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

    Gene ID: 5252, updated on 3-Dec-2024

    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; AllianceGenome:HGNC:8919
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PHF1 in Genome Data Viewer
    Location:
    6p21.32
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (33410412..33416439)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (33231158..33237801)
    RS_2024_09 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 synaptic Ras GTPase activating protein 1 Neighboring gene cutA divalent cation tolerance homolog Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33393157-33393699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33396849-33397470 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:33405630-33405807 Neighboring gene SYNGAP1 antisense RNA 1 Neighboring gene microRNA 5004

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
     
    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 
    Process Evidence Code Pubs
    involved_in DNA repair-dependent chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of gene expression, epigenetic IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    part_of ESC/E(Z) complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    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
     
    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)

    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.

    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
      UniProtKB/TrEMBL
      A0A140VJR4, A0A1U9X8A3
      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
      UniProtKB/Swiss-Prot
      B1AZX2, B1AZX3, O43189, O60929, Q5SU07, Q5SU08, Q96KM7
      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: 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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      33410412..33416439
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418879.1XP_047274835.1  PHD finger protein 1 isoform X6

      UniProtKB/Swiss-Prot
      B1AZX2, B1AZX3, O43189, O60929, Q5SU07, Q5SU08, Q96KM7
    2. XM_011514665.2XP_011512967.2  PHD finger protein 1 isoform X4

    3. XM_011514666.2XP_011512968.2  PHD finger protein 1 isoform X5

    4. XM_011514662.2XP_011512964.2  PHD finger protein 1 isoform X1

    5. XM_011514663.2XP_011512965.2  PHD finger protein 1 isoform X2

    6. XM_011514669.2XP_011512971.2  PHD finger protein 1 isoform X7

      UniProtKB/TrEMBL
      A0A140VJR4
    7. XM_011514664.2XP_011512966.2  PHD finger protein 1 isoform X3

    8. XM_011514670.3XP_011512972.2  PHD finger protein 1 isoform X8

      UniProtKB/TrEMBL
      E9PQT8
    9. XM_047418881.1XP_047274837.1  PHD finger protein 1 isoform X9

    RNA

    1. XR_007059274.1 RNA Sequence

    2. XR_926250.2 RNA Sequence

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      4858494..4865164
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331354.1XP_054187329.1  PHD finger protein 1 isoform X6

    2. XM_054331356.1XP_054187331.1  PHD finger protein 1 isoform X11

    3. XM_054331362.1XP_054187337.1  PHD finger protein 1 isoform X13

    4. XM_054331358.1XP_054187333.1  PHD finger protein 1 isoform X12

    5. XM_054331353.1XP_054187328.1  PHD finger protein 1 isoform X5

    6. XM_054331360.1XP_054187335.1  PHD finger protein 1 isoform X8

      UniProtKB/TrEMBL
      B4DI51
    7. XM_054331352.1XP_054187327.1  PHD finger protein 1 isoform X4

    8. XM_054331351.1XP_054187326.1  PHD finger protein 1 isoform X10

    9. XM_054331348.1XP_054187323.1  PHD finger protein 1 isoform X1

    10. XM_054331349.1XP_054187324.1  PHD finger protein 1 isoform X2

    11. XM_054331359.1XP_054187334.1  PHD finger protein 1 isoform X7

      UniProtKB/TrEMBL
      A0A140VJR4
    12. XM_054331350.1XP_054187325.1  PHD finger protein 1 isoform X3

    13. XM_054331361.1XP_054187336.1  PHD finger protein 1 isoform X13

    14. XM_054331355.1XP_054187330.1  PHD finger protein 1 isoform X11

    15. XM_054331357.1XP_054187332.1  PHD finger protein 1 isoform X12

    16. XM_054331364.1XP_054187339.1  PHD finger protein 1 isoform X9

    17. XM_054331363.1XP_054187338.1  PHD finger protein 1 isoform X14

    RNA

    1. XR_008485716.1 RNA Sequence

    2. XR_008485717.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      33231158..33237801
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355619.1XP_054211594.1  PHD finger protein 1 isoform X6

      UniProtKB/Swiss-Prot
      B1AZX2, B1AZX3, O43189, O60929, Q5SU07, Q5SU08, Q96KM7
    2. XM_054355621.1XP_054211596.1  PHD finger protein 1 isoform X16

    3. XM_054355627.1XP_054211602.1  PHD finger protein 1 isoform X18

    4. XM_054355623.1XP_054211598.1  PHD finger protein 1 isoform X17

    5. XM_054355618.1XP_054211593.1  PHD finger protein 1 isoform X5

    6. XM_054355625.1XP_054211600.1  PHD finger protein 1 isoform X8

      UniProtKB/TrEMBL
      E9PQT8
    7. XM_054355617.1XP_054211592.1  PHD finger protein 1 isoform X4

    8. XM_054355616.1XP_054211591.1  PHD finger protein 1 isoform X15

    9. XM_054355613.1XP_054211588.1  PHD finger protein 1 isoform X1

    10. XM_054355614.1XP_054211589.1  PHD finger protein 1 isoform X2

    11. XM_054355624.1XP_054211599.1  PHD finger protein 1 isoform X7

      UniProtKB/TrEMBL
      A0A140VJR4
    12. XM_054355615.1XP_054211590.1  PHD finger protein 1 isoform X3

    13. XM_054355626.1XP_054211601.1  PHD finger protein 1 isoform X18

    14. XM_054355620.1XP_054211595.1  PHD finger protein 1 isoform X16

    15. XM_054355622.1XP_054211597.1  PHD finger protein 1 isoform X17

    16. XM_054355629.1XP_054211604.1  PHD finger protein 1 isoform X9

    17. XM_054355628.1XP_054211603.1  PHD finger protein 1 isoform X19

    RNA

    1. XR_008487345.1 RNA Sequence

    2. XR_008487346.1 RNA Sequence