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    PHF7 PHD finger protein 7 [ Homo sapiens (human) ]

    Gene ID: 51533, updated on 27-Nov-2024

    Summary

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    Official Symbol
    PHF7provided by HGNC
    Official Full Name
    PHD finger protein 7provided by HGNC
    Primary source
    HGNC:HGNC:18458
    See related
    Ensembl:ENSG00000010318 MIM:620057; AllianceGenome:HGNC:18458
    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
    HSPC045; HSPC226; NYD-SP6
    Summary
    Spermatogenesis is a complex process regulated by extracellular and intracellular factors as well as cellular interactions among interstitial cells of the testis, Sertoli cells, and germ cells. This gene is expressed in the testis in Sertoli cells but not germ cells. The protein encoded by this gene contains plant homeodomain (PHD) finger domains, also known as leukemia associated protein (LAP) domains, believed to be involved in transcriptional regulation. The protein, which localizes to the nucleus of transfected cells, has been implicated in the transcriptional regulation of spermatogenesis. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]
    Expression
    Restricted expression toward testis (RPKM 610.5) See more
    Orthologs
    mouse all
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    Genomic context

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    See PHF7 in Genome Data Viewer
    Location:
    3p21.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52410660..52423641)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52443570..52456620)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52444676..52457657)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene dynein axonemal heavy chain 1 Neighboring gene protein phosphatase 2 regulatory subunit B'gamma pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:52443144-52443692 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:52443693-52444241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19941 Neighboring gene BRCA1 associated deubiquitinase 1 Neighboring gene VISTA enhancer hs2179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52471583-52472088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52478216-52479092 Neighboring gene semaphorin 3G Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52479093-52479969 Neighboring gene Sharpr-MPRA regulatory region 2927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52486099-52486919 Neighboring gene troponin C1, slow skeletal and cardiac type

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. NYD-SP6, a novel gene potentially involved in regulating testicular development/spermatogenesis. Xiao J, et al. Biochem Biophys Res Commun, 2002 Feb 15. PMID 11829468
    2. Genome wide identification of promoter binding sites for H4K12ac in human sperm and its relevance for early embryonic development. Paradowska AS, et al. Epigenetics, 2012 Sep. PMID 22894908, Free PMC Article
    3. The PHD finger: implications for chromatin-mediated transcriptional regulation. Aasland R, et al. Trends Biochem Sci, 1995 Feb. PMID 7701562
    4. Phf7 controls male sex determination in the Drosophila germline. Yang SY, et al. Dev Cell, 2012 May 15. PMID 22595675, Free PMC Article
    5. The melanoma-associated antigen 1 (MAGEA1) protein stimulates the E3 ubiquitin-ligase activity of TRIM31 within a TRIM31-MAGEA1-NSE4 complex. Kozakova L, et al. Cell Cycle, 2015. PMID 25590999, Free PMC Article

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHF7 promoter binds H4K12ac in mature spermatozoa.
      Title: Genome wide identification of promoter binding sites for H4K12ac in human sperm and its relevance for early embryonic development.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    EBI GWAS Catalog
    Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC26088, DKFZp434L1850

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus HDA PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    PHD finger protein 7
    Names
    testicular secretory protein Li 34
    testis development protein NYD-SP6

    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_001278221.3 → NP_001265150.1  PHD finger protein 7 isoform 2

      See identical proteins and their annotated locations for NP_001265150.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.
      Source sequence(s)
      AY014283, BC022002, BG704704, BG723964, BU853281
      Consensus CDS
      CCDS2855.1
      UniProtKB/TrEMBL
      A8K856, Q53EV8
      Related
      ENSP00000246282.4, ENST00000347025.6
      Conserved Domains (2) summary
      cd15669
      Location:33 → 144
      ePHD_PHF7_G2E3_like; Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3)
      cl22851
      Location:225 → 261
      PHD_SF; PHD finger superfamily

    2. NM_001321126.2 → NP_001308055.1  PHD finger protein 7 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AK292221, AY014283, BC022002, BG704704
      Consensus CDS
      CCDS2854.1
      UniProtKB/Swiss-Prot
      K4DI82, Q9BWX1
      UniProtKB/TrEMBL
      A0A024R336, A0A140VK34, A8K856, Q53EV8
      Related
      ENSP00000417712.1, ENST00000461861.5
      Conserved Domains (2) summary
      cd15496
      Location:247 → 300
      PHD_PHF7_G2E3_like; PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3)
      cd15669
      Location:33 → 144
      ePHD_PHF7_G2E3_like; Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3)

    3. NM_001321127.2 → NP_001308056.1  PHD finger protein 7 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AK292221, AY014283, BC022002, BG704704, BQ669125
      Consensus CDS
      CCDS2854.1
      UniProtKB/Swiss-Prot
      K4DI82, Q9BWX1
      UniProtKB/TrEMBL
      A0A024R336, A0A140VK34, A8K856, Q53EV8
      Conserved Domains (2) summary
      cd15496
      Location:247 → 300
      PHD_PHF7_G2E3_like; PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3)
      cd15669
      Location:33 → 144
      ePHD_PHF7_G2E3_like; Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3)

    4. NM_016483.7 → NP_057567.3  PHD finger protein 7 isoform 1

      See identical proteins and their annotated locations for NP_057567.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AY014283, BC022002, BG704704
      Consensus CDS
      CCDS2854.1
      UniProtKB/Swiss-Prot
      K4DI82, Q9BWX1
      UniProtKB/TrEMBL
      A0A024R336, A0A140VK34, A8K856, Q53EV8
      Related
      ENSP00000333024.3, ENST00000327906.8
      Conserved Domains (2) summary
      cd15496
      Location:247 → 300
      PHD_PHF7_G2E3_like; PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3)
      cd15669
      Location:33 → 144
      ePHD_PHF7_G2E3_like; Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3)

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      52410660..52423641
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024453589.2 → XP_024309357.1  PHD finger protein 7 isoform X1

      UniProtKB/Swiss-Prot
      K4DI82, Q9BWX1
      UniProtKB/TrEMBL
      A0A024R336, A0A140VK34, A8K856, Q53EV8
      Conserved Domains (2) summary
      cd15496
      Location:247 → 300
      PHD_PHF7_G2E3_like; PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3)
      cd15669
      Location:33 → 144
      ePHD_PHF7_G2E3_like; Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3)

    2. XM_047448296.1 → XP_047304252.1  PHD finger protein 7 isoform X3

    3. XM_047448295.1 → XP_047304251.1  PHD finger protein 7 isoform X2

    4. XM_011533826.4 → XP_011532128.1  PHD finger protein 7 isoform X3

      Conserved Domains (1) summary
      cd15669
      Location:33 → 144
      ePHD_PHF7_G2E3_like; Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      52443570..52456620
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346814.1 → XP_054202789.1  PHD finger protein 7 isoform X1

      UniProtKB/Swiss-Prot
      K4DI82, Q9BWX1
      UniProtKB/TrEMBL
      A0A024R336, A0A140VK34

    2. XM_054346817.1 → XP_054202792.1  PHD finger protein 7 isoform X3

    3. XM_054346815.1 → XP_054202790.1  PHD finger protein 7 isoform X2

    4. XM_054346816.1 → XP_054202791.1  PHD finger protein 7 isoform X3

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_173341.1: Suppressed sequence

      Description
      NM_173341.1: This RefSeq was permanently suppressed because currently there is support for the protein but not for the 5' UTR of the transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BWX1.1 GenPept UniProtKB/Swiss-Prot:Q9BWX1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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