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    PHF12 PHD finger protein 12 [ Homo sapiens (human) ]

    Gene ID: 57649, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PHF12provided by HGNC
    Official Full Name
    PHD finger protein 12provided by HGNC
    Primary source
    HGNC:HGNC:20816
    See related
    Ensembl:ENSG00000109118 MIM:618645; AllianceGenome:HGNC:20816
    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
    PF1
    Summary
    Enables phosphatidylinositol binding activity and transcription corepressor activity. Involved in negative regulation of transcription, DNA-templated. Acts upstream of or within negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of Sin3 complex and transcription repressor complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in bone marrow (RPKM 8.9), spleen (RPKM 8.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    17q11.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (28905250..28951518, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (29848033..29894279, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (27232268..27278536, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11955 Neighboring gene flotillin 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:27223968-27224468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8359 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:27228996-27229188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:27232864-27233364 Neighboring gene Sharpr-MPRA regulatory region 2481 Neighboring gene dehydrogenase/reductase 13 Neighboring gene uncharacterized LOC101927018 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11956 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:27275797-27276417 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:27276418-27277037 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8362 Neighboring gene uncharacterized LOC105371716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11959 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:27279039-27279660 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:27285966-27286466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:27286467-27286967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11961 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27295422-27296072 Neighboring gene seizure related 6 homolog Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27298966-27299843 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27304487-27305060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11962 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27312673-27313313 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:27314841-27315342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:27318844-27319528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:27319529-27320212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:27325005-27325504 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27330212-27330838 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27330839-27331463 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:27332814-27332997 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27346329-27346969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27346970-27347609 Neighboring gene NADH:ubiquinone oxidoreductase subunit S5 pseudogene 7

    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. Structural basis for molecular interactions involving MRG domains: implications in chromatin biology. Xie T, et al. Structure, 2012 Jan 11. PMID 22244764, Free PMC Article
    2. Solution structure of the mSin3A PAH2-Pf1 SID1 complex: a Mad1/Mxd1-like interaction disrupted by MRG15 in the Rpd3S/Sin3S complex. Kumar GS, et al. J Mol Biol, 2011 May 20. PMID 21440557, Free PMC Article
    3. The polybasic region that follows the plant homeodomain zinc finger 1 of Pf1 is necessary and sufficient for specific phosphoinositide binding. Kaadige MR, et al. J Biol Chem, 2006 Sep 29. PMID 16893883
    4. Peptidoglycan recognition protein Pglyrp2 protects mice from psoriasis-like skin inflammation by promoting regulatory T cells and limiting Th17 responses. Park SY, et al. J Immunol, 2011 Dec 1. PMID 22048773, Free PMC Article
    5. Role for the mortality factors MORF4, MRGX, and MRG15 in transcriptional repression via associations with Pf1, mSin3A, and Transducin-Like Enhancer of Split. Yochum GS, et al. Mol Cell Biol, 2002 Nov. PMID 12391155, Free PMC Article

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of PHD finger protein 12 (PHF12) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34122, KIAA1523, MGC131914

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription corepressor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription corepressor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription corepressor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Sin3-type complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Sin3-type complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of transcription repressor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    PHD finger protein 12
    Names
    PHD factor 1
    PHD zinc finger transcription factor

    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_001033561.2 → NP_001028733.1  PHD finger protein 12 isoform 1

      See identical proteins and their annotated locations for NP_001028733.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB040956, AC024267, AL161953, AY030283
      Consensus CDS
      CCDS32598.1
      UniProtKB/Swiss-Prot
      Q0VAI5, Q2TAK2, Q6ZML2, Q96QT6, Q9BV34, Q9H7U9, Q9P205
      UniProtKB/TrEMBL
      A8K5V5
      Related
      ENSP00000329933.4, ENST00000332830.9
      Conserved Domains (4) summary
      cd00060
      Location:813 → 868
      FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
      cd15533
      Location:58 → 102
      PHD1_PHF12; PHD finger 1 found in PHD finger protein 12 (PHF12)
      cd15534
      Location:273 → 318
      PHD2_PHF12_Rco1; PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins
      pfam16737
      Location:203 → 241
      PHF12_MRG_bd; PHD finger protein 12 MRG binding domain

    2. NM_001290131.2 → NP_001277060.1  PHD finger protein 12 isoform 3

      See identical proteins and their annotated locations for NP_001277060.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC024267, AY030283, BC110882
      Consensus CDS
      CCDS76981.1
      UniProtKB/TrEMBL
      C9J9G2
      Related
      ENSP00000465161.1, ENST00000577226.5
      Conserved Domains (3) summary
      cd15533
      Location:58 → 102
      PHD1_PHF12; PHD finger 1 found in PHD finger protein 12 (PHF12)
      cd15534
      Location:273 → 318
      PHD2_PHF12_Rco1; PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins
      pfam16737
      Location:203 → 241
      PHF12_MRG_bd; PHD finger protein 12 MRG binding domain

    3. NM_020889.3 → NP_065940.1  PHD finger protein 12 isoform 2

      See identical proteins and their annotated locations for NP_065940.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC024267, AL161953, AY030283, BC001657
      Consensus CDS
      CCDS11247.1
      UniProtKB/TrEMBL
      Q0VAI6
      Related
      ENSP00000268756.3, ENST00000268756.7
      Conserved Domains (3) summary
      cd15533
      Location:58 → 102
      PHD1_PHF12; PHD finger 1 found in PHD finger protein 12 (PHF12)
      cd15534
      Location:273 → 318
      PHD2_PHF12_Rco1; PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins
      pfam16737
      Location:203 → 241
      PHF12_MRG_bd; PHD finger protein 12 MRG binding domain

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      28905250..28951518 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      29848033..29894279 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96QT6.2 GenPept UniProtKB/Swiss-Prot:Q96QT6

    Gene LinkOut

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

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