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Aliases for JADE3 Gene

Aliases for JADE3 Gene

  • Jade Family PHD Finger 3 2 3 5
  • PHD Finger Protein 16 2 3 4
  • Jade Family PHD Finger Protein 3 3 4
  • PHF16 3 4
  • Protein Jade-3 3
  • KIAA0215 4
  • JADE-3 3

External Ids for JADE3 Gene

Previous HGNC Symbols for JADE3 Gene

  • PHF16

Previous GeneCards Identifiers for JADE3 Gene

  • GC0XP046773

Summaries for JADE3 Gene

Entrez Gene Summary for JADE3 Gene

  • This gene encodes a member of a family of large proteins containing PHD (plant homeo domain)-type zinc fingers. The encoded protein may be associated in a nuclear complex that functions in histone H4 acetylation. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Aug 2013]

GeneCards Summary for JADE3 Gene

JADE3 (Jade Family PHD Finger 3) is a Protein Coding gene. Among its related pathways are Chromatin organization. An important paralog of this gene is JADE1.

UniProtKB/Swiss-Prot for JADE3 Gene

  • Component of the HBO1 complex which has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3 and is responsible for the bulk of histone H4 acetylation in vivo.

Gene Wiki entry for JADE3 Gene

Additional gene information for JADE3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for JADE3 Gene

Genomics for JADE3 Gene

Regulatory Elements for JADE3 Gene

Enhancers for JADE3 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
GH0XH046912 0.9 ENCODE 0.7 +1.0 1027 2.6 RB1 ZSCAN4 ARID4B ZNF76 SIN3A BMI1 RAD21 GLIS2 EGR1 ZSCAN5C JADE3 RGN
GH0XH046903 1.2 Ensembl ENCODE 0.4 -8.3 -8341 1.3 PKNOX1 ARID4B SIN3A ZNF2 GLIS2 ZNF143 MXD4 REST NBN KDM1A SLC9A7 LINC01545 JADE3
GH0XH046951 1.1 Ensembl ENCODE 0.3 +40.9 40947 2.6 PKNOX1 FOXA2 DMAP1 BATF RARA ZNF366 RUNX3 IKZF2 SP5 REST JADE3 RGN
GH0XH046978 1.1 Ensembl ENCODE 0.2 +67.0 66965 2.1 ZNF2 RAD21 RFX5 YY1 ZSCAN5C ZNF143 RCOR1 FOS SMARCA5 ZNF654 JADE3 RGN
GH0XH046963 0.9 Ensembl ENCODE 0.2 +51.3 51318 1 TFAP4 ZNF687 NR2F1 EBF1 DPF2 YY1 IKZF1 RUNX3 IKZF2 TRIM28 JADE3 RGN
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around JADE3 on UCSC Golden Path with GeneCards custom track

Promoters for JADE3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000246369 924 2400 RB1 ZSCAN4 ARID4B ZNF76 SIN3A BMI1 RAD21 RARA GLIS2 EGR1

Genomic Locations for JADE3 Gene

Genomic Locations for JADE3 Gene
chrX:46,912,276-47,061,242
(GRCh38/hg38)
Size:
148,967 bases
Orientation:
Plus strand
chrX:46,771,711-46,920,641
(GRCh37/hg19)

Genomic View for JADE3 Gene

Genes around JADE3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
JADE3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for JADE3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for JADE3 Gene

Proteins for JADE3 Gene

  • Protein details for JADE3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92613-JADE3_HUMAN
    Recommended name:
    Protein Jade-3
    Protein Accession:
    Q92613
    Secondary Accessions:
    • Q6IE79

    Protein attributes for JADE3 Gene

    Size:
    823 amino acids
    Molecular mass:
    93808 Da
    Quaternary structure:
    • Component of the HBO1 complex composed at least of ING4 or ING5, KAT7/HBO1, MEAF6, and one of JADE1, JADE2 and JADE3.
    SequenceCaution:
    • Sequence=BAA13205.2; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for JADE3 Gene

Post-translational modifications for JADE3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for JADE3 Gene

No data available for DME Specific Peptides for JADE3 Gene

Domains & Families for JADE3 Gene

Gene Families for JADE3 Gene

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

Suggested Antigen Peptide Sequences for JADE3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q92613

UniProtKB/Swiss-Prot:

JADE3_HUMAN :
  • Belongs to the JADE family.
Family:
  • Belongs to the JADE family.
genes like me logo Genes that share domains with JADE3: view

Function for JADE3 Gene

Molecular function for JADE3 Gene

UniProtKB/Swiss-Prot Function:
Component of the HBO1 complex which has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3 and is responsible for the bulk of histone H4 acetylation in vivo.
UniProtKB/Swiss-Prot Induction:
By estradiol in estrogen-responsive breast cancer cells.

Gene Ontology (GO) - Molecular Function for JADE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with JADE3: view
genes like me logo Genes that share phenotypes with JADE3: view

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for JADE3 Gene

Localization for JADE3 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 JADE3 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for JADE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000123 histone acetyltransferase complex IDA 16387653
genes like me logo Genes that share ontologies with JADE3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for JADE3 Gene

Pathways & Interactions for JADE3 Gene

genes like me logo Genes that share pathways with JADE3: view

Pathways by source for JADE3 Gene

Interacting Proteins for JADE3 Gene

Gene Ontology (GO) - Biological Process for JADE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043966 histone H3 acetylation IDA 16387653
GO:0043981 histone H4-K5 acetylation IDA 16387653
GO:0043982 histone H4-K8 acetylation IDA 16387653
GO:0043983 histone H4-K12 acetylation IDA 16387653
GO:0043984 NOT histone H4-K16 acetylation IDA 16387653
genes like me logo Genes that share ontologies with JADE3: view

No data available for SIGNOR curated interactions for JADE3 Gene

Drugs & Compounds for JADE3 Gene

No Compound Related Data Available

Transcripts for JADE3 Gene

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for JADE3 Gene

No ASD Table

Relevant External Links for JADE3 Gene

GeneLoc Exon Structure for
JADE3
ECgene alternative splicing isoforms for
JADE3

Expression for JADE3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for JADE3 Gene

Protein differential expression in normal tissues from HIPED for JADE3 Gene

This gene is overexpressed in Plasma (59.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for JADE3 Gene



Protein tissue co-expression partners for JADE3 Gene

NURSA nuclear receptor signaling pathways regulating expression of JADE3 Gene:

JADE3

mRNA Expression by UniProt/SwissProt for JADE3 Gene:

Q92613-JADE3_HUMAN
Tissue specificity: Ubiquitously expressed, with highest levels in placenta and uterus.

Evidence on tissue expression from TISSUES for JADE3 Gene

  • Bone marrow(4)
genes like me logo Genes that share expression patterns with JADE3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for JADE3 Gene

Orthologs for JADE3 Gene

This gene was present in the common ancestor of animals.

Orthologs for JADE3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHF16 33
  • 99.04 (n)
JADE3 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PHF16 33
  • 90.64 (n)
JADE3 34
  • 88 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PHF16 33
  • 88.01 (n)
JADE3 34
  • 84 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Jade3 33
  • 85.34 (n)
mouse
(Mus musculus)
Mammalia Jade3 33 16
  • 84.89 (n)
Phf16 34
  • 82 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia JADE3 34
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia JADE3 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHF16 33
  • 75.05 (n)
JADE3 34
  • 74 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia JADE3 34
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia jade3 33
  • 67.64 (n)
Str.566 33
zebrafish
(Danio rerio)
Actinopterygii jade3 33 33 34
  • 64.38 (n)
fruit fly
(Drosophila melanogaster)
Insecta rno 34
  • 10 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 43 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.659 33
Species where no ortholog for JADE3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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 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 JADE3 Gene

ENSEMBL:
Gene Tree for JADE3 (if available)
TreeFam:
Gene Tree for JADE3 (if available)

Paralogs for JADE3 Gene

Paralogs for JADE3 Gene

(3) SIMAP similar genes for JADE3 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with JADE3: view

Variants for JADE3 Gene

Sequence variations from dbSNP and Humsavar for JADE3 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs1000004661 -- 46,934,456(+) ACCAC(A/G)CCTGG intron-variant
rs1000008219 -- 46,975,058(+) GGGGG(G/T)GCAAA intron-variant
rs1000054742 -- 46,985,108(+) GATAG(A/C)TAAAT intron-variant
rs1000097859 -- 46,955,555(+) TTCCC(A/G)GGTAA intron-variant
rs1000211679 -- 46,926,972(+) ATGTA(C/T)ATGTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for JADE3 Gene

Variant ID Type Subtype PubMed ID
nsv818024 CNV gain 17921354
nsv7440 OTHER inversion 18451855
nsv508767 CNV insertion 20534489
nsv203 OTHER inversion 15895083
nsv1110082 CNV deletion 24896259
nsv1077228 CNV deletion 25765185
esv2670040 CNV deletion 23128226
esv2427673 OTHER inversion 19546169
esv22153 CNV loss 19812545
esv1121377 OTHER inversion 17803354
esv1006962 OTHER inversion 20482838
dgv62n50 OTHER inversion 21212237
dgv61n47 OTHER inversion 21111241
dgv4585e59 OTHER inversion 20981092
dgv139n16 OTHER inversion 17901297

Variation tolerance for JADE3 Gene

Residual Variation Intolerance Score: 10.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.85; 17.80% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for JADE3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
JADE3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for JADE3 Gene

Disorders for JADE3 Gene

Relevant External Links for JADE3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
JADE3

No disorders were found for JADE3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for JADE3 Gene

Publications for JADE3 Gene

  1. ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation. (PMID: 16387653) Doyon Y … Côté J (Molecular cell 2006) 3 4 60
  2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 60
  3. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 60
  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 60
  5. Identification of Jade1, a gene encoding a PHD zinc finger protein, in a gene trap mutagenesis screen for genes involved in anteroposterior axis development. (PMID: 14612400) Tzouanacou E … Wilson V (Molecular and cellular biology 2003) 3 4 60

Products for JADE3 Gene

Sources for JADE3 Gene

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