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

    Gene ID: 9767, updated on 10-Dec-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
    mouse all
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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
    • 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 (43) 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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    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)

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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