Human Gene PHF19 (uc004bks.1) Description and Page Index
  Description: Homo sapiens PHD finger protein 19 (PHF19), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:123,617,931-123,639,606 Size: 21,676 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr9:123,620,222-123,637,019 Size: 16,798 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr9:123,617,931-123,639,606)mRNA (may differ from genome)Protein (580 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  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;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PHF19
CDC HuGE Published Literature: PHF19
Positive Disease Associations: Arthritis, Rheumatoid , Autoimmune Diseases
Related Studies:
  1. Arthritis, Rheumatoid
    Peter K Gregersen et al. Nature genetics 2009, REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis., Nature genetics. [PubMed 19503088]
  2. Autoimmune Diseases
    Alexandra Zhernakova et al. PLoS genetics 2011, Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci., PLoS genetics. [PubMed 21383967]

-  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

+  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: 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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -121.20253-0.479 Picture PostScript Text
3' UTR -938.462291-0.410 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:
PF00628 - PHD-finger
PF14061 - Polycomb-like MTF2 factor 2

SCOP Domains:
63748 - Tudor/PWWP/MBT
57903 - FYVE/PHD zinc 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
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene 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.
BC044224 - Homo sapiens PHD finger protein 19, mRNA (cDNA clone IMAGE:5729468), containing frame-shift errors.
AL117477 - Homo sapiens mRNA; cDNA DKFZp727G051 (from clone DKFZp727G051); partial cds.
JD264851 - Sequence 245875 from Patent EP1572962.
JD324947 - Sequence 305971 from Patent EP1572962.
JD527102 - Sequence 508126 from Patent EP1572962.
JD240182 - Sequence 221206 from Patent EP1572962.
JD126415 - Sequence 107439 from Patent EP1572962.
JD509697 - Sequence 490721 from Patent EP1572962.
JD289699 - Sequence 270723 from Patent EP1572962.
JD045601 - Sequence 26625 from Patent EP1572962.
JD318424 - Sequence 299448 from Patent EP1572962.
JD098636 - Sequence 79660 from Patent EP1572962.
JD248742 - Sequence 229766 from Patent EP1572962.
JD281780 - Sequence 262804 from Patent EP1572962.
JD077467 - Sequence 58491 from Patent EP1572962.
JD477308 - Sequence 458332 from Patent EP1572962.
JD134760 - Sequence 115784 from Patent EP1572962.
JD159600 - Sequence 140624 from Patent EP1572962.
JD424325 - Sequence 405349 from Patent EP1572962.
JD095712 - Sequence 76736 from Patent EP1572962.
JD356085 - Sequence 337109 from Patent EP1572962.
JD215033 - Sequence 196057 from Patent EP1572962.
JD446171 - Sequence 427195 from Patent EP1572962.
JD173736 - Sequence 154760 from Patent EP1572962.
JD163340 - Sequence 144364 from Patent EP1572962.
JD040699 - Sequence 21723 from Patent EP1572962.
JD094941 - Sequence 75965 from Patent EP1572962.
JD301306 - Sequence 282330 from Patent EP1572962.
JD457760 - Sequence 438784 from Patent EP1572962.
JD503182 - Sequence 484206 from Patent EP1572962.
JD150408 - Sequence 131432 from Patent EP1572962.
JD152730 - Sequence 133754 from Patent EP1572962.
JD189076 - Sequence 170100 from Patent EP1572962.
JD334293 - Sequence 315317 from Patent EP1572962.
JD312407 - Sequence 293431 from Patent EP1572962.
JD121326 - Sequence 102350 from Patent EP1572962.
JD075207 - Sequence 56231 from Patent EP1572962.
JD313364 - Sequence 294388 from Patent EP1572962.
JD103030 - Sequence 84054 from Patent EP1572962.
JD050766 - Sequence 31790 from Patent EP1572962.
JD103225 - Sequence 84249 from Patent EP1572962.
JD320674 - Sequence 301698 from Patent EP1572962.
JD103224 - Sequence 84248 from Patent EP1572962.
JD111499 - Sequence 92523 from Patent EP1572962.
JD223325 - Sequence 204349 from Patent EP1572962.
JD147825 - Sequence 128849 from Patent EP1572962.
JD175404 - Sequence 156428 from Patent EP1572962.
JD248014 - Sequence 229038 from Patent EP1572962.
JD163327 - Sequence 144351 from Patent EP1572962.
JD334906 - Sequence 315930 from Patent EP1572962.
JD439762 - Sequence 420786 from Patent EP1572962.
AK303433 - Homo sapiens cDNA FLJ53261 complete cds, highly similar to Homo sapiens PHD finger protein 19 (PHF19), transcript variant 1, mRNA.
JD549880 - Sequence 530904 from Patent EP1572962.
JD124078 - Sequence 105102 from Patent EP1572962.
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.
AK302996 - Homo sapiens cDNA FLJ55009 complete cds, highly similar to Homo sapiens PHD finger protein 19 (PHF19), transcript variant 1, mRNA.
JD140934 - Sequence 121958 from Patent EP1572962.
JD365672 - Sequence 346696 from Patent EP1572962.
JD194010 - Sequence 175034 from Patent EP1572962.
JD048995 - Sequence 30019 from Patent EP1572962.
JD063304 - Sequence 44328 from Patent EP1572962.
JD537135 - Sequence 518159 from Patent EP1572962.
JD065303 - Sequence 46327 from Patent EP1572962.
JD426442 - Sequence 407466 from Patent EP1572962.
JD383959 - Sequence 364983 from Patent EP1572962.
JD426441 - Sequence 407465 from Patent EP1572962.
JD480336 - Sequence 461360 from Patent EP1572962.
JD241966 - Sequence 222990 from Patent EP1572962.
JD286228 - Sequence 267252 from Patent EP1572962.
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_015651, NP_056466, PCL3, PHF19_HUMAN, Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9
UCSC ID: uc004bks.1
RefSeq Accession: NM_015651
Protein: Q5T6S3 (aka PHF19_HUMAN)
CCDS: CCDS35116.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_015651.1
exon count: 15CDS single in 3' UTR: no RNA size: 4287
ORF size: 1743CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3619.50frame 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.