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    PHF11 PHD finger protein 11 [ Homo sapiens (human) ]

    Gene ID: 51131, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PHF11provided by HGNC
    Official Full Name
    PHD finger protein 11provided by HGNC
    Primary source
    HGNC:HGNC:17024
    See related
    Ensembl:ENSG00000136147 MIM:607796; AllianceGenome:HGNC:17024
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    APY; BCAP; IGEL; IGER; IGHER; NYREN34; NY-REN-34
    Summary
    This gene encodes a protein containing a PHD (plant homeodomain) type zinc finger. This gene has been identified in some studies as a candidate gene for asthma. Naturally-occurring readthrough transcription may occur from the upstream SETDB2 (SET domain bifurcated 2) gene to this locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
    Expression
    Ubiquitous expression in lymph node (RPKM 13.0), spleen (RPKM 12.7) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See PHF11 in Genome Data Viewer
    Location:
    13q14.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (49495953..49528976)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (48714592..48747507)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (50070089..50103112)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:49888093-49889292 Neighboring gene calcium binding protein 39 like Neighboring gene NANOG hESC enhancer GRCh37_chr13:49961302-49961803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7746 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:50018017-50018789 Neighboring gene SETDB2-PHF11 readthrough Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:50018790-50019563 Neighboring gene SET domain bifurcated histone lysine methyltransferase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:50068895-50069580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7749 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 14 Neighboring gene RCC1 and BTB domain containing protein 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:50139673-50140480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7750 Neighboring gene uncharacterized LOC105370204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:50194124-50194624

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Functional characterization of the atopy-associated gene PHF11. Clarke E, et al. J Allergy Clin Immunol, 2008 May. PMID 18405956
    2. A role for the atopy-associated gene PHF11 in T-cell activation and viability. Rahman N, et al. Immunol Cell Biol, 2010 Nov-Dec. PMID 20421878
    3. Association of PHF11 polymorphisms with asthma and allergy. Jones G, et al. Thorax, 2010 Jul. PMID 20627928
    4. PHF11 is not a major candidate gene for asthma or eczema in Chinese children. Sy HY, et al. Pediatr Pulmonol, 2010 Sep. PMID 20717939
    5. PHF11 and DPP10: a tale of two genes in asthma. Adcock IM, et al. Respiration, 2010. PMID 19729874

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. data suggest that BCAP exists as two isoforms with subtly different roles in inhibition of ciliogenesis. Both are required to prevent ciliogenesis and one additionally controls cilium length after ciliogenesis has completed.
      Title: BCAP is a centriolar satellite protein and inhibitor of ciliogenesis.
    2. contributes to T-cell activation and viability
      Title: A role for the atopy-associated gene PHF11 in T-cell activation and viability.
    3. the single nucleotide polymorphism rs1046295 of PHF11 modulates allele-specific binding by the octamer-binding transcription factor 1
      Title: Allele-specific transcription of the asthma-associated PHD finger protein 11 gene (PHF11) modulated by octamer-binding transcription factor 1 (Oct-1).
    4. PHF11 (PHD finger protein 11) is not a major candidate gene for asthma or eczema in Chinese children
      Title: PHF11 is not a major candidate gene for asthma or eczema in Chinese children.
    5. We were unable to confirm associations of single nucleotide polymorphisms of the positional candidates DPP10 and PHF11 with wheeze. Significant associations with reported and examined eczema were only observed for DPP10.
      Title: A multi-centre study of candidate genes for wheeze and allergy: the International Study of Asthma and Allergies in Childhood Phase 2.
    6. rs1046295 and rs16659 associated with asthma susceptibility in a Han Chinese population
      Title: Polymorphisms of PHF11 and DPP10 are associated with asthma and related traits in a Chinese population.
    7. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Postural changes in blood pressure associated with interactions between candidate genes for chronic respiratory diseases and exposure to particulate matter.
    8. PHF11 is unlikely to contain polymorphic loci that have a major impact on asthma susceptibility in two independent populations.
      Title: The PHF11 gene is not associated with asthma or asthma phenotypes in two independent populations.
    9. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Early life environment, neurodevelopment and the interrelation with atopy.
    10. PHF11 is a regulator of T(H)1-type cytokine gene expression
      Title: Functional characterization of the atopy-associated gene PHF11.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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

    EBI GWAS Catalog

    Description
    Hypertrophy-associated polymorphisms ascertained in a founder cohort applied to heart failure risk and mortality.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough SETDB2-PHF11

    Readthrough gene: SETDB2-PHF11, Included gene: SETDB2

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    PHD finger protein 11
    Names
    BRCA1 C-terminus-associated protein
    IgE responsiveness (atopic)
    renal carcinoma antigen NY-REN-34

    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_001040443.3 → NP_001035533.1  PHD finger protein 11 isoform a

      See identical proteins and their annotated locations for NP_001035533.1

      Status: REVIEWED

      Source sequence(s)
      AK026228, DA652444
      Consensus CDS
      CCDS31975.1
      UniProtKB/Swiss-Prot
      Q5W0A4, Q5W0A6, Q9UIL8, Q9Y5A2
      Related
      ENSP00000367570.3, ENST00000378319.8
      Conserved Domains (1) summary
      cd15712
      Location:45 → 159
      ePHD_PHF11; Extended PHD finger found in PHD finger protein 11 (PHF11)

    2. NM_001040444.3 → NP_001035534.1  PHD finger protein 11 isoform b

      See identical proteins and their annotated locations for NP_001035534.1

      Status: REVIEWED

      Source sequence(s)
      AL139321
      Consensus CDS
      CCDS41887.1
      UniProtKB/TrEMBL
      H0Y4X7
      Related
      ENSP00000417539.1, ENST00000488958.5
      Conserved Domains (1) summary
      cl22851
      Location:6 → 120
      PHD_SF; PHD finger superfamily

    3. NM_001419873.1 → NP_001406802.1  PHD finger protein 11 isoform b

      Status: REVIEWED

      Source sequence(s)
      AL139321
      UniProtKB/TrEMBL
      H0Y4X7

    4. NM_001419874.1 → NP_001406803.1  PHD finger protein 11 isoform b

      Status: REVIEWED

      Source sequence(s)
      AL139321
      UniProtKB/TrEMBL
      H0Y4X7
      Related
      ENSP00000350209.3, ENST00000357596.7

    5. NM_001419875.1 → NP_001406804.1  PHD finger protein 11 isoform b

      Status: REVIEWED

      Source sequence(s)
      AL139321
      UniProtKB/TrEMBL
      H0Y4X7

    6. NM_001419876.1 → NP_001406805.1  PHD finger protein 11 isoform b

      Status: REVIEWED

      Source sequence(s)
      AL139321
      UniProtKB/TrEMBL
      H0Y4X7

    RNA

    1. NR_135322.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AK026228, AK293242, BX461254

    2. NR_135323.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL139321

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      49495953..49528976
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      48714592..48747507
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UIL8.3 GenPept UniProtKB/Swiss-Prot:Q9UIL8

    Gene LinkOut

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

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