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

Gene ID: 5253, updated on 22-Sep-2022

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
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Genomic context

See PHF2 in Genome Data Viewer
Location:
9q22.31
Exon count:
23
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (93576584..93679587)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (105744005..105847110)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (96338866..96441869)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 4009 Neighboring gene family with sequence similarity 120A opposite strand Neighboring gene family with sequence similarity 120A Neighboring gene MIA SH3 domain ER export factor 2 pseudogene Neighboring gene Sharpr-MPRA regulatory region 10393 Neighboring gene microRNA 548au Neighboring gene keratin-associated protein 5-5-like Neighboring gene microRNA 4291 Neighboring gene uncharacterized LOC101928014

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

Homology

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
PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in histone modification IEA
Inferred from Electronic Annotation
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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)

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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.

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, 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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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)

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.