Human Gene PCGF5 (ENST00000336126.6_4) from GENCODE V47lift37
  Description: polycomb group ring finger 5, transcript variant 1 (from RefSeq NM_032373.5)
Gencode Transcript: ENST00000336126.6_4
Gencode Gene: ENSG00000180628.15_8
Transcript (Including UTRs)
   Position: hg19 chr10:92,980,420-93,044,094 Size: 63,675 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr10:92,982,629-93,038,073 Size: 55,445 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:92,980,420-93,044,094)mRNA (may differ from genome)Protein (256 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PCGF5_HUMAN
DESCRIPTION: RecName: Full=Polycomb group RING finger protein 5; AltName: Full=RING finger protein 159;
FUNCTION: Component of a Polycomb group (PcG) multiprotein PRC1- like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility.
SUBUNIT: Component of a PRC1-like complex. Interacts with CBX6, CBX7 and CBX8.
INTERACTION: Q9HC52:CBX8; NbExp=2; IntAct=EBI-2827999, EBI-712912; Q06587:RING1; NbExp=2; IntAct=EBI-2827999, EBI-752313; Q99496:RNF2; NbExp=2; IntAct=EBI-2827999, EBI-722416;
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Contains 1 RING-type zinc finger.

-  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: PCGF5
Diseases sorted by gene-association score: interleukin-7 receptor alpha deficiency (2)

-  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: 20.43 RPKM in Artery - Aorta
Total median expression: 453.69 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 -145.70357-0.408 Picture PostScript Text
3' UTR -1366.406021-0.227 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
IPR018957 - Znf_C3HC4_RING-type
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00097 - Zinc finger, C3HC4 type (RING finger)
PF13445 - RING-type zinc-finger
PF13923 - Zinc finger, C3HC4 type (RING finger)
PF16207 - RAWUL domain RING finger- and WD40-associated ubiquitin-like

SCOP Domains:
48695 - Multiheme cytochromes
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on Q86SE9
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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 DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0036353 histone H2A-K119 monoubiquitination
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0060819 inactivation of X chromosome by genetic imprinting

Cellular Component:
GO:0000805 X chromosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005813 centrosome
GO:0031519 PcG protein complex


-  Descriptions from all associated GenBank mRNAs
  BC007377 - Homo sapiens polycomb group ring finger 5, mRNA (cDNA clone IMAGE:3640258), complete cds.
BC051845 - Homo sapiens polycomb group ring finger 5, mRNA (cDNA clone MGC:60159 IMAGE:5199133), complete cds.
AK303014 - Homo sapiens cDNA FLJ51751 complete cds, highly similar to Homo sapiens polycomb group ring finger 5 (PCGF5), mRNA.
AL832496 - Homo sapiens mRNA; cDNA DKFZp686I1251 (from clone DKFZp686I1251); complete cds.
JD111649 - Sequence 92673 from Patent EP1572962.
JD307374 - Sequence 288398 from Patent EP1572962.
KJ903419 - Synthetic construct Homo sapiens clone ccsbBroadEn_12813 PCGF5 gene, encodes complete protein.
AB528204 - Synthetic construct DNA, clone: pF1KE0185, Homo sapiens PCGF5 gene for polycomb group ring finger 5, without stop codon, in Flexi system.
AM393626 - Synthetic construct Homo sapiens clone IMAGE:100002317 for hypothetical protein (PCGF5 gene).
CU690856 - Synthetic construct Homo sapiens gateway clone IMAGE:100021308 5' read PCGF5 mRNA.
KJ894989 - Synthetic construct Homo sapiens clone ccsbBroadEn_04383 PCGF5 gene, encodes complete protein.
AL832003 - Homo sapiens mRNA; cDNA DKFZp451N213 (from clone DKFZp451N213).
AK055625 - Homo sapiens cDNA FLJ31063 fis, clone HSYRA2001105.
BC044910 - Homo sapiens polycomb group ring finger 5, mRNA (cDNA clone IMAGE:5273745).
JD283289 - Sequence 264313 from Patent EP1572962.
JD144561 - Sequence 125585 from Patent EP1572962.
JD144559 - Sequence 125583 from Patent EP1572962.
JD144560 - Sequence 125584 from Patent EP1572962.
JD375910 - Sequence 356934 from Patent EP1572962.
JD496996 - Sequence 478020 from Patent EP1572962.
JD274895 - Sequence 255919 from Patent EP1572962.
JD274896 - Sequence 255920 from Patent EP1572962.
MP014882 - Sequence 85 from Patent WO2019016252.

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

Protein Q86SE9 (Reactome details) participates in the following event(s):

R-HSA-8937989 RUNX1 binds PRC1 complexes
R-HSA-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z892, D3DR33, ENST00000336126.1, ENST00000336126.2, ENST00000336126.3, ENST00000336126.4, ENST00000336126.5, NM_032373, PCGF5_HUMAN, Q6PK47, Q86SE9, Q86TD0, RNF159, uc317ulj.1, uc317ulj.2
UCSC ID: ENST00000336126.6_4
RefSeq Accession: NM_032373.5
Protein: Q86SE9 (aka PCGF5_HUMAN)

-  Gene Model Information
  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.