Human Gene PHC3 (uc003fgl.2) Description and Page Index
  Description: Homo sapiens polyhomeotic homolog 3 (Drosophila) (PHC3), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:169,805,368-169,899,537 Size: 94,170 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr3:169,815,018-169,899,503 Size: 84,486 Coding Exon Count: 15 

Page IndexSequence and LinksCTDGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr3:169,805,368-169,899,537)mRNA (may differ from genome)Protein (995 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  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: 6.33 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 204.67 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 -2.7034-0.079 Picture PostScript Text
3' UTR -2829.989650-0.293 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
  Pfam Domains:
PF00536 - SAM domain (Sterile alpha motif)
PF07647 - SAM domain (Sterile alpha motif)

SCOP Domains:
47769 - SAM/Pointed domain

ModBase Predicted Comparative 3D Structure on Q8NDX5-7
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Protein Sequence   

-  Descriptions from all associated GenBank mRNAs
  LF206092 - JP 2014500723-A/13595: Polycomb-Associated Non-Coding RNAs.
BX647868 - Homo sapiens mRNA; cDNA DKFZp313K1221 (from clone DKFZp313K1221).
BC112944 - Homo sapiens cDNA clone IMAGE:5553866, containing frame-shift errors.
AF380154 - Homo sapiens early development regulator 3 (EDR3) mRNA, complete cds.
AF444193 - Homo sapiens polyhomeotic 3 protein (HPH3) mRNA, complete cds.
AJ320486 - Homo sapiens mRNA for homolog of polyhomeotic 3 (PHC3 gene).
EF560717 - Homo sapiens clone DKFZp781A2228 PHC3 protein (PHC3) mRNA, complete cds.
BC131772 - Homo sapiens polyhomeotic homolog 3 (Drosophila), mRNA (cDNA clone MGC:156272 IMAGE:40123356), complete cds.
BC131773 - Homo sapiens cDNA clone IMAGE:40123357.
GQ129247 - Synthetic construct Homo sapiens clone HAIB:100068502; DKFZo004E0834 polyhomeotic homolog 3 (Drosophila) protein (PHC3) gene, partial cds.
EU832812 - Synthetic construct Homo sapiens clone HAIB:100067841; DKFZo008E0833 polyhomeotic homolog 3 (Drosophila) protein (PHC3) gene, encodes complete protein.
AK304411 - Homo sapiens cDNA FLJ58230 complete cds, highly similar to Polyhomeotic-like protein 3.
AK302371 - Homo sapiens cDNA FLJ57231 complete cds, moderately similar to Homo sapiens polyhomeotic like 3 (PHC3), mRNA.
AK300151 - Homo sapiens cDNA FLJ57195 complete cds, highly similar to Polyhomeotic-like protein 3.
AK023029 - Homo sapiens cDNA FLJ12967 fis, clone NT2RP2005806.
MA441669 - JP 2018138019-A/13595: Polycomb-Associated Non-Coding RNAs.
BC026001 - Homo sapiens, clone IMAGE:4617948, mRNA.
LF351271 - JP 2014500723-A/158774: Polycomb-Associated Non-Coding RNAs.
LF351272 - JP 2014500723-A/158775: Polycomb-Associated Non-Coding RNAs.
JD312193 - Sequence 293217 from Patent EP1572962.
JD560898 - Sequence 541922 from Patent EP1572962.
JD300908 - Sequence 281932 from Patent EP1572962.
JD359572 - Sequence 340596 from Patent EP1572962.
LF351273 - JP 2014500723-A/158776: Polycomb-Associated Non-Coding RNAs.
LF351274 - JP 2014500723-A/158777: Polycomb-Associated Non-Coding RNAs.
JD051042 - Sequence 32066 from Patent EP1572962.
JD097572 - Sequence 78596 from Patent EP1572962.
JD491797 - Sequence 472821 from Patent EP1572962.
JD512579 - Sequence 493603 from Patent EP1572962.
JD346188 - Sequence 327212 from Patent EP1572962.
JD375050 - Sequence 356074 from Patent EP1572962.
JD329115 - Sequence 310139 from Patent EP1572962.
JD522283 - Sequence 503307 from Patent EP1572962.
JD556342 - Sequence 537366 from Patent EP1572962.
JD070834 - Sequence 51858 from Patent EP1572962.
JD319327 - Sequence 300351 from Patent EP1572962.
JD319326 - Sequence 300350 from Patent EP1572962.
JD340834 - Sequence 321858 from Patent EP1572962.
LF351275 - JP 2014500723-A/158778: Polycomb-Associated Non-Coding RNAs.
DQ572004 - Homo sapiens piRNA piR-40116, complete sequence.
LF351276 - JP 2014500723-A/158779: Polycomb-Associated Non-Coding RNAs.
LF351277 - JP 2014500723-A/158780: Polycomb-Associated Non-Coding RNAs.
LF351278 - JP 2014500723-A/158781: Polycomb-Associated Non-Coding RNAs.
JD434331 - Sequence 415355 from Patent EP1572962.
JD301650 - Sequence 282674 from Patent EP1572962.
LF351281 - JP 2014500723-A/158784: Polycomb-Associated Non-Coding RNAs.
LF351284 - JP 2014500723-A/158787: Polycomb-Associated Non-Coding RNAs.
LF351289 - JP 2014500723-A/158792: Polycomb-Associated Non-Coding RNAs.
LF351290 - JP 2014500723-A/158793: Polycomb-Associated Non-Coding RNAs.
MA586848 - JP 2018138019-A/158774: Polycomb-Associated Non-Coding RNAs.
MA586849 - JP 2018138019-A/158775: Polycomb-Associated Non-Coding RNAs.
MA586850 - JP 2018138019-A/158776: Polycomb-Associated Non-Coding RNAs.
MA586851 - JP 2018138019-A/158777: Polycomb-Associated Non-Coding RNAs.
MA586852 - JP 2018138019-A/158778: Polycomb-Associated Non-Coding RNAs.
MA586853 - JP 2018138019-A/158779: Polycomb-Associated Non-Coding RNAs.
MA586854 - JP 2018138019-A/158780: Polycomb-Associated Non-Coding RNAs.
MA586855 - JP 2018138019-A/158781: Polycomb-Associated Non-Coding RNAs.
MA586858 - JP 2018138019-A/158784: Polycomb-Associated Non-Coding RNAs.
MA586861 - JP 2018138019-A/158787: Polycomb-Associated Non-Coding RNAs.
MA586866 - JP 2018138019-A/158792: Polycomb-Associated Non-Coding RNAs.
MA586867 - JP 2018138019-A/158793: Polycomb-Associated Non-Coding RNAs.
BC022325 - Homo sapiens polyhomeotic homolog 3 (Drosophila), mRNA (cDNA clone IMAGE:4774329), complete cds.
AK022791 - Homo sapiens cDNA FLJ12729 fis, clone NT2RP2000076, weakly similar to Homo sapiens partial mRNA for polyhomeotic 2 protein (PH2 gene).
BC070164 - Homo sapiens polyhomeotic homolog 3 (Drosophila), mRNA (cDNA clone IMAGE:6105365), complete cds.
CU687058 - Synthetic construct Homo sapiens gateway clone IMAGE:100023094 5' read PHC3 mRNA.
KJ906327 - Synthetic construct Homo sapiens clone ccsbBroadEn_15997 PHC3 gene, encodes complete protein.
AK093027 - Homo sapiens cDNA FLJ35708 fis, clone SPLEN2020467.
AX747865 - Sequence 1390 from Patent EP1308459.
LF351293 - JP 2014500723-A/158796: Polycomb-Associated Non-Coding RNAs.
LF351296 - JP 2014500723-A/158799: Polycomb-Associated Non-Coding RNAs.
MA586870 - JP 2018138019-A/158796: Polycomb-Associated Non-Coding RNAs.
MA586873 - JP 2018138019-A/158799: Polycomb-Associated Non-Coding RNAs.

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

Protein Q8NDX5 (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: EDR3, NM_024947, NP_079223, PH3, Q8NDX5-7
UCSC ID: uc003fgl.2
RefSeq Accession: NM_024947
Protein: Q8NDX5-7, splice isoform of Q8NDX5 CCDS: CCDS46952.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_024947.3
exon count: 15CDS single in 3' UTR: no RNA size: 12687
ORF size: 2988CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6152.00frame shift in genome: no % Coverage: 99.88
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
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.