Human Gene PHC1 (ENST00000544916.6_6) from GENCODE V47lift37
  Description: 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. Required for proper control of cellular levels of GMNN expression. (from UniProt P78364)
Gencode Transcript: ENST00000544916.6_6
Gencode Gene: ENSG00000111752.11_15
Transcript (Including UTRs)
   Position: hg19 chr12:9,067,105-9,094,063 Size: 26,959 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr12:9,070,274-9,092,055 Size: 21,782 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:9,067,105-9,094,063)mRNA (may differ from genome)Protein (1004 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsHGNC
MalacardsMGIPubMedReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PHC1_HUMAN
DESCRIPTION: RecName: Full=Polyhomeotic-like protein 1; Short=hPH1; AltName: Full=Early development regulatory protein 1;
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: Homodimer. Component of a PRC1-like complex.
SUBCELLULAR LOCATION: Nucleus.
MISCELLANEOUS: The hPRC-H complex purification reported by PubMed:12167701 probably presents a mixture of different PRC1-like complexes.
SIMILARITY: Contains 1 FCS-type zinc finger.
SIMILARITY: Contains 1 SAM (sterile alpha motif) domain.
SEQUENCE CAUTION: Sequence=AAH17748.1; 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: PHC1
Diseases sorted by gene-association score: microcephaly 11, primary, autosomal recessive* (979), microcephaly (5)
* = Manually curated disease association

-  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: 9.34 RPKM in Pituitary
Total median expression: 130.70 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 -198.70367-0.541 Picture PostScript Text
3' UTR -579.602008-0.289 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
IPR001660 - SAM
IPR013761 - SAM/pointed
IPR021129 - SAM_type1
IPR012313 - Znf_FCS
IPR010507 - Znf_MYM

Pfam Domains:
PF00536 - SAM domain (Sterile alpha motif)
PF07647 - SAM domain (Sterile alpha motif)
PF16616 - Unstructured region on Polyhomeotic-like protein 1 and 2

SCOP Domains:
47769 - SAM/Pointed domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2L8E - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P78364
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding

Biological Process:
GO:0007275 multicellular organism development
GO:0016574 histone ubiquitination
GO:0070317 negative regulation of G0 to G1 transition

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0031519 PcG protein complex
GO:0035102 PRC1 complex


-  Descriptions from all associated GenBank mRNAs
  AB209063 - Homo sapiens mRNA for Polyhomeotic-like protein 1 variant protein.
JD124755 - Sequence 105779 from Patent EP1572962.
AK293893 - Homo sapiens cDNA FLJ60101 complete cds, highly similar to Polyhomeotic-like protein 1.
JD179700 - Sequence 160724 from Patent EP1572962.
BC073964 - Homo sapiens polyhomeotic homolog 1 (Drosophila), mRNA (cDNA clone MGC:87926 IMAGE:5788132), complete cds.
JD443872 - Sequence 424896 from Patent EP1572962.
JD456944 - Sequence 437968 from Patent EP1572962.
U89277 - Human polyhomeotic 1 homolog (HPH1) mRNA, partial cds.
BC157850 - Homo sapiens polyhomeotic homolog 1 (Drosophila), mRNA (cDNA clone MGC:189745 IMAGE:9057069), complete cds.
BX640639 - Homo sapiens mRNA; cDNA DKFZp686A1782 (from clone DKFZp686A1782); complete cds.
JD266693 - Sequence 247717 from Patent EP1572962.
JD176781 - Sequence 157805 from Patent EP1572962.
JD101319 - Sequence 82343 from Patent EP1572962.
AB384829 - Synthetic construct DNA, clone: pF1KB3651, Homo sapiens PHC1 gene for polyhomeotic-like protein 1, complete cds, without stop codon, in Flexi system.
BC017748 - Homo sapiens polyhomeotic homolog 1 (Drosophila), mRNA (cDNA clone IMAGE:4419551), complete cds.
BC002871 - Homo sapiens polyhomeotic homolog 1 (Drosophila), mRNA (cDNA clone IMAGE:3944202), partial cds.
CU676042 - Synthetic construct Homo sapiens gateway clone IMAGE:100019446 5' read PHC1 mRNA.
KJ901402 - Synthetic construct Homo sapiens clone ccsbBroadEn_10796 PHC1 gene, encodes complete protein.
JD392356 - Sequence 373380 from Patent EP1572962.
JD434780 - Sequence 415804 from Patent EP1572962.
JD402801 - Sequence 383825 from Patent EP1572962.
JD077199 - Sequence 58223 from Patent EP1572962.
JD311530 - Sequence 292554 from Patent EP1572962.
JD299143 - Sequence 280167 from Patent EP1572962.
JD561754 - Sequence 542778 from Patent EP1572962.
JD561753 - Sequence 542777 from Patent EP1572962.
JD134831 - Sequence 115855 from Patent EP1572962.
JD341175 - Sequence 322199 from Patent EP1572962.
JD363869 - Sequence 344893 from Patent EP1572962.
JD537548 - Sequence 518572 from Patent EP1572962.
LF207373 - JP 2014500723-A/14876: Polycomb-Associated Non-Coding RNAs.
LF206257 - JP 2014500723-A/13760: Polycomb-Associated Non-Coding RNAs.
LF365680 - JP 2014500723-A/173183: Polycomb-Associated Non-Coding RNAs.
LF365679 - JP 2014500723-A/173182: Polycomb-Associated Non-Coding RNAs.
LF352707 - JP 2014500723-A/160210: Polycomb-Associated Non-Coding RNAs.
LF352706 - JP 2014500723-A/160209: Polycomb-Associated Non-Coding RNAs.
MA601257 - JP 2018138019-A/173183: Polycomb-Associated Non-Coding RNAs.
MA601256 - JP 2018138019-A/173182: Polycomb-Associated Non-Coding RNAs.
MA588284 - JP 2018138019-A/160210: Polycomb-Associated Non-Coding RNAs.
MA588283 - JP 2018138019-A/160209: Polycomb-Associated Non-Coding RNAs.
MA442950 - JP 2018138019-A/14876: Polycomb-Associated Non-Coding RNAs.
MA441834 - JP 2018138019-A/13760: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_prc2Pathway - The PRC2 Complex Sets Long-term Gene Silencing Through Modification of Histone Tails

Reactome (by CSHL, EBI, and GO)

Protein P78364 (Reactome details) participates in the following event(s):

R-HSA-4551727 CBX4 SUMOylates CBX4 in PRC1 with SUMO1
R-HSA-4551655 CBX4 SUMOylates BMI1 in PRC1 with SUMO1
R-HSA-3229089 PRC1.4 complex binds H3K27Me3 nucleosomes on CDKN2A promoter
R-HSA-3229102 p-MAPKAPK3 phosphorylates BMI1
R-HSA-8954082 E2F6 binds the PRC1 complex
R-HSA-4570463 CBX4 (Pc2) SUMOylates CETN2 with SUMO2,3
R-HSA-4570499 CBX4 (Pc2) SUMOylates HNRNPK with SUMO2
R-HSA-8937989 RUNX1 binds PRC1 complexes
R-HSA-8943817 MECOM (EVI1) recruits polycomb repressor complexes (PRCs) to the PTEN gene promoter
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-2559580 Oxidative Stress Induced Senescence
R-HSA-8953750 Transcriptional Regulation by E2F6
R-HSA-2990846 SUMOylation
R-HSA-3108214 SUMOylation of DNA damage response and repair proteins
R-HSA-4570464 SUMOylation of RNA binding proteins
R-HSA-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-8943724 Regulation of PTEN gene transcription
R-HSA-2559583 Cellular Senescence
R-HSA-212436 Generic Transcription Pathway
R-HSA-597592 Post-translational protein modification
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-6807070 PTEN Regulation
R-HSA-2262752 Cellular responses to stress
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-392499 Metabolism of proteins
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-74160 Gene expression (Transcription)
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: D3DUV4, EDR1, ENST00000544916.1, ENST00000544916.2, ENST00000544916.3, ENST00000544916.4, ENST00000544916.5, NR_182209, P78364, PH1, PHC1_HUMAN, Q8WVM3, Q9BU63, uc324vzh.1, uc324vzh.2
UCSC ID: ENST00000544916.6_6
RefSeq Accession: NM_004426.3
Protein: P78364 (aka PHC1_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.