Human Gene PHF19 (ENST00000373896.8_12) from GENCODE V47lift37

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Description: PHD finger protein 19, transcript variant 1 (from RefSeq NM_015651.3)
Gencode Transcript: ENST00000373896.8_12
Gencode Gene: ENSG00000119403.15_17
Transcript (Including UTRs)
Position: hg19 chr9:123,617,929-123,639,466 Size: 21,538 Total Exon Count: 15 Strand: -
Coding Region
Position: hg19 chr9:123,620,222-123,637,019 Size: 16,798 Coding Exon Count: 14

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr9:123,617,929-123,639,466)			mRNA (may differ from genome)		Protein (580 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: PHF19_HUMAN 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. SUBCELLULAR LOCATION: Nucleus. 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;

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

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 D013749 Tetrachlorodibenzodioxin D014212 Tretinoin C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone D001564 Benzo(a)pyrene D019256 Cadmium Chloride D002117 Calcitriol D003300 Copper D003375 Coumestrol D004958 Estradiol C558013 NSC 689534 more ... click here to view the complete list

Common Gene Haplotype Alleles


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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

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-50.60	113	-0.448	Picture	PostScript	Text
3' UTR	-906.70	2293	-0.395	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
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00628 - PHD-finger
PF14061 - Polycomb-like MTF2 factor 2
PF18104 - Jumonji domain-containing protein 2A Tudor domain

SCOP Domains:
48695 - Multiheme cytochromes
54160 - Chromo domain-like
63748 - Tudor/PWWP/MBT
57603 - FnI-like domain
57889 - Cysteine-rich domain
57903 - FYVE/PHD zinc finger

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

2E5Q - NMR MuPIT

ModBase Predicted Comparative 3D Structure on Q5T6S3


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

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: ENST00000373896.1, ENST00000373896.2, ENST00000373896.3, ENST00000373896.4, ENST00000373896.5, ENST00000373896.6, ENST00000373896.7, NM_015651, PCL3, PHF19_HUMAN, Q32NF2, Q5T6S3, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9, uc318ldq.1, uc318ldq.2 UCSC ID: ENST00000373896.8_12 RefSeq Accession: NM_015651.3 Protein: Q5T6S3 (aka PHF19_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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