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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
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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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