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    Jade1 jade family PHD finger 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 310352, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Jade1provided by RGD
    Official Full Name
    jade family PHD finger 1provided by RGD
    Primary source
    RGD:1306920
    See related
    EnsemblRapid:ENSRNOG00000014066 AllianceGenome:RGD:1306920
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Phf17
    Summary
    Predicted to enable transcription coactivator activity. Predicted to contribute to histone acetyltransferase activity. Predicted to be involved in several processes, including negative regulation of canonical Wnt signaling pathway; regulation of cell growth; and regulation of nucleobase-containing compound metabolic process. Predicted to act upstream of or within negative regulation of G1/S transition of mitotic cell cycle. Predicted to be located in several cellular components, including cytosol; microtubule organizing center; and nuclear speck. Predicted to be part of histone acetyltransferase complex. Orthologous to human JADE1 (jade family PHD finger 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 162.6), Adrenal (RPKM 124.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Jade1 in Genome Data Viewer
    Location:
    2q26
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (126471124..126524252)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (124543233..124596361)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (128461147..128514298)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORD22 Neighboring gene uncharacterized LOC102553773 Neighboring gene ribosome biogenesis protein NSA2 homolog Neighboring gene sodium channel and clathrin linker 1 Neighboring gene similar to human chromosome 4 open reading frame 33

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Cell cycle-dependent chromatin shuttling of HBO1-JADE1 histone acetyl transferase (HAT) complex. Siriwardana NS, et al. Cell Cycle, 2014. PMID 24739512, Free PMC Article
    2. The ciliary protein nephrocystin-4 translocates the canonical Wnt regulator Jade-1 to the nucleus to negatively regulate β-catenin signaling. Borgal L, et al. J Biol Chem, 2012 Jul 20. PMID 22654112, Free PMC Article
    3. The von Hippel-Lindau tumor suppressor stabilizes novel plant homeodomain protein Jade-1. Zhou MI, et al. J Biol Chem, 2002 Oct 18. PMID 12169691
    4. Polycystin-1 regulates the stability and ubiquitination of transcription factor Jade-1. Foy RL, et al. Hum Mol Genet, 2012 Dec 15. PMID 23001567, Free PMC Article
    5. ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation. Doyon Y, et al. Mol Cell, 2006 Jan 6. PMID 16387653

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    contributes_to histone H3K14 acetyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    contributes_to histone H4K12 acetyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT contributes_to histone H4K16 acetyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    contributes_to histone H4K5 acetyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    contributes_to histone H4K8 acetyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coactivator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of G1/S transition of mitotic cell cycle ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of canonical Wnt signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of DNA biosynthetic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA replication ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cell cycle ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cell growth ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in ciliary basal body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of histone acetyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of histone acetyltransferase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    protein Jade-1
    Names
    PHD finger protein 17

    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.

    mRNA and Protein(s)

    1. NM_001415052.1 → NP_001401981.1  protein Jade-1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/TrEMBL
      D3ZM64
      Related
      ENSRNOP00000018872.7, ENSRNOT00000018872.8

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086020.1 Reference GRCr8

      Range
      126471124..126524252
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006232303.5 → XP_006232365.1  protein Jade-1 isoform X2

      See identical proteins and their annotated locations for XP_006232365.1

      UniProtKB/TrEMBL
      A6II53, D3ZM64
      Conserved Domains (3) summary
      cd15671
      Location:258 → 368
      ePHD_JADE; Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins
      cd15679
      Location:205 → 250
      PHD_JADE1; PHD finger found in protein Jade-1 and similar proteins
      pfam10513
      Location:92 → 180
      EPL1; Enhancer of polycomb-like

    2. XM_006232304.5 → XP_006232366.1  protein Jade-1 isoform X2

      See identical proteins and their annotated locations for XP_006232366.1

      UniProtKB/TrEMBL
      A6II53, D3ZM64
      Conserved Domains (3) summary
      cd15671
      Location:258 → 368
      ePHD_JADE; Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins
      cd15679
      Location:205 → 250
      PHD_JADE1; PHD finger found in protein Jade-1 and similar proteins
      pfam10513
      Location:92 → 180
      EPL1; Enhancer of polycomb-like

    3. XM_008760928.4 → XP_008759150.2  protein Jade-1 isoform X2

      UniProtKB/TrEMBL
      A6II53, D3ZM64
      Related
      ENSRNOP00000105202.1, ENSRNOT00000172515.1
      Conserved Domains (3) summary
      cd15671
      Location:258 → 368
      ePHD_JADE; Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins
      cd15679
      Location:205 → 250
      PHD_JADE1; PHD finger found in protein Jade-1 and similar proteins
      pfam10513
      Location:92 → 180
      EPL1; Enhancer of polycomb-like

    4. XM_006232301.5 → XP_006232363.1  protein Jade-1 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AB02, A6II53
      Related
      ENSRNOP00000090026.1, ENSRNOT00000098865.2
      Conserved Domains (3) summary
      cd15679
      Location:220 → 265
      PHD_JADE1; PHD finger found in protein Jade-1 and similar proteins
      cd15704
      Location:270 → 387
      ePHD_JADE1; Extended PHD finger found in protein Jade-1 and similar proteins
      pfam10513
      Location:107 → 195
      EPL1; Enhancer of polycomb-like

    5. XM_063281777.1 → XP_063137847.1  protein Jade-1 isoform X3

    6. XM_039102248.2 → XP_038958176.1  protein Jade-1 isoform X3

      UniProtKB/TrEMBL
      A0A8I6GJ46
      Conserved Domains (2) summary
      COG5141
      Location:32 → 367
      COG5141; PHD zinc finger-containing protein [General function prediction only]
      cd15704
      Location:93 → 210
      ePHD_JADE1; Extended PHD finger found in protein Jade-1 and similar proteins

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001107670.1: Suppressed sequence

      Description
      NM_001107670.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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