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PYGO2 pygopus family PHD finger 2 [ Homo sapiens (human) ]

Gene ID: 90780, updated on 27-Nov-2024

Summary

Official Symbol
PYGO2provided by HGNC
Official Full Name
pygopus family PHD finger 2provided by HGNC
Primary source
HGNC:HGNC:30257
See related
Ensembl:ENSG00000163348 MIM:606903; AllianceGenome:HGNC:30257
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
1190004M21Rik
Summary
Predicted to enable several functions, including chromatin binding activity; histone acetyltransferase regulator activity; and histone binding activity. Predicted to be involved in kidney development and spermatid nucleus differentiation. Predicted to act upstream of or within several processes, including canonical Wnt signaling pathway; lens development in camera-type eye; and regulation of mammary gland epithelial cell proliferation. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in thyroid (RPKM 16.3), ovary (RPKM 15.1) and 25 other tissues See more
Orthologs
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Genomic context

See PYGO2 in Genome Data Viewer
Location:
1q21.3
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (154957026..154961782, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (154096387..154101143, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (154929502..154934258, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene phosphomevalonate kinase Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154908701-154909643 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154909644-154910585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154914379-154915254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154917055-154917556 Neighboring gene PBX homeobox interacting protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154924461-154924960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154931761-154932260 Neighboring gene H3K27ac hESC enhancers GRCh37_chr1:154933865-154934605 and GRCh37_chr1:154934606-154935345 Neighboring gene PYGO2 and SHC1 antisense RNA 1 Neighboring gene SHC adaptor protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154942000-154942550 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154942551-154943101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1800 Neighboring gene microRNA 4258 Neighboring gene CDC28 protein kinase regulatory subunit 1B

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: PBXIP1

Clone Names

  • FLJ33226

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
 
enables histone acetyltransferase regulator activity IEA
Inferred from Electronic Annotation
more info
 
enables histone binding IEA
Inferred from Electronic Annotation
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in brain development IEA
Inferred from Electronic Annotation
more info
 
involved_in canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in developmental growth IEA
Inferred from Electronic Annotation
more info
 
involved_in kidney development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in lens development in camera-type eye IEA
Inferred from Electronic Annotation
more info
 
involved_in mammary gland development IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of mammary gland epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
involved_in roof of mouth development IEA
Inferred from Electronic Annotation
more info
 
involved_in spermatid nucleus differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
part_of beta-catenin-TCF complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
pygopus homolog 2
Names
pygopus 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_138300.4NP_612157.1  pygopus homolog 2

    See identical proteins and their annotated locations for NP_612157.1

    Status: VALIDATED

    Source sequence(s)
    BC006132, CN260857
    Consensus CDS
    CCDS1075.1
    UniProtKB/Swiss-Prot
    Q8WYZ4, Q96CY2, Q9BRQ0
    UniProtKB/TrEMBL
    Q5T170, Q5T171
    Related
    ENSP00000357442.2, ENST00000368457.3
    Conserved Domains (1) summary
    cd15636
    Location:329382
    PHD_PYGO2; PHD finger found in pygopus homolog 2 (PYGO2)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    154957026..154961782 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    154096387..154101143 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)