Human Gene PHF19 (ENST00000312189.10) Description and Page Index
  Description: Homo sapiens PHD finger protein 19 (PHF19), transcript variant 5, mRNA. (from RefSeq NM_001286843)
Gencode Transcript: ENST00000312189.10
Gencode Gene: ENSG00000119403.15
Transcript (Including UTRs)
   Position: hg38 chr9:120,869,587-120,877,188 Size: 7,602 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg38 chr9:120,869,686-120,874,741 Size: 5,056 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr9:120,869,587-120,877,188)mRNA (may differ from genome)Protein (207 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
Stanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=PHD finger protein 19; AltName: Full=Polycomb-like protein 3; Short=hPCL3;
FUNCTION: Acts as a transcritpional repressor. Isoform 1 and isoform 2 inhibit transcription from an HSV-tk promoter.
SUBUNIT: Interacts with EZH2 via its Tudor domain.
TISSUE SPECIFICITY: Isoform 1 is expressed in thymus, heart, lung and kidney. Isoform 2 is predominantly expressed in placenta, skeletal muscle and kidney, whereas isoform 1 is predominantly expressed in liver and peripheral blood leukocytes. Overexpressed in many types of cancers, including colon, skin, lung, rectal, cervical, uterus, liver cancers, in cell lines derived from different stages of melanoma and in glioma cell lines.
SIMILARITY: Contains 2 PHD-type zinc fingers.
SIMILARITY: Contains 1 Tudor domain.
SEQUENCE CAUTION: Sequence=CAE45832.1; Type=Erroneous initiation;

-  MalaCards Disease Associations
  MalaCards Gene Search: PHF19
Diseases sorted by gene-association score: cataract 7 (6), leukoencephalopathy with vanishing white matter (4), melanoma (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.25 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 328.13 RPKM

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

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -50.60113-0.448 Picture PostScript Text
3' UTR -19.9099-0.201 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
IPR025894 - Mtf2_C_dom
IPR002999 - Tudor
IPR019786 - Zinc_finger_PHD-type_CS
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger

Pfam Domains:
PF14061 - Polycomb-like MTF2 factor 2
PF00628 - PHD-finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help


ModBase Predicted Comparative 3D Structure on Q5T6S3
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0035064 methylated histone binding
GO:0046872 metal ion binding

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0045814 negative regulation of gene expression, epigenetic
GO:0061087 positive regulation of histone H3-K27 methylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0035098 ESC/E(Z) complex

-  Descriptions from all associated GenBank mRNAs
  BX640713 - Homo sapiens mRNA; cDNA DKFZp686C07187 (from clone DKFZp686C07187).
AK122744 - Homo sapiens cDNA FLJ16269 fis, clone MESAN2016552, highly similar to Homo sapiens PHD finger protein 19 (PHF19), transcript variant 1, mRNA.
AL117477 - Homo sapiens mRNA; cDNA DKFZp727G051 (from clone DKFZp727G051); partial cds.
AK303433 - Homo sapiens cDNA FLJ53261 complete cds, highly similar to Homo sapiens PHD finger protein 19 (PHF19), transcript variant 1, mRNA.
BC125076 - Homo sapiens PHD finger protein 19, mRNA (cDNA clone MGC:149712 IMAGE:40117657), complete cds.
BC125077 - Homo sapiens PHD finger protein 19, mRNA (cDNA clone MGC:149713 IMAGE:40117658), complete cds.
KJ893530 - Synthetic construct Homo sapiens clone ccsbBroadEn_02924 PHF19 gene, encodes complete protein.
AB527540 - Synthetic construct DNA, clone: pF1KB6107, Homo sapiens PHF19 gene for PHD finger protein 19, without stop codon, in Flexi system.
BC022374 - Homo sapiens PHD finger protein 19, mRNA (cDNA clone IMAGE:4807540), complete cds.
BC108663 - Homo sapiens PHD finger protein 19, mRNA (cDNA clone IMAGE:6164954), complete cds.
CU692586 - Synthetic construct Homo sapiens gateway clone IMAGE:100022118 5' read PHF19 mRNA.
HQ447719 - Synthetic construct Homo sapiens clone IMAGE:100071050; CCSB013122_01 PHD finger protein 19 (PHF19) gene, encodes complete protein.
KJ893529 - Synthetic construct Homo sapiens clone ccsbBroadEn_02923 PHF19 gene, encodes complete protein.

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

Protein Q5T6S3 (Reactome details) participates in the following event(s):

R-HSA-212263 PRC2 trimethylates histone H3 at lysine-27
R-HSA-212300 PRC2 methylates histones and DNA
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001286843, PCL3, PHF19_HUMAN, Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9, uc004bkt.1, uc004bkt.2, uc004bkt.3, uc004bkt.4, uc004bkt.5
UCSC ID: uc004bkt.5
RefSeq Accession: NM_001009936
Protein: Q5T6S3 (aka PHF19_HUMAN)
CCDS: CCDS35117.1

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