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PHF1 PHD finger protein 1 [ Homo sapiens (human) ]

Gene ID: 5252, updated on 17-Oct-2021

Summary

Official Symbol
PHF1provided by HGNC
Official Full Name
PHD finger protein 1provided by HGNC
Primary source
HGNC:HGNC:8919
See related
Ensembl:ENSG00000112511 MIM:602881
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
PCL1; PHF2; hPHF1; MTF2L2; TDRD19C
Summary
This gene encodes a Polycomb group protein. The protein is a component of a histone H3 lysine-27 (H3K27)-specific methyltransferase complex, and functions in transcriptional repression of homeotic genes. The protein is also recruited to double-strand breaks, and reduced protein levels results in X-ray sensitivity and increased homologous recombination. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]
Expression
Ubiquitous expression in ovary (RPKM 47.5), testis (RPKM 44.7) and 25 other tissues See more
Orthologs
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Genomic context

See PHF1 in Genome Data Viewer
Location:
6p21.32
Exon count:
16
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (33410751..33416443)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33378791..33384216)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L35a pseudogene 4 Neighboring gene kinesin family member C1 Neighboring gene ribosomal protein L12 pseudogene 1 Neighboring gene cutA divalent cation tolerance homolog Neighboring gene synaptic Ras GTPase activating protein 1 Neighboring gene microRNA 5004 Neighboring gene zinc finger and BTB domain containing 9

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?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of PHD finger protein 1 (PHF1) by siRNA has both activating and inhibiting activities on HIV-1 replication in HeLa P4/R5 cells, suggesting a regulatory role in HIV replication PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone methyltransferase binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables methylated histone binding IBA
Inferred from Biological aspect of Ancestor
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 corepressor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
colocalizes_with centrosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in site of double-strand break IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
PHD finger protein 1
Names
hPCl1
polycomb-like 1
polycomb-like protein 1
testicular tissue protein Li 140
tudor domain containing 19C

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_002636.5NP_002627.2  PHD finger protein 1 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), uses an alternate splice site and lacks an alternate exon in the 3' coding region resulting in a frameshift, compared to variant 2. The resulting isoform (a) has a shorter and distinct C-terminus, compared to isoform b.
    Source sequence(s)
    AL662799
    Consensus CDS
    CCDS4778.1
    Related
    ENSP00000363636.3, ENST00000374512.7
    Conserved Domains (3) summary
    cd15500
    Location:89139
    PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)
    cd15582
    Location:188239
    PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)
    pfam18104
    Location:3469
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
  2. NM_024165.3NP_077084.2  PHD finger protein 1 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also called variant PHF2, represents the longest transcript and encodes the longer isoform (b).
    Source sequence(s)
    AL662799
    Consensus CDS
    CCDS4777.1
    Related
    ENSP00000363640.3, ENST00000374516.8
    Conserved Domains (4) summary
    cd15500
    Location:89139
    PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)
    cd15582
    Location:188239
    PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)
    pfam14061
    Location:539565
    Mtf2_C; Polycomb-like MTF2 factor 2
    pfam18104
    Location:3469
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain

RNA

  1. NR_027692.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site, compared to variant 2. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL662799

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    33410751..33416443
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514665.1XP_011512967.1  PHD finger protein 1 isoform X4

    Conserved Domains (3) summary
    smart00333
    Location:2980
    TUDOR; Tudor domain
    cd15500
    Location:89139
    PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)
    cd15582
    Location:188239
    PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)
  2. XM_011514666.1XP_011512968.1  PHD finger protein 1 isoform X5

    Conserved Domains (3) summary
    smart00333
    Location:2980
    TUDOR; Tudor domain
    cd15500
    Location:89139
    PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)
    cd15582
    Location:188239
    PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)
  3. XM_011514662.1XP_011512964.1  PHD finger protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011512964.1

    UniProtKB/Swiss-Prot
    O43189
    Conserved Domains (4) summary
    cd15500
    Location:89139
    PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)
    cd15582
    Location:188239
    PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)
    pfam14061
    Location:539565
    Mtf2_C; Polycomb-like MTF2 factor 2
    pfam18104
    Location:3469
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
  4. XM_011514663.1XP_011512965.1  PHD finger protein 1 isoform X2

    Conserved Domains (4) summary
    smart00333
    Location:2980
    TUDOR; Tudor domain
    cd15500
    Location:89139
    PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)
    cd15582
    Location:188239
    PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)
    pfam14061
    Location:538563
    Mtf2_C; Polycomb-like MTF2 factor 2
  5. XM_011514669.1XP_011512971.1  PHD finger protein 1 isoform X6

    Conserved Domains (3) summary
    smart00333
    Location:2980
    TUDOR; Tudor domain
    cd15500
    Location:89139
    PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)
    cd15582
    Location:188239
    PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)
  6. XM_011514664.1XP_011512966.1  PHD finger protein 1 isoform X3

    Conserved Domains (4) summary
    smart00333
    Location:2980
    TUDOR; Tudor domain
    cd15500
    Location:89139
    PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)
    pfam14061
    Location:507532
    Mtf2_C; Polycomb-like MTF2 factor 2
    cl22851
    Location:188206
    PHD_SF; PHD finger superfamily
  7. XM_011514670.2XP_011512972.1  PHD finger protein 1 isoform X7

    Related
    ENSP00000432419.1, ENST00000487667.5
    Conserved Domains (3) summary
    smart00333
    Location:2980
    TUDOR; Tudor domain
    cd15500
    Location:89139
    PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)
    cd15582
    Location:188239
    PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)
  8. XM_017010939.1XP_016866428.1  PHD finger protein 1 isoform X8

    Conserved Domains (1) summary
    pfam14061
    Location:306331
    Mtf2_C; Polycomb-like MTF2 factor 2

RNA

  1. XR_926249.2 RNA Sequence

  2. XR_926250.1 RNA Sequence

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    4859741..4865164
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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