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    PHF2 PHD finger protein 2 [ Homo sapiens (human) ]

    Gene ID: 5253, updated on 9-Dec-2024

    Summary

    Official Symbol
    PHF2provided by HGNC
    Official Full Name
    PHD finger protein 2provided by HGNC
    Primary source
    HGNC:HGNC:8920
    See related
    Ensembl:ENSG00000197724 MIM:604351; AllianceGenome:HGNC:8920
    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
    GRC5; KDM7C; JHDM1E; CENP-35
    Summary
    This gene encodes a protein which contains a zinc finger-like PHD (plant homeodomain) finger, distinct from other classes of zinc finger motifs, and a hydrophobic and highly conserved domain. The PHD finger shows the typical Cys4-His-Cys3 arrangement. PHD finger genes are thought to belong to a diverse group of transcriptional regulators possibly affecting eukaryotic gene expression by influencing chromatin structure. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in ovary (RPKM 14.2), endometrium (RPKM 13.4) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PHF2 in Genome Data Viewer
    Location:
    9q22.31
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (93576584..93679587)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (105744005..105847110)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (96338866..96441869)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:96213447-96213996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20045 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28621 Neighboring gene Sharpr-MPRA regulatory region 4009 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96222857-96223356 Neighboring gene family with sequence similarity 120 member A opposite strand Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96228924-96229490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28623 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:96244807-96245307 Neighboring gene family with sequence similarity 120 member A Neighboring gene MIA SH3 domain ER export factor 2 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr9:96271147-96271342 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:96273606-96273793 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96337173-96337768 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20048 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20049 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96337769-96338363 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96350491-96350991 Neighboring gene Sharpr-MPRA regulatory region 10393 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96360469-96361050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28626 Neighboring gene microRNA 548au Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96397750-96398479 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96405763-96406603 Neighboring gene keratin-associated protein 5-5-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96431943-96432456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96440627-96441126 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109906 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109914 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:96562895-96563100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96569945-96570665 Neighboring gene uncharacterized LOC101928014 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96571818-96572396 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96572397-96572974 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96572975-96573552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96573553-96574130 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109955 Neighboring gene microRNA 4291 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96632251-96632981 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96656649-96657524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96658478-96658978 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96664804-96665335 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96670812-96671504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96682210-96682710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96683612-96684112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96710391-96711318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96711319-96712244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96715091-96715655 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96715656-96716219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96717631-96718162 Neighboring gene BARX homeobox 1

    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?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2019-02-27)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2019-02-27)

    ClinGen Genome Curation PagePubMed

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of PHD finger protein 2 (PHF2) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0662, MGC176680

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone H3K9 demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H4K20 demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT enables histone demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables iron ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in liver development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of rDNA heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein demethylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in transcription initiation-coupled chromatin remodeling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in kinetochore IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    lysine-specific demethylase PHF2
    Names
    centromere protein 35
    jumonji C domain-containing histone demethylase 1E

    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.

    Genomic

    1. NG_047001.1 RefSeqGene

      Range
      4958..107961
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005392.4NP_005383.3  lysine-specific demethylase PHF2

      See identical proteins and their annotated locations for NP_005383.3

      Status: REVIEWED

      Source sequence(s)
      AL353629, AL359181, AL834263, BQ716020, CB990295
      Consensus CDS
      CCDS35069.1
      UniProtKB/Swiss-Prot
      O75151, Q4VXG0, Q8N3K2, Q9Y6N4
      Related
      ENSP00000352185.4, ENST00000359246.9
      Conserved Domains (3) summary
      pfam02373
      Location:236336
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:201264
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15554
      Location:753
      PHD_PHF2_like; PHD finger found in PHF2, PHF8 and KDM7

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      93576584..93679587
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005252051.3XP_005252108.1  lysine-specific demethylase PHF2 isoform X1

      See identical proteins and their annotated locations for XP_005252108.1

      Conserved Domains (3) summary
      pfam02373
      Location:236336
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:201264
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15554
      Location:753
      PHD_PHF2_like; PHD finger found in PHF2, PHF8 and KDM7
    2. XM_006717143.3XP_006717206.1  lysine-specific demethylase PHF2 isoform X3

      Conserved Domains (3) summary
      smart00558
      Location:201263
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cd15554
      Location:753
      PHD_PHF2_like; PHD finger found in PHF2, PHF8 and KDM7
      cl21464
      Location:236301
      cupin_like; Conserved domain found in cupin and related proteins
    3. XM_047423475.1XP_047279431.1  lysine-specific demethylase PHF2 isoform X4

    4. XM_047423474.1XP_047279430.1  lysine-specific demethylase PHF2 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      105744005..105847110
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363110.1XP_054219085.1  lysine-specific demethylase PHF2 isoform X1

    2. XM_054363112.1XP_054219087.1  lysine-specific demethylase PHF2 isoform X3

    3. XM_054363113.1XP_054219088.1  lysine-specific demethylase PHF2 isoform X4

    4. XM_054363111.1XP_054219086.1  lysine-specific demethylase PHF2 isoform X2

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_024517.1: Suppressed sequence

      Description
      NM_024517.1: This RefSeq was temporarily suppressed because currently there are not sufficient data to support this transcript.