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JADE3 jade family PHD finger 3 [ Homo sapiens (human) ]

Gene ID: 9767, updated on 2-Nov-2024

Summary

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Official Symbol
JADE3provided by HGNC
Official Full Name
jade family PHD finger 3provided by HGNC
Primary source
HGNC:HGNC:22982
See related
Ensembl:ENSG00000102221 MIM:300618; AllianceGenome:HGNC:22982
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PHF16; JADE-3
Summary
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]
Expression
Broad expression in testis (RPKM 8.9), placenta (RPKM 7.4) and 25 other tissues See more
Orthologs
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Genomic context

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See JADE3 in Genome Data Viewer
Location:
Xp11.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (46912301..47061242)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (46319282..46468244)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (46771736..46920641)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29577 Neighboring gene RP2 activator of ARL3 GTPase Neighboring gene long intergenic non-protein coding RNA 1545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29578 Neighboring gene Sharpr-MPRA regulatory region 4088 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20797 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29579 Neighboring gene Sharpr-MPRA regulatory region 7060 Neighboring gene RNA, U6 small nuclear 1189, pseudogene Neighboring gene regucalcin Neighboring gene uncharacterized LOC105373193 Neighboring gene uncharacterized LOC107985720

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Identification of human estrogen-inducible transcripts that potentially mediate the apoptotic response in breast cancer. Szelei J, et al. J Steroid Biochem Mol Biol, 2000 Mar. PMID 10775800
  2. Whole-exome sequencing identifies mutated PCK2 and HUWE1 associated with carcinoma cell proliferation in a hepatocellular carcinoma patient. Liu YX, et al. Oncol Lett, 2012 Oct. PMID 23205112, Free PMC Article
  3. Genome-wide CRISPR activation screen identifies JADE3 as an antiviral activator of NF-kB-dependent IFITM3 expression. Munir M, et al. J Biol Chem, 2024 Apr. PMID 38462163, Free PMC Article
  4. Jade family PHD finger 3 (JADE3) increases cancer stem cell-like properties and tumorigenicity in colon cancer. Jian Y, et al. Cancer Lett, 2018 Aug 1. PMID 29660380
  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. Tzouanacou E, et al. Mol Cell Biol, 2003 Dec. PMID 14612400, Free PMC Article

See all (42) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genome-wide CRISPR activation screen identifies JADE3 as an antiviral activator of NF-kB-dependent IFITM3 expression.
    Title: Genome-wide CRISPR activation screen identifies JADE3 as an antiviral activator of NF-kB-dependent IFITM3 expression.
  2. JADE3 was markedly upregulated in colon cancer tissues and correlated with cancer progression and predicted shorter patient survival. JADE3 interacted with the promoters of LGR5 and activated its transcription, by increasing the occupancy of p300 acetyltransferase and histone acetylation on the promoters. These findings suggest an oncogenic role of JADE3 by regulating cancer stem cell-like traits in the colon cancer.
    Title: Jade family PHD finger 3 (JADE3) increases cancer stem cell-like properties and tumorigenicity in colon cancer.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0215, MGC138748, MGC138749

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in regulation of DNA biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA replication IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of cell cycle IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of cell growth ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of histone acetyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of histone acetyltransferase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
protein Jade-3
Names
PHD finger protein 16
jade family PHD finger protein 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_013324.3 RefSeqGene

    Range
    5121..153942
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001077445.3 → NP_001070913.1  protein Jade-3

    See identical proteins and their annotated locations for NP_001070913.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AF127774, AL704455, AW071647, BN000289
    Consensus CDS
    CCDS14271.1
    UniProtKB/Swiss-Prot
    Q6IE79, Q92613
    UniProtKB/TrEMBL
    A8K5A5
    Related
    ENSP00000479377.1, ENST00000611250.4
    Conserved Domains (3) summary
    cd15681
    Location:202 → 251
    PHD_JADE3; PHD finger found in protein Jade-3 and similar proteins
    cd15706
    Location:255 → 365
    ePHD_JADE3; Extended PHD finger found in protein Jade-3 and similar proteins
    pfam10513
    Location:88 → 177
    EPL1; Enhancer of polycomb-like

  2. NM_014735.5 → NP_055550.1  protein Jade-3

    See identical proteins and their annotated locations for NP_055550.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AF127774, AL627143, AW071647, BN000289
    Consensus CDS
    CCDS14271.1
    UniProtKB/Swiss-Prot
    Q6IE79, Q92613
    UniProtKB/TrEMBL
    A8K5A5
    Related
    ENSP00000481850.1, ENST00000614628.5
    Conserved Domains (3) summary
    cd15681
    Location:202 → 251
    PHD_JADE3; PHD finger found in protein Jade-3 and similar proteins
    cd15706
    Location:255 → 365
    ePHD_JADE3; Extended PHD finger found in protein Jade-3 and similar proteins
    pfam10513
    Location:88 → 177
    EPL1; Enhancer of polycomb-like

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    46912301..47061242
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    46319282..46468244
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92613.1 GenPept UniProtKB/Swiss-Prot:Q92613

Gene LinkOut

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