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    PYGO1 pygopus family PHD finger 1 [ Homo sapiens (human) ]

    Gene ID: 26108, updated on 27-Nov-2024

    Summary

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    Official Symbol
    PYGO1provided by HGNC
    Official Full Name
    pygopus family PHD finger 1provided by HGNC
    Primary source
    HGNC:HGNC:30256
    See related
    Ensembl:ENSG00000171016 MIM:606902; AllianceGenome:HGNC:30256
    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
    Summary
    Enables methylated histone binding activity. Predicted to be involved in kidney development and spermatid nucleus differentiation. Predicted to act upstream of or within several processes, including hematopoietic progenitor cell differentiation; positive regulation of transcription by RNA polymerase II; and spermatid development. Predicted to be located in nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in thyroid (RPKM 4.1), endometrium (RPKM 3.0) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PYGO1 in Genome Data Viewer
    Location:
    15q21.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (55538884..55588971, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (53342076..53392120, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (55831082..55881169, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene DNAAF4-CCPG1 readthrough (NMD candidate) Neighboring gene thioesterase superfamily member 4 pseudogene Neighboring gene dynein axonemal assembly factor 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9448 Neighboring gene uncharacterized mitochondrial protein AtMg00860-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6454 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6455 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6456 Neighboring gene uncharacterized LOC124903497 Neighboring gene NANOG hESC enhancer GRCh37_chr15:55953352-55954256 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:55957303-55957803 Neighboring gene protogenin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9449 Neighboring gene NANOG hESC enhancer GRCh37_chr15:56028112-56028613 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:56034229-56035192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:56036083-56036584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:56036585-56037084 Neighboring gene NEDD4 intron nontranscribed DNase I hypersensitive site-defined enhancer Neighboring gene NEDD4 E3 ubiquitin protein ligase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40173 Neighboring gene small nucleolar RNA U13

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Pygo1 Regulates the Behavior of Human Non-Small-Cell Lung Cancer via the Wnt/β-Catenin Pathway. Wen Y, et al. Dis Markers, 2022. PMID 36398031, Free PMC Article
    2. Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex. Fiedler M, et al. Mol Cell, 2008 May 23. PMID 18498752, Free PMC Article
    3. A new nuclear component of the Wnt signalling pathway. Thompson B, et al. Nat Cell Biol, 2002 May. PMID 11988739
    4. Single nucleotide polymorphisms in Wnt signaling and cell death pathway genes and susceptibility to colorectal cancer. Frank B, et al. Carcinogenesis, 2010 Aug. PMID 20403915
    5. Pygopus residues required for its binding to Legless are critical for transcription and development. Townsley FM, et al. J Biol Chem, 2004 Feb 13. PMID 14612447

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Pygo1 Regulates the Behavior of Human Non-Small-Cell Lung Cancer via the Wnt/beta-Catenin Pathway.
      Title: Pygo1 Regulates the Behavior of Human Non-Small-Cell Lung Cancer via the Wnt/β-Catenin Pathway.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Single nucleotide polymorphisms in Wnt signaling and cell death pathway genes and susceptibility to colorectal cancer.
    3. Data show that human and Drosophila Pygo PHD fingers associate with their cognate HD1 domains from BCL9/Legless to bind specifically to the histone H3 tail methylated at lysine 4 (H3K4me).
      Title: Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ30808, FLJ38221, DKFZp547G0910, DKFZp686P07116

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in canonical Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in hematopoietic progenitor cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in kidney development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein localization to nucleus 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
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    pygopus homolog 1
    Names
    pygopus-like protein 1

    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_001330326.2 → NP_001317255.1  pygopus homolog 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' and 3' UTRs, and uses an alternate start codon, compared to variant 1. The encoded isoform (2) is the same length as isoform 1, but has a distinct N-terminus.
      Source sequence(s)
      AC012378, AC022083
      Consensus CDS
      CCDS81885.1
      UniProtKB/Swiss-Prot
      Q9Y3Y4
      Related
      ENSP00000496139.1, ENST00000645724.1
      Conserved Domains (1) summary
      cd15635
      Location:341 → 397
      PHD_PYGO1; PHD finger found in pygopus homolog 1 (PYGO1)

    2. NM_001367806.1 → NP_001354735.1  pygopus homolog 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC012378, AC022083
      Consensus CDS
      CCDS81885.1
      Related
      ENSP00000457777.1, ENST00000563719.4

    3. NM_015617.3 → NP_056432.1  pygopus homolog 1 isoform 1

      See identical proteins and their annotated locations for NP_056432.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform 1. Variants 1 and 2 encode isoforms that are the same length, but have distinct protein sequences.
      Source sequence(s)
      AC012378, AC022083, AF457207
      Consensus CDS
      CCDS10155.1
      UniProtKB/Swiss-Prot
      A7Y2D6, Q9Y3Y4
      Related
      ENSP00000302327.6, ENST00000302000.10
      Conserved Domains (1) summary
      cd15635
      Location:341 → 397
      PHD_PYGO1; PHD finger found in pygopus homolog 1 (PYGO1)

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      55538884..55588971 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047432381.1 → XP_047288337.1  pygopus homolog 1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      53342076..53392120 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377719.1 → XP_054233694.1  pygopus homolog 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y3Y4.2 GenPept UniProtKB/Swiss-Prot:Q9Y3Y4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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