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Aliases for SETD4 Gene

Aliases for SETD4 Gene

  • SET Domain Containing 4 2 3 5
  • C21orf18 3 4
  • C21orf27 3 4
  • Chromosome 21 Open Reading Frame 27 2
  • Chromosome 21 Open Reading Frame 18 2
  • SET Domain-Containing Protein 4 3
  • EC 2.1.1.- 4

External Ids for SETD4 Gene

Previous HGNC Symbols for SETD4 Gene

  • C21orf27
  • C21orf18

Previous GeneCards Identifiers for SETD4 Gene

  • GC21M036329
  • GC21M037406
  • GC21M022885

Summaries for SETD4 Gene

GeneCards Summary for SETD4 Gene

SETD4 (SET Domain Containing 4) is a Protein Coding gene. Among its related pathways are PKMTs methylate histone lysines. GO annotations related to this gene include methyltransferase activity.

Additional gene information for SETD4 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SETD4 Gene

Genomics for SETD4 Gene

Regulatory Elements for SETD4 Gene

Enhancers for SETD4 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
GH21H037071 1.2 ENCODE 80.2 -993.8 -993755 4.2 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 ZNF416 SETD4 TTC3 ENSG00000242553 PIGP DYRK1A MORC3 TTC3-AS1 MRPL20P1 RN7SL678P DSCR4-IT1
GH21H036697 1.6 FANTOM5 ENCODE dbSUPER 59.4 -621.7 -621734 6.9 HDGF SIN3A GLI4 ZNF2 GLIS2 SP3 SP5 YY2 REST TSHZ1 SETD4 ENSG00000242553 RIMKLBP1 MORC3 SIM2 TTC3-AS1 DYRK1A TTC3 MRPL20P1 RN7SL678P
GH21H036155 1.6 FANTOM5 ENCODE dbSUPER 52.9 -77.1 -77118 2.6 HDGF PKNOX1 SIN3A YY1 ZNF121 GLIS2 ZNF207 KLF7 ATF7 SP3 SETD4 RIMKLBP1 DOPEY2 MORC3 CBR3 CBR1 GC21P036137
GH21H036133 1.3 ENCODE dbSUPER 49.8 -56.0 -56008 2.9 SIN3A GLI4 ZNF2 ZNF121 GLIS2 ZNF416 KLF7 ZNF548 ATF7 SP3 SETD4 DOPEY2 MORC3 RIMKLBP1 LOC105369295 ENSG00000230794 MRPL20P1 CBR3 TTC3 RPL23AP3
GH21H036989 1.1 ENCODE 42.7 -910.8 -910769 2 HDGF ARNT ZFP64 SIN3A DMAP1 ZNF2 YY1 ZNF766 CBX5 ZNF143 ENSG00000242553 SETD4 HLCS DYRK1A MORC3 RIMKLBP1 GC21M036965
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SETD4 on UCSC Golden Path with GeneCards custom track

Genomic Locations for SETD4 Gene

Genomic Locations for SETD4 Gene
chr21:36,034,541-36,079,389
(GRCh38/hg38)
Size:
44,849 bases
Orientation:
Minus strand
chr21:37,406,839-37,451,687
(GRCh37/hg19)

Genomic View for SETD4 Gene

Genes around SETD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETD4 Gene

Proteins for SETD4 Gene

  • Protein details for SETD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NVD3-SETD4_HUMAN
    Recommended name:
    SET domain-containing protein 4
    Protein Accession:
    Q9NVD3
    Secondary Accessions:
    • B4DT14
    • D3DSG2
    • D3DSG4
    • Q8NE19
    • Q9BU46

    Protein attributes for SETD4 Gene

    Size:
    440 amino acids
    Molecular mass:
    50416 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SETD4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SETD4 Gene

Post-translational modifications for SETD4 Gene

  • Ubiquitination at isoforms=3, 4127
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SETD4 Gene

Domains & Families for SETD4 Gene

Gene Families for SETD4 Gene

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

Protein Domains for SETD4 Gene

Suggested Antigen Peptide Sequences for SETD4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NVD3

UniProtKB/Swiss-Prot:

SETD4_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 SETD4: view

Function for SETD4 Gene

Enzyme Numbers (IUBMB) for SETD4 Gene

Phenotypes From GWAS Catalog for SETD4 Gene

Gene Ontology (GO) - Molecular Function for SETD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008168 methyltransferase activity IEA --
GO:0016279 protein-lysine N-methyltransferase activity IBA --
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with SETD4: view
genes like me logo Genes that share phenotypes with SETD4: view

Animal Models for SETD4 Gene

MGI Knock Outs for SETD4:

Animal Model Products

miRNA for SETD4 Gene

miRTarBase miRNAs that target SETD4

Clone Products

No data available for Molecular function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SETD4 Gene

Localization for SETD4 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 SETD4 gene
Compartment Confidence
nucleus 5
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SETD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IBA --
genes like me logo Genes that share ontologies with SETD4: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SETD4 Gene

Pathways & Interactions for SETD4 Gene

SuperPathways for SETD4 Gene

SuperPathway Contained pathways
1 PKMTs methylate histone lysines
genes like me logo Genes that share pathways with SETD4: view

Pathways by source for SETD4 Gene

1 BioSystems pathway for SETD4 Gene

Gene Ontology (GO) - Biological Process for SETD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0018023 peptidyl-lysine trimethylation IBA --
GO:0018026 peptidyl-lysine monomethylation IBA --
GO:0032259 methylation IEA --
GO:0042254 ribosome biogenesis IBA --
genes like me logo Genes that share ontologies with SETD4: view

No data available for SIGNOR curated interactions for SETD4 Gene

Drugs & Compounds for SETD4 Gene

No Compound Related Data Available

Transcripts for SETD4 Gene

Unigene Clusters for SETD4 Gene

SET domain containing 4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SETD4 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b · 11c ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^
SP1: - - - - - - -
SP2: - - - - - - - - -
SP3: - - - - - - - - - - -
SP4: - - -
SP5: - - - - -
SP6: - - - - -
SP7: - - - - -
SP8: - - - -
SP9: - - -
SP10: - - - - -
SP11: -
SP12:
SP13: -
SP14:

ExUns: 16a · 16b ^ 17
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for SETD4 Gene

GeneLoc Exon Structure for
SETD4
ECgene alternative splicing isoforms for
SETD4

Expression for SETD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SETD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of SETD4 Gene:

SETD4

SOURCE GeneReport for Unigene cluster for SETD4 Gene:

Hs.606200

Evidence on tissue expression from TISSUES for SETD4 Gene

  • Lung(4.2)
  • Nervous system(2.8)
genes like me logo Genes that share expression patterns with SETD4: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SETD4 Gene

Orthologs for SETD4 Gene

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

Orthologs for SETD4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SETD4 33 34
  • 99.55 (n)
dog
(Canis familiaris)
Mammalia SETD4 33 34
  • 87.4 (n)
cow
(Bos Taurus)
Mammalia SETD4 33 34
  • 84.47 (n)
mouse
(Mus musculus)
Mammalia Setd4 33 16 34
  • 78.28 (n)
rat
(Rattus norvegicus)
Mammalia Setd4 33
  • 78.16 (n)
oppossum
(Monodelphis domestica)
Mammalia SETD4 34
  • 64 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETD4 34
  • 64 (a)
OneToOne
chicken
(Gallus gallus)
Aves SETD4 33 34
  • 67.51 (n)
lizard
(Anolis carolinensis)
Reptilia SETD4 34
  • 60 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia setd4 33
  • 58.07 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC53706 33
zebrafish
(Danio rerio)
Actinopterygii setd4 33 34
  • 55.37 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP013401 33
  • 42.24 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG33230 33 34
  • 41.96 (n)
worm
(Caenorhabditis elegans)
Secernentea set-29 33 34
  • 42.97 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes EFM1 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 22 (a)
OneToOne
Species where no ortholog for SETD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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 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 SETD4 Gene

ENSEMBL:
Gene Tree for SETD4 (if available)
TreeFam:
Gene Tree for SETD4 (if available)

Paralogs for SETD4 Gene

No data available for Paralogs for SETD4 Gene

Variants for SETD4 Gene

Sequence variations from dbSNP and Humsavar for SETD4 Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type
VAR_035988 A colorectal cancer sample
rs1000184863 -- 36,035,128(+) GGCCT(C/G)AACAG nc-transcript-variant, utr-variant-3-prime
rs1000216089 -- 36,034,920(+) AAAGT(A/G)TATAT nc-transcript-variant, utr-variant-3-prime
rs1000409769 -- 36,041,274(+) AACTA(-/C)CCTGG intron-variant
rs1000444826 -- 36,062,268(+) CAATA(A/G)GATAC nc-transcript-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for SETD4 Gene

Variant ID Type Subtype PubMed ID
nsv964547 CNV deletion 23825009
nsv587461 CNV loss 21841781
nsv470899 CNV loss 18288195
nsv459247 CNV loss 19166990
nsv3504 CNV insertion 18451855
esv3646959 CNV loss 21293372
esv2723389 CNV deletion 23290073
esv2723388 CNV deletion 23290073
esv2665899 CNV deletion 23128226
esv1004462 CNV deletion 20482838

Variation tolerance for SETD4 Gene

Residual Variation Intolerance Score: 40.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.03; 50.21% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SETD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SETD4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETD4 Gene

Disorders for SETD4 Gene

Relevant External Links for SETD4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SETD4

No disorders were found for SETD4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SETD4 Gene

Publications for SETD4 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  2. An unappreciated role for RNA surveillance. (PMID: 14759258) Hillman RT … Brenner SE (Genome biology 2004) 3 4 60
  3. 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 60
  4. From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map. (PMID: 11707072) Reymond A … Antonarakis SE (Genomics 2001) 3 4 60
  5. The DNA sequence of human chromosome 21. (PMID: 10830953) Hattori M … Chromosome 21 mapping and sequencing consortium (Nature 2000) 3 4 60

Products for SETD4 Gene

Sources for SETD4 Gene

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