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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. Gene Ontology (GO) annotations related to this gene include methyltransferase activity. An important paralog of this gene is SETD3.

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

GeneHancer (GH) Regulatory Elements for SETD4 Gene

Promoters and enhancers for SETD4 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
GH21I036059 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 557 +19.0 18951 2.5 CLOCK SMAD1 ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B CBX5 E2F8 SETD4 LOC105369295 LINC01436 CBR1 LOC105369306 RNU6-992P
GH21I036078 Enhancer 1.2 Ensembl ENCODE dbSUPER 562.1 +0.1 149 2 HDAC1 NFRKB ZBTB40 YY1 CHAMP1 ZNF766 EGR1 CAVIN1 ZNF592 ZNF148 SETD4 LINC01436 CBR1 RIMKLBP1 LOC105369306 CBR3-AS1 LOC100133286
GH21I036080 Enhancer 0.8 ENCODE dbSUPER 550.8 -1.2 -1209 0.2 FOXA2 RXRA HLF MAX REST RAD21 FOXA1 GABPA YY1 JUND SETD4 LOC105369306 ENSG00000236119 LOC100133286
GH21I037071 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 69.8 -993.8 -993755 4.2 DMAP1 YY1 ZNF213 ZNF416 ZNF143 ZNF548 SP3 NFYC ZNF610 GLIS1 TTC3 PIGP SETD4 ENSG00000242553 DYRK1A MORC3 TTC3-AS1 ENSG00000224790 LOC105372795 GC21M037042
GH21I036697 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 59.4 -621.7 -621734 6.9 HDGF SIN3A GLI4 ZNF2 GLIS2 SP3 SP5 YY2 ZNF662 REST SIM2 ENSG00000224269 SETD4 ENSG00000242553 RIMKLBP1 TTC3-AS1 TTC3 DSCR9 MORC3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SETD4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SETD4 gene promoter:

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

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

Paralogs for SETD4 Gene

genes like me logo Genes that share paralogs with SETD4: view

Variants for SETD4 Gene

Sequence variations from dbSNP and Humsavar for SETD4 Gene

SNP ID Clin Chr 21 pos Variation AA Info Type
VAR_035988 A colorectal cancer sample p.Glu420Gly
rs1000184863 -- 36,035,128(-) G/C 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1000216089 -- 36,034,920(-) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1000409769 -- 36,041,274(-) CCC/CC genic_downstream_transcript_variant, intron_variant
rs1000444826 -- 36,062,268(-) A/G upstream_transcript_variant

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)

Additional Variant Information 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

Additional Disease Information for 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 58
  2. An unappreciated role for RNA surveillance. (PMID: 14759258) Hillman RT … Brenner SE (Genome biology 2004) 3 4 58
  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 58
  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 58
  5. The DNA sequence of human chromosome 21. (PMID: 10830953) Hattori M … Chromosome 21 mapping and sequencing consortium (Nature 2000) 3 4 58

Products for SETD4 Gene

Sources for SETD4 Gene

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