
SP8:

Relevant External Links for SETD3 Gene

GeneLoc Exon Structure for
SETD3

Expression for SETD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SETD3 Gene

Protein differential expression in normal tissues from HIPED for SETD3 Gene

This gene is overexpressed in Testis (11.2), Peripheral blood mononuclear cells (7.3), and Spleen (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SETD3 Gene



Protein tissue co-expression partners for SETD3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SETD3

SOURCE GeneReport for Unigene cluster for SETD3 Gene:

Hs.510407

Evidence on tissue expression from TISSUES for SETD3 Gene

  • Nervous system(4.6)
  • Lung(4.4)
  • Eye(4.2)
  • Muscle(2.8)
  • Kidney(2.7)
  • Liver(2.5)
  • Heart(2.4)
  • Intestine(2.4)
  • Skin(2.3)
genes like me logo Genes that share expression patterns with SETD3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SETD3 Gene

Orthologs for SETD3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SETD3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SETD3 30 31
  • 99.49 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 92 (a)
OneToMany
-- 31
  • 85 (a)
OneToMany
-- 31
  • 81 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Setd3 30
  • 87.77 (n)
Mouse
(Mus musculus)
Mammalia Setd3 30 17 31
  • 87.44 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SETD3 31
  • 87 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia SETD3 30 31
  • 86.6 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SETD3 30 31
  • 86.58 (n)
OneToOne
Chicken
(Gallus gallus)
Aves -- 31
  • 88 (a)
OneToMany
-- 31
  • 81 (a)
OneToMany
LOC100859337 30
  • 79.73 (n)
SETD3 31
  • 78 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 83 (a)
OneToMany
-- 31
  • 80 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia setd3 30
  • 74.48 (n)
Str.4852 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.15711 30
Zebrafish
(Danio rerio)
Actinopterygii setd3 30 31
  • 69.03 (n)
OneToOne
wufb01d12 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002018 30
  • 45.15 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG32732 31
  • 27 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea set-27 30 31
  • 45.37 (n)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU08733 30
  • 41.06 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 38 (a)
OneToOne
Species where no ortholog for SETD3 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)
  • 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 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 SETD3 Gene

ENSEMBL:
Gene Tree for SETD3 (if available)
TreeFam:
Gene Tree for SETD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SETD3: view image

Paralogs for SETD3 Gene

Paralogs for SETD3 Gene

genes like me logo Genes that share paralogs with SETD3: view

Variants for SETD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SETD3 Gene

SNP ID Clinical significance and condition Chr 14 pos Variation AA Info Type
709144 Benign: not provided 99,405,261(-) T/C SYNONYMOUS_VARIANT
710040 Benign: not provided 99,413,068(-) A/G INTRON_VARIANT
710041 Benign: not provided 99,458,390(-) G/A SYNONYMOUS_VARIANT
710042 Benign: not provided 99,465,734(-) T/C SYNONYMOUS_VARIANT
715670 Benign: not provided 99,461,306(-) A/G SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for SETD3 Gene

Structural Variations from Database of Genomic Variants (DGV) for SETD3 Gene

Variant ID Type Subtype PubMed ID
esv3635481 CNV gain 21293372
esv997017 OTHER inversion 20482838
nsv832871 CNV gain 17160897
nsv832872 CNV loss 17160897

Variation tolerance for SETD3 Gene

Residual Variation Intolerance Score: 10.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.12; 22.80% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SETD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SETD3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETD3 Gene

Disorders for SETD3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SETD3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
meier-gorlin syndrome 1
  • eps
- elite association - COSMIC cancer census association via MalaCards
Search SETD3 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with SETD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SETD3 Gene

Publications for SETD3 Gene

  1. SETD3 protein is the actin-specific histidine N-methyltransferase. (PMID: 30526847) Kwiatkowski S … Drozak J (eLife 2018) 2 3 4
  2. An engineered variant of SETD3 methyltransferase alters target specificity from histidine to lysine methylation. (PMID: 31911441) Dai S … Cheng X (The Journal of biological chemistry 2020) 2 3
  3. SETD3 is an actin histidine methyltransferase that prevents primary dystocia. (PMID: 30626964) Wilkinson AW … Gozani O (Nature 2019) 3 4
  4. Structural insights into SETD3-mediated histidine methylation on β-actin. (PMID: 30785395) Guo Q … Xu C (eLife 2019) 3 4
  5. Cell cycle-dependent degradation of the methyltransferase SETD3 attenuates cell proliferation and liver tumorigenesis. (PMID: 28442573) Cheng X … Du HN (The Journal of biological chemistry 2017) 3 4

Products for SETD3 Gene

  • Signalway Proteins for SETD3

Sources for SETD3 Gene