Human Gene JADE1 (uc003igk.3)
  Description: Homo sapiens PHD finger protein 17 (JADE1), transcript variant L, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr4:129,730,779-129,796,379 Size: 65,601 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr4:129,752,914-129,793,417 Size: 40,504 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:129,730,779-129,796,379)mRNA (may differ from genome)Protein (842 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHPRDLynxMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: JADE1_HUMAN
DESCRIPTION: RecName: Full=Protein Jade-1; AltName: Full=PHD finger protein 17;
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. Transcriptional coactivator it may also promote acetylation of nucleosomal histone H4 by KAT5. Promotes apoptosis. May act as a renal tumor suppressor.
SUBUNIT: Component of the HBO1 complex composed at least of ING4 or ING5, KAT7/HBO1, MEAF6, and one of PHF15, PHF16 and PHF17. Isoform 3 interacts with VHL and KAT5.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: Highly expressed in kidney. Also present in pancreas, liver and heart (at protein level). Down-regulated in renal cancer cells.
DOMAIN: The 2 PHD-type zinc fingers are required for transcriptional activity.
SIMILARITY: Belongs to the JADE family.
SIMILARITY: Contains 2 PHD-type zinc fingers.
SEQUENCE CAUTION: Sequence=BAB15371.1; Type=Erroneous initiation; Sequence=BAC11335.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.10 RPKM in Thyroid
Total median expression: 227.62 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -110.61280-0.395 Picture PostScript Text
3' UTR -752.502962-0.254 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019542 - Enhancer_polycomb-like_N
IPR019786 - Zinc_finger_PHD-type_CS
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00628 - PHD-finger
PF10513 - Enhancer of polycomb-like
PF13771 - PHD-like zinc-binding domain
PF13831 - PHD-finger
PF13832 - PHD-zinc-finger like domain

SCOP Domains:
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q6IE81
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001105 RNA polymerase II transcription coactivator activity
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0006915 apoptotic process
GO:0030308 negative regulation of cell growth
GO:0043966 histone H3 acetylation
GO:0043981 histone H4-K5 acetylation
GO:0043982 histone H4-K8 acetylation
GO:0043983 histone H4-K12 acetylation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0090090 negative regulation of canonical Wnt signaling pathway
GO:2000134 negative regulation of G1/S transition of mitotic cell cycle
GO:0043984 histone H4-K16 acetylation

Cellular Component:
GO:0000123 histone acetyltransferase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0016607 nuclear speck
GO:0036064 ciliary basal body
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  AK027620 - Homo sapiens cDNA FLJ14714 fis, clone NT2RP3001107, weakly similar to PEREGRIN.
AF520952 - Homo sapiens PHD protein Jade-1 mRNA, complete cds.
AK304815 - Homo sapiens cDNA FLJ53388 complete cds, highly similar to Homo sapiens PHD finger protein 17 (PHF17), transcript variant L, mRNA.
AK127326 - Homo sapiens cDNA FLJ45397 fis, clone BRHIP3027651, weakly similar to Bromodomain-containing protein 1.
AK297357 - Homo sapiens cDNA FLJ60695 complete cds, highly similar to Homo sapiens PHD finger protein 17 (PHF17), transcript variant L, mRNA.
AK304235 - Homo sapiens cDNA FLJ53490 complete cds, highly similar to Homo sapiens PHD finger protein 17 (PHF17), transcript variant L, mRNA.
BC032376 - Homo sapiens PHD finger protein 17, mRNA (cDNA clone MGC:40386 IMAGE:5111727), complete cds.
AB590320 - Synthetic construct DNA, clone: pFN21AE1296, Homo sapiens PHF17 gene for PHD finger protein 17, without stop codon, in Flexi system.
DQ894766 - Synthetic construct Homo sapiens clone IMAGE:100009226; FLH178248.01L; RZPDo839B01127D PHD finger protein 17 (PHF17) gene, encodes complete protein.
KJ894759 - Synthetic construct Homo sapiens clone ccsbBroadEn_04153 PHF17 gene, encodes complete protein.
DQ891572 - Synthetic construct clone IMAGE:100004202; FLH178252.01X; RZPDo839B01128D PHD finger protein 17 (PHF17) gene, encodes complete protein.
AB058710 - Homo sapiens mRNA for KIAA1807 protein, partial cds.
AK074986 - Homo sapiens cDNA FLJ90505 fis, clone NT2RP3004119, weakly similar to PEREGRIN.
AK026132 - Homo sapiens cDNA: FLJ22479 fis, clone HRC10831.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q6IE81 (Reactome details) participates in the following event(s):

R-HSA-3318413 KAT7-containing ING4/5 complexes acetylate Me3K-histone H3
R-HSA-3214847 HATs acetylate histones
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: D3DNY0, D3DNY1, JADE1_HUMAN, KIAA1807, NM_199320, NP_955352, PHF17, Q4W5D5, Q6IE81, Q6ZSL7, Q8NC41, Q96JL8, Q96SQ1, Q9H692
UCSC ID: uc003igk.3
RefSeq Accession: NM_199320
Protein: Q6IE81 (aka JADE1_HUMAN)
CCDS: CCDS34062.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_199320.2
exon count: 11CDS single in 3' UTR: no RNA size: 5771
ORF size: 2529CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5180.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.