Human Gene PYGO2 (ENST00000368457.3_9) from GENCODE V47lift37
  Description: pygopus family PHD finger 2 (from RefSeq NM_138300.4)
Gencode Transcript: ENST00000368457.3_9
Gencode Gene: ENSG00000163348.4_12
Transcript (Including UTRs)
   Position: hg19 chr1:154,929,502-154,934,258 Size: 4,757 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr1:154,931,255-154,934,052 Size: 2,798 Coding Exon Count: 3 

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 (chr1:154,929,502-154,934,258)mRNA (may differ from genome)Protein (406 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PYGO2_HUMAN
DESCRIPTION: RecName: Full=Pygopus homolog 2;
FUNCTION: Involved in signal transduction through the Wnt pathway.
SUBUNIT: Binds to BCL9 via the PHD-type zinc finger motif, and thereby becomes part of the nuclear beta-catenin/TCF complex.
SUBCELLULAR LOCATION: Nucleus (Probable).
SIMILARITY: Contains 1 PHD-type zinc finger.
SEQUENCE CAUTION: Sequence=AAL55782.1; Type=Miscellaneous discrepancy; Note=Sequencing errors;

-  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: PYGO2
Diseases sorted by gene-association score: oligospermia (12), treacher collins syndrome 1 (4)

-  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: 28.76 RPKM in Pituitary
Total median expression: 792.03 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 -97.80206-0.475 Picture PostScript Text
3' UTR -608.201753-0.347 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
IPR019786 - Zinc_finger_PHD-type_CS
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00628 - PHD-finger

SCOP Domains:
57903 - FYVE/PHD zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2XB1 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9BRQ0
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 Details  
Gene SorterGene Sorter Gene Sorter  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0035034 histone acetyltransferase regulator activity
GO:0042393 histone binding
GO:0046872 metal ion binding

Biological Process:
GO:0001701 in utero embryonic development
GO:0001822 kidney development
GO:0002088 lens development in camera-type eye
GO:0007286 spermatid development
GO:0007289 spermatid nucleus differentiation
GO:0007420 brain development
GO:0009791 post-embryonic development
GO:0016055 Wnt signaling pathway
GO:0030879 mammary gland development
GO:0033599 regulation of mammary gland epithelial cell proliferation
GO:0035065 regulation of histone acetylation
GO:0035563 positive regulation of chromatin binding
GO:0048589 developmental growth
GO:0051569 regulation of histone H3-K4 methylation
GO:0060021 palate development
GO:0060070 canonical Wnt signaling pathway
GO:1904837 beta-catenin-TCF complex assembly

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:1990907 beta-catenin-TCF complex


-  Descriptions from all associated GenBank mRNAs
  LF206188 - JP 2014500723-A/13691: Polycomb-Associated Non-Coding RNAs.
BC013725 - Homo sapiens pygopus homolog 2 (Drosophila), mRNA (cDNA clone IMAGE:3859726), partial cds.
AF289598 - Homo sapiens clone pp7910 unknown mRNA.
BC006132 - Homo sapiens pygopus homolog 2 (Drosophila), mRNA (cDNA clone MGC:13050 IMAGE:3627860), complete cds.
BC032099 - Homo sapiens pygopus homolog 2 (Drosophila), mRNA (cDNA clone MGC:20502 IMAGE:4126360), complete cds.
AK095425 - Homo sapiens cDNA FLJ38106 fis, clone D3OST2001598.
AK090545 - Homo sapiens cDNA FLJ33226 fis, clone ASTRO2001029.
AX746503 - Sequence 28 from Patent EP1308459.
AK092389 - Homo sapiens cDNA FLJ35070 fis, clone PLACE5000139.
AX747515 - Sequence 1040 from Patent EP1308459.
JD206980 - Sequence 188004 from Patent EP1572962.
JD158331 - Sequence 139355 from Patent EP1572962.
JD559479 - Sequence 540503 from Patent EP1572962.
JD547262 - Sequence 528286 from Patent EP1572962.
JD123507 - Sequence 104531 from Patent EP1572962.
JD371191 - Sequence 352215 from Patent EP1572962.
JD067419 - Sequence 48443 from Patent EP1572962.
JD113808 - Sequence 94832 from Patent EP1572962.
JD137418 - Sequence 118442 from Patent EP1572962.
JD501349 - Sequence 482373 from Patent EP1572962.
JD279206 - Sequence 260230 from Patent EP1572962.
JD312889 - Sequence 293913 from Patent EP1572962.
JD171406 - Sequence 152430 from Patent EP1572962.
JD060837 - Sequence 41861 from Patent EP1572962.
JD492336 - Sequence 473360 from Patent EP1572962.
JD303989 - Sequence 285013 from Patent EP1572962.
JD500454 - Sequence 481478 from Patent EP1572962.
JD094282 - Sequence 75306 from Patent EP1572962.
JD402288 - Sequence 383312 from Patent EP1572962.
JD235747 - Sequence 216771 from Patent EP1572962.
JD098396 - Sequence 79420 from Patent EP1572962.
JD219022 - Sequence 200046 from Patent EP1572962.
LF352249 - JP 2014500723-A/159752: Polycomb-Associated Non-Coding RNAs.
JD485139 - Sequence 466163 from Patent EP1572962.
JD302399 - Sequence 283423 from Patent EP1572962.
JD155520 - Sequence 136544 from Patent EP1572962.
JD199853 - Sequence 180877 from Patent EP1572962.
JD233201 - Sequence 214225 from Patent EP1572962.
JD471913 - Sequence 452937 from Patent EP1572962.
JD158146 - Sequence 139170 from Patent EP1572962.
JD526601 - Sequence 507625 from Patent EP1572962.
JD158145 - Sequence 139169 from Patent EP1572962.
JD301160 - Sequence 282184 from Patent EP1572962.
JD175762 - Sequence 156786 from Patent EP1572962.
JD448550 - Sequence 429574 from Patent EP1572962.
JD446779 - Sequence 427803 from Patent EP1572962.
JD111953 - Sequence 92977 from Patent EP1572962.
JD328245 - Sequence 309269 from Patent EP1572962.
JD554330 - Sequence 535354 from Patent EP1572962.
JD550912 - Sequence 531936 from Patent EP1572962.
LF352248 - JP 2014500723-A/159751: Polycomb-Associated Non-Coding RNAs.
JD052978 - Sequence 34002 from Patent EP1572962.
JD534360 - Sequence 515384 from Patent EP1572962.
AK095899 - Homo sapiens cDNA FLJ38580 fis, clone HCHON2008582, highly similar to FERRITIN HEAVY CHAIN.
JD220311 - Sequence 201335 from Patent EP1572962.
DQ597490 - Homo sapiens piRNA piR-35556, complete sequence.
LF352247 - JP 2014500723-A/159750: Polycomb-Associated Non-Coding RNAs.
AF457208 - Homo sapiens pygopus 2 (PYGO2) mRNA, complete cds.
DQ893379 - Synthetic construct clone IMAGE:100006009; FLH199451.01X; RZPDo839A0782D pygopus homolog 2 (Drosophila) (PYGO2) gene, encodes complete protein.
DQ895952 - Synthetic construct Homo sapiens clone IMAGE:100010412; FLH199357.01L; RZPDo839A0781D pygopus homolog 2 (Drosophila) (PYGO2) gene, encodes complete protein.
AB528446 - Synthetic construct DNA, clone: pF1KB7682, Homo sapiens PYGO2 gene for pygopus homolog 2, without stop codon, in Flexi system.
DQ587922 - Homo sapiens piRNA piR-55034, complete sequence.
JD485592 - Sequence 466616 from Patent EP1572962.
JD256688 - Sequence 237712 from Patent EP1572962.
JD077936 - Sequence 58960 from Patent EP1572962.
MA587826 - JP 2018138019-A/159752: Polycomb-Associated Non-Coding RNAs.
MA587825 - JP 2018138019-A/159751: Polycomb-Associated Non-Coding RNAs.
MA587824 - JP 2018138019-A/159750: Polycomb-Associated Non-Coding RNAs.
MA441765 - JP 2018138019-A/13691: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9BRQ0 (Reactome details) participates in the following event(s):

R-HSA-201712 Beta-catenin:TCF associates with BCL9 and PYGO
R-HSA-3364014 Recruitment of SET1 methyltransferase complex
R-HSA-3364026 SET1 complex trimethylates H3K4 at the MYC gene
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-195721 Signaling by WNT
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000368457.1, ENST00000368457.2, NM_138300, PP7910, PYGO2_HUMAN, Q8WYZ4, Q96CY2, Q9BRQ0, uc318gud.1, uc318gud.2
UCSC ID: ENST00000368457.3_9
RefSeq Accession: NM_138300.4
Protein: Q9BRQ0 (aka PYGO2_HUMAN or PYG2_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.