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

Gene ID: 5253, updated on 21-Mar-2015
Official Symbol
PHF2provided by HGNC
Official Full Name
PHD finger protein 2provided by HGNC
Primary source
HGNC:HGNC:8920
See related
Ensembl:ENSG00000197724; HPRD:05071; MIM:604351; Vega:OTTHUMG00000020253
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; 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]
Orthologs
See PHF2 in MapViewer
Location:
9q22.31
Exon count:
23
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 9 NC_000009.12 (93576627..93679587)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (96338909..96441869)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 120A opposite strand Neighboring gene family with sequence similarity 120A Neighboring gene CTAGE family, member 5 pseudogene Neighboring gene microRNA 548au Neighboring gene mucin-2-like Neighboring gene uncharacterized LOC101928014 Neighboring gene microRNA 4291 Neighboring gene BARX homeobox 1

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
    HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • KIAA0662, MGC176680

Gene Ontology Provided by GOA

Function Evidence Code Pubs
dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
NOT histone demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H3-K9 specific) IDA
Inferred from Direct Assay
more info
PubMed 
iron ion binding IDA
Inferred from Direct Assay
more info
PubMed 
methylated histone binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to transcription coactivator activity IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
chromatin organization TAS
Traceable Author Statement
more info
 
histone H3-K9 demethylation IEA
Inferred from Electronic Annotation
more info
 
liver development TAS
Traceable Author Statement
more info
PubMed 
negative regulation of chromatin silencing at rDNA IMP
Inferred from Mutant Phenotype
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
protein demethylation IDA
Inferred from Direct Assay
more info
PubMed 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
condensed chromosome kinetochore IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
Preferred Names
lysine-specific demethylase PHF2
Names
lysine-specific demethylase PHF2
centromere protein 35
jumonji C domain-containing histone demethylase 1E

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_005392.3NP_005383.3  lysine-specific demethylase PHF2

    See proteins identical to NP_005383.3

    Status: REVIEWED

    Source sequence(s)
    AL359181, AL834263, BQ716020, CB990295
    Consensus CDS
    CCDS35069.1
    UniProtKB/Swiss-Prot
    O75151
    Related
    ENSP00000352185, OTTHUMP00000021685, ENST00000359246, OTTHUMT00000053162
    Conserved Domains (4) summary
    pfam02373
    Location:236336
    JmjC; JmjC domain, hydroxylase
    smart00249
    Location:753
    PHD; PHD zinc finger
    smart00558
    Location:201264
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00023
    Location:753
    PHD; canonical plant homeodomain (PHD) finger

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p2 Primary Assembly

    Range
    93576627..93679587
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005252051.2XP_005252108.1  

    See proteins identical to XP_005252108.1

    Conserved Domains (4) summary
    pfam02373
    Location:236336
    JmjC; JmjC domain, hydroxylase
    smart00249
    Location:753
    PHD; PHD zinc finger
    smart00558
    Location:201264
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00023
    Location:753
    PHD; canonical plant homeodomain (PHD) finger
  2. XM_006717143.2XP_006717206.1  

    Conserved Domains (4) summary
    smart00249
    Location:753
    PHD; PHD zinc finger
    smart00558
    Location:201263
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    sd00023
    Location:753
    PHD; canonical plant homeodomain (PHD) finger
    cl21464
    Location:236301
    ABD; Alpha-Mannosidase Binding Domain of Atg19/34
  3. XM_011518784.1XP_011517086.1  

    Conserved Domains (2) summary
    pfam02373
    Location:233333
    JmjC; JmjC domain, hydroxylase
    smart00558
    Location:198261
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily

Alternate CHM1_1.1

Genomic

  1. NC_018920.2 Alternate CHM1_1.1

    Range
    96485947..96588795
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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.