Human Gene PCGF1 (uc002slz.3) Description and Page Index
  Description: Homo sapiens polycomb group ring finger 1 (PCGF1), mRNA.
RefSeq Summary (NM_032673): PCGF1 is a mammalian homolog of the Drosophila polycomb group genes, which act as transcriptional repressors to regulate anterior-posterior patterning in early embryonic development (Nunes et al., 2001 [PubMed 11287196]). See also PCGF2 (MIM 600346).[supplied by OMIM, Aug 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR5189667.331340.1, SRR1163655.595382.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000233630.11/ ENSP00000233630.6 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr2:74,732,170-74,734,821 Size: 2,652 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr2:74,732,270-74,734,795 Size: 2,526 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:74,732,170-74,734,821)mRNA (may differ from genome)Protein (259 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: PCGF1_HUMAN
DESCRIPTION: RecName: Full=Polycomb group RING finger protein 1; AltName: Full=Nervous system Polycomb-1; Short=NSPc1; AltName: Full=RING finger protein 68;
FUNCTION: Component of the Polycomb group (PcG) multiprotein BCOR complex, a complex required to maintain the transcriptionally repressive state of some genes, such as BCL6 and the cyclin- dependent kinase inhibitor, CDKN1A. Transcriptional repressor that may be targeted to the DNA by BCL6; this transcription repressor activity may be related to PKC signaling pathway. Represses CDKN1A expression by binding to its promoter, and this repression is dependent on the retinoic acid response element (RARE element). Promotes cell cycle progression and enhances cell proliferation as well. May have a positive role in tumor cell growth by down- regulating CDKN1A. 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 repressive BCOR complex containing Polycomb group subcomplex at least composed of RYBP, RING1 and RNF2/RING2. Specifically interacts with BCOR, RING1 and RNF2/RING2. Component of a PRC1-like complex. Interacts with CBX6, CBX7 and CBX8.
INTERACTION: Q6W2J9:BCOR; NbExp=6; IntAct=EBI-749901, EBI-950027; Q9HC52:CBX8; NbExp=2; IntAct=EBI-749901, EBI-712912; Q06587:RING1; NbExp=5; IntAct=EBI-749901, EBI-752313; Q99496:RNF2; NbExp=4; IntAct=EBI-749901, EBI-722416;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Contains 1 RING-type zinc finger.
SEQUENCE CAUTION: Sequence=AAH04952.1; Type=Erroneous initiation; Sequence=AAP97183.1; Type=Erroneous initiation;

-  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: 8.84 RPKM in Pituitary
Total median expression: 294.67 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 -8.0026-0.308 Picture PostScript Text
3' UTR -11.42100-0.114 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:
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on Q9BSM1
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0046872 metal ion binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0035518 histone H2A monoubiquitination
GO:0036353 histone H2A-K119 monoubiquitination

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


-  Descriptions from all associated GenBank mRNAs
  LF207218 - JP 2014500723-A/14721: Polycomb-Associated Non-Coding RNAs.
AL049296 - Homo sapiens mRNA; cDNA DKFZp564P013 (from clone DKFZp564P013).
AF087884 - Homo sapiens RNF3A-2 mRNA, complete cds.
BC004952 - Homo sapiens polycomb group ring finger 1, mRNA (cDNA clone MGC:10882 IMAGE:3621400), complete cds.
LF207045 - JP 2014500723-A/14548: Polycomb-Associated Non-Coding RNAs.
AK125742 - Homo sapiens cDNA FLJ43754 fis, clone TESTI2044796, weakly similar to Homo sapiens ring finger protein 3 (RNF3).
HQ447406 - Synthetic construct Homo sapiens clone IMAGE:100070728; CCSB004263_01 polycomb group ring finger 1 (PCGF1) gene, encodes complete protein.
KJ903459 - Synthetic construct Homo sapiens clone ccsbBroadEn_12853 PCGF1 gene, encodes complete protein.
JD027113 - Sequence 8137 from Patent EP1572962.
JD035592 - Sequence 16616 from Patent EP1572962.
JD023543 - Sequence 4567 from Patent EP1572962.
JD027610 - Sequence 8634 from Patent EP1572962.
LF360513 - JP 2014500723-A/168016: Polycomb-Associated Non-Coding RNAs.
DQ573969 - Homo sapiens piRNA piR-42081, complete sequence.
LF360512 - JP 2014500723-A/168015: Polycomb-Associated Non-Coding RNAs.
LF363227 - JP 2014500723-A/170730: Polycomb-Associated Non-Coding RNAs.
MA598804 - JP 2018138019-A/170730: Polycomb-Associated Non-Coding RNAs.
MA442795 - JP 2018138019-A/14721: Polycomb-Associated Non-Coding RNAs.
MA442622 - JP 2018138019-A/14548: Polycomb-Associated Non-Coding RNAs.
MA596090 - JP 2018138019-A/168016: Polycomb-Associated Non-Coding RNAs.
MA596089 - JP 2018138019-A/168015: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_032673, NP_116062, NSPC1, PCGF1_HUMAN, Q7Z506, Q9BSM1, RNF68
UCSC ID: uc002slz.3
RefSeq Accession: NM_032673
Protein: Q9BSM1 (aka PCGF1_HUMAN)
CCDS: CCDS1946.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_032673.2
exon count: 9CDS single in 3' UTR: no RNA size: 939
ORF size: 780CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1712.00frame shift in genome: no % Coverage: 96.49
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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.