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

    Gene ID: 26108, updated on 17-Jun-2024

    Summary

    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; protein localization to nucleus; and spermatid development. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in thyroid (RPKM 4.1), endometrium (RPKM 3.0) and 20 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See PYGO1 in Genome Data Viewer
    Location:
    15q21.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (55538884..55588971, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (53342076..53392120, complement)
    105.20220307 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

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    Preferred Names
    pygopus homolog 1
    Names
    pygopus-like protein 1

    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_001330326.2NP_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:341397
      PHD_PYGO1; PHD finger found in pygopus homolog 1 (PYGO1)
    2. NM_001367806.1NP_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_015617.3NP_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:341397
      PHD_PYGO1; PHD finger found in pygopus homolog 1 (PYGO1)

    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_000015.10 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_047432381.1XP_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_054377719.1XP_054233694.1  pygopus homolog 1 isoform X1