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

    Gene ID: 90780, updated on 5-Mar-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 animal organ development; positive regulation of chromatin binding activity; and regulation of histone H3-K4 methylation. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 16.3), ovary (RPKM 15.1) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    Location:
    1q21.3
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (154957026..154961782, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (154096387..154101143, complement)
    105.20220307 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)

    NEW Try the new Transcript table

    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_2023_10

    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)