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

Gene ID: 51533, updated on 3-Apr-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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Location:
3p21.1
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52410660..52423641)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52443570..52456620)
105.20220307 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 protein 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. 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
  2. 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
  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)

Genotypes

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_2023_10

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

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