Human Gene PCGF3 (uc003gbe.3) Description and Page Index
  Description: Homo sapiens polycomb group ring finger 3 (PCGF3), mRNA.
RefSeq Summary (NM_006315): The protein encoded by this gene contains a C3HC4 type RING finger, which is a motif known to be involved in protein-protein interactions. The specific function of this protein has not yet been determined. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr4:699,573-764,427 Size: 64,855 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr4:727,470-759,867 Size: 32,398 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:699,573-764,427)mRNA (may differ from genome)Protein (242 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: PCGF3_HUMAN
DESCRIPTION: RecName: Full=Polycomb group RING finger protein 3; AltName: Full=RING finger protein 3A;
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: O95503:CBX6; NbExp=2; IntAct=EBI-2339807, EBI-3951758; O95931:CBX7; NbExp=2; IntAct=EBI-2339807, EBI-3923843; Q9HC52:CBX8; NbExp=3; IntAct=EBI-2339807, EBI-712912; Q06587:RING1; NbExp=2; IntAct=EBI-2339807, EBI-752313; Q99496:RNF2; NbExp=2; IntAct=EBI-2339807, EBI-722416;
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Contains 1 RING-type zinc finger.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PCGF3
CDC HuGE Published Literature: PCGF3
Positive Disease Associations: Anticoagulants , Body Mass Index
Related Studies:
  1. Anticoagulants
    Tiphaine Oudot-Mellakh et al. British journal of haematology 2012, Genome wide association study for plasma levels of natural anticoagulant inhibitors and protein C anticoagulant pathway: the MARTHA project., British journal of haematology. [PubMed 22443383]
  2. Body Mass Index
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 28.92 RPKM in Brain - Cerebellum
Total median expression: 794.66 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -180.60376-0.480 Picture PostScript Text
3' UTR -1429.834560-0.314 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
PF13639 - Ring finger domain
PF13923 - Zinc finger, C3HC4 type (RING finger)
PF16207 - RAWUL domain RING finger- and WD40-associated ubiquitin-like

SCOP Domains:
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on Q3KNV8
FrontTopSide
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     
Gene Sorter     
      
      
      

-  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:0060819 inactivation of X chromosome by genetic imprinting

Cellular Component:
GO:0000805 X chromosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0031519 PcG protein complex


-  Descriptions from all associated GenBank mRNAs
  AK225892 - Homo sapiens mRNA for ring finger protein 3 variant, clone: FCC121A10.
LF383991 - JP 2014500723-A/191494: Polycomb-Associated Non-Coding RNAs.
AK300290 - Homo sapiens cDNA FLJ54810 complete cds, highly similar to Homo sapiens polycomb group ring finger 3 (PCGF3), mRNA.
AK057124 - Homo sapiens cDNA FLJ32562 fis, clone SPLEN1000165, highly similar to Homo sapiens polycomb group ring finger 3 (PCGF3), mRNA.
AK125801 - Homo sapiens cDNA FLJ43813 fis, clone TESTI4001467, highly similar to Homo sapiens polycomb group ring finger 3 (PCGF3), mRNA.
JD202504 - Sequence 183528 from Patent EP1572962.
JD141583 - Sequence 122607 from Patent EP1572962.
LF359261 - JP 2014500723-A/166764: Polycomb-Associated Non-Coding RNAs.
BC107061 - Homo sapiens polycomb group ring finger 3, mRNA (cDNA clone MGC:129615 IMAGE:40006331), complete cds.
JD440503 - Sequence 421527 from Patent EP1572962.
AJ001019 - Homo sapiens mRNA for RNF3A (DONG1) ring finger protein.
KJ904650 - Synthetic construct Homo sapiens clone ccsbBroadEn_14044 PCGF3-like gene, encodes complete protein.
BX648409 - Homo sapiens mRNA; cDNA DKFZp686D20235 (from clone DKFZp686D20235).
LF359262 - JP 2014500723-A/166765: Polycomb-Associated Non-Coding RNAs.
LF359263 - JP 2014500723-A/166766: Polycomb-Associated Non-Coding RNAs.
LF359264 - JP 2014500723-A/166767: Polycomb-Associated Non-Coding RNAs.
LF206914 - JP 2014500723-A/14417: Polycomb-Associated Non-Coding RNAs.
JD316757 - Sequence 297781 from Patent EP1572962.
JD061741 - Sequence 42765 from Patent EP1572962.
JD168926 - Sequence 149950 from Patent EP1572962.
JD292754 - Sequence 273778 from Patent EP1572962.
JD081715 - Sequence 62739 from Patent EP1572962.
JD268530 - Sequence 249554 from Patent EP1572962.
BC050044 - Homo sapiens polycomb group ring finger 3, mRNA (cDNA clone IMAGE:5284446).
JD428746 - Sequence 409770 from Patent EP1572962.
LF359265 - JP 2014500723-A/166768: Polycomb-Associated Non-Coding RNAs.
JD466851 - Sequence 447875 from Patent EP1572962.
JD289324 - Sequence 270348 from Patent EP1572962.
JD493183 - Sequence 474207 from Patent EP1572962.
JD141054 - Sequence 122078 from Patent EP1572962.
JD170570 - Sequence 151594 from Patent EP1572962.
JD297043 - Sequence 278067 from Patent EP1572962.
JD495840 - Sequence 476864 from Patent EP1572962.
JD436934 - Sequence 417958 from Patent EP1572962.
JD535032 - Sequence 516056 from Patent EP1572962.
JD427913 - Sequence 408937 from Patent EP1572962.
JD335914 - Sequence 316938 from Patent EP1572962.
JD356910 - Sequence 337934 from Patent EP1572962.
JD454301 - Sequence 435325 from Patent EP1572962.
JD546893 - Sequence 527917 from Patent EP1572962.
JD308497 - Sequence 289521 from Patent EP1572962.
BX640894 - Homo sapiens mRNA; cDNA DKFZp686G1435 (from clone DKFZp686G1435).
JD244397 - Sequence 225421 from Patent EP1572962.
LF359266 - JP 2014500723-A/166769: Polycomb-Associated Non-Coding RNAs.
JD359415 - Sequence 340439 from Patent EP1572962.
JD219720 - Sequence 200744 from Patent EP1572962.
JD429520 - Sequence 410544 from Patent EP1572962.
LF359267 - JP 2014500723-A/166770: Polycomb-Associated Non-Coding RNAs.
AL832536 - Homo sapiens mRNA; cDNA DKFZp547K2416 (from clone DKFZp547K2416).
JD196622 - Sequence 177646 from Patent EP1572962.
JD544087 - Sequence 525111 from Patent EP1572962.
JD137369 - Sequence 118393 from Patent EP1572962.
JD429602 - Sequence 410626 from Patent EP1572962.
JD552428 - Sequence 533452 from Patent EP1572962.
JD080070 - Sequence 61094 from Patent EP1572962.
JD409869 - Sequence 390893 from Patent EP1572962.
JD422475 - Sequence 403499 from Patent EP1572962.
JD462575 - Sequence 443599 from Patent EP1572962.
JD301304 - Sequence 282328 from Patent EP1572962.
JD307854 - Sequence 288878 from Patent EP1572962.
BC028026 - Homo sapiens polycomb group ring finger 3, mRNA (cDNA clone IMAGE:4181035).
JD295609 - Sequence 276633 from Patent EP1572962.
LF359268 - JP 2014500723-A/166771: Polycomb-Associated Non-Coding RNAs.
JD528216 - Sequence 509240 from Patent EP1572962.
BC061897 - Homo sapiens cDNA clone IMAGE:4780592, partial cds.
KJ906033 - Synthetic construct Homo sapiens clone ccsbBroadEn_15703 PCGF3 gene, encodes complete protein.
JD544036 - Sequence 525060 from Patent EP1572962.
JD209177 - Sequence 190201 from Patent EP1572962.
JD515764 - Sequence 496788 from Patent EP1572962.
JD079888 - Sequence 60912 from Patent EP1572962.
JD341889 - Sequence 322913 from Patent EP1572962.
JD361263 - Sequence 342287 from Patent EP1572962.
JD451251 - Sequence 432275 from Patent EP1572962.
LF359269 - JP 2014500723-A/166772: Polycomb-Associated Non-Coding RNAs.
JD286227 - Sequence 267251 from Patent EP1572962.
JD060127 - Sequence 41151 from Patent EP1572962.
JD040506 - Sequence 21530 from Patent EP1572962.
JD361983 - Sequence 343007 from Patent EP1572962.
JD055502 - Sequence 36526 from Patent EP1572962.
JD518664 - Sequence 499688 from Patent EP1572962.
JD173275 - Sequence 154299 from Patent EP1572962.
JD323754 - Sequence 304778 from Patent EP1572962.
JD450597 - Sequence 431621 from Patent EP1572962.
JD468439 - Sequence 449463 from Patent EP1572962.
JD436106 - Sequence 417130 from Patent EP1572962.
JD371069 - Sequence 352093 from Patent EP1572962.
LF359270 - JP 2014500723-A/166773: Polycomb-Associated Non-Coding RNAs.
JD097135 - Sequence 78159 from Patent EP1572962.
JD269035 - Sequence 250059 from Patent EP1572962.
JD100770 - Sequence 81794 from Patent EP1572962.
JD413110 - Sequence 394134 from Patent EP1572962.
JD184735 - Sequence 165759 from Patent EP1572962.
MA619568 - JP 2018138019-A/191494: Polycomb-Associated Non-Coding RNAs.
MA594838 - JP 2018138019-A/166764: Polycomb-Associated Non-Coding RNAs.
MA594839 - JP 2018138019-A/166765: Polycomb-Associated Non-Coding RNAs.
MA594840 - JP 2018138019-A/166766: Polycomb-Associated Non-Coding RNAs.
MA594841 - JP 2018138019-A/166767: Polycomb-Associated Non-Coding RNAs.
MA442491 - JP 2018138019-A/14417: Polycomb-Associated Non-Coding RNAs.
MA594842 - JP 2018138019-A/166768: Polycomb-Associated Non-Coding RNAs.
MA594843 - JP 2018138019-A/166769: Polycomb-Associated Non-Coding RNAs.
MA594844 - JP 2018138019-A/166770: Polycomb-Associated Non-Coding RNAs.
MA594845 - JP 2018138019-A/166771: Polycomb-Associated Non-Coding RNAs.
MA594846 - JP 2018138019-A/166772: Polycomb-Associated Non-Coding RNAs.
MA594847 - JP 2018138019-A/166773: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: D3DVN1, NM_006315, NP_006306, O15262, PCGF3_HUMAN, Q3KNV8, RNF3, RNF3A
UCSC ID: uc003gbe.3
RefSeq Accession: NM_006315
Protein: Q3KNV8 (aka PCGF3_HUMAN)
CCDS: CCDS3339.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006315.4
exon count: 11CDS single in 3' UTR: no RNA size: 5666
ORF size: 729CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 1509.50frame shift in genome: no % Coverage: 99.98
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 4234# 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.