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    PHRF1 PHD and ring finger domains 1 [ Homo sapiens (human) ]

    Gene ID: 57661, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PHRF1provided by HGNC
    Official Full Name
    PHD and ring finger domains 1provided by HGNC
    Primary source
    HGNC:HGNC:24351
    See related
    Ensembl:ENSG00000070047 MIM:611780; AllianceGenome:HGNC:24351
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RNF221; PPP1R125
    Summary
    Predicted to enable RNA polymerase binding activity. Predicted to be involved in protein ubiquitination. Located in membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in testis (RPKM 9.2), spleen (RPKM 7.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHRF1 in Genome Data Viewer
    Location:
    11p15.5
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (576470..612222)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (619076..660868)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (576470..612222)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene MIR210 host gene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:569389-570139 Neighboring gene translation initiation factor IF-2-like Neighboring gene microRNA 210 Neighboring gene uncharacterized LOC143666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:583763-584264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:584265-584764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:595501-596000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:604659-605277 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:612434-613028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:613623-614217 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:614812-615406 Neighboring gene interferon regulatory factor 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:620099-620704 Neighboring gene cadherin related family member 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of PHRF1 as a tumor suppressor that promotes the TGF-β cytostatic program through selective release of TGIF-driven PML inactivation. Ettahar A, et al. Cell Rep, 2013 Aug 15. PMID 23911286
    2. Overexpression of PHRF1 attenuates the proliferation and tumorigenicity of non-small cell lung cancer cells. Wang Y, et al. Oncotarget, 2016 Sep 27. PMID 27608840, Free PMC Article
    3. Downregulation of a putative tumor suppressor gene PHRF1 in gastric and colorectal cancers. An CH, et al. Pathol Res Pract, 2020 Jun. PMID 32360246
    4. PHRF1 Promotes Cell Invasion by Modulating SOX4 Expression in Colorectal Cancer HCT116-p53(-/-) Cells. Lin HW, et al. Anticancer Res, 2023 Dec. PMID 38030167
    5. Association of PHRF1-IRF7 region polymorphism with clinical manifestations of systemic lupus erythematosus in a Japanese population. Kawasaki A, et al. Lupus, 2012 Jul. PMID 22433914

    See all (52) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHRF1 Promotes Cell Invasion by Modulating SOX4 Expression in Colorectal Cancer HCT116-p53[-/-] Cells.
      Title: PHRF1 Promotes Cell Invasion by Modulating SOX4 Expression in Colorectal Cancer HCT116-p53(-/-) Cells.
    2. Downregulation of a putative tumor suppressor gene PHRF1 in gastric and colorectal cancers.
      Title: Downregulation of a putative tumor suppressor gene PHRF1 in gastric and colorectal cancers.
    3. Overexpression of PHRF1 attenuated the proliferation and tumorigenicity of non-small cell lung cancer cell lines.
      Title: Overexpression of PHRF1 attenuates the proliferation and tumorigenicity of non-small cell lung cancer cells.
    4. Results suggest that PHRF1 may combine with H3K36 methylation and NBS1 to promote NHEJ and stabilize genomic integrity upon DNA damage insults.
      Title: PHRF1 promotes genome integrity by modulating non-homologous end-joining.
    5. The PHRF1 gene is deleted or silenced in a high proportion of human breast cancer samples and cancer cell lines.
      Title: Identification of PHRF1 as a tumor suppressor that promotes the TGF-β cytostatic program through selective release of TGIF-driven PML inactivation.
    6. we independently replicated the association of PHRF1 SNP rs4963128T with anti-Sm antibody recently reported in African- American populations, and also detected association with the presence of renal disorder.
      Title: Association of PHRF1-IRF7 region polymorphism with clinical manifestations of systemic lupus erythematosus in a Japanese population.
    7. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Early disease onset is predicted by a higher genetic risk for lupus and is associated with a more severe phenotype in lupus patients.
    8. Observational study and meta-analysis of gene-disease association. (HuGE Navigator)
      Title: Study of the common genetic background for rheumatoid arthritis and systemic lupus erythematosus.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: A targeted association study in systemic lupus erythematosus identifies multiple susceptibility alleles.
    10. Genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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
    A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci.
    EBI GWAS Catalog
    Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
    EBI GWAS Catalog
    Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci.
    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

    • KIAA1542

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA polymerase binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in membrane HDA PubMed 

    General protein information

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    Preferred Names
    PHD and RING finger domain-containing protein 1
    Names
    CTD-binding SR-like protein rA9
    protein phosphatase 1, regulatory subunit 125

    NCBI Reference Sequences (RefSeq)

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    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_001286581.2 → NP_001273510.1  PHD and RING finger domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001273510.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AP006284, BC146771, DA656880
      Consensus CDS
      CCDS65988.1
      UniProtKB/Swiss-Prot
      A6H8W1, B7ZM64, B9EGP0, C9JS82, Q6PJP2, Q8IVY2, Q8N2Y7, Q9BSM2, Q9P1Y6
      UniProtKB/TrEMBL
      A0A0J9YWD5
      Related
      ENSP00000264555.5, ENST00000264555.10
      Conserved Domains (3) summary
      cd15536
      Location:185 → 230
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam12678
      Location:92 → 149
      zf-rbx1; RING-H2 zinc finger
      pfam13639
      Location:106 → 149
      zf-RING_2; Ring finger domain

    2. NM_001286582.2 → NP_001273511.1  PHD and RING finger domain-containing protein 1 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses two alternate in-frame splice sites, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      BC144293, BC144295, BC146771, DA656880
      Consensus CDS
      CCDS65989.1
      UniProtKB/TrEMBL
      A0A0J9YYB5, B7ZM66, F8WEF5
      Related
      ENSP00000388589.2, ENST00000413872.6
      Conserved Domains (3) summary
      cd15536
      Location:184 → 229
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam12678
      Location:91 → 148
      zf-rbx1; RING-H2 zinc finger
      pfam13639
      Location:105 → 148
      zf-RING_2; Ring finger domain

    3. NM_001286583.2 → NP_001273512.1  PHD and RING finger domain-containing protein 1 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses two alternate in-frame splice sites, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AP006284, BC144293, BC144294, BC146771, DA656880
      Consensus CDS
      CCDS65987.1
      UniProtKB/TrEMBL
      B7ZM65, E9PJ24
      Related
      ENSP00000431870.1, ENST00000533464.5
      Conserved Domains (3) summary
      cd15536
      Location:181 → 226
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam12678
      Location:88 → 145
      zf-rbx1; RING-H2 zinc finger
      pfam13639
      Location:102 → 145
      zf-RING_2; Ring finger domain

    4. NM_020901.4 → NP_065952.2  PHD and RING finger domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_065952.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      BC144293, BC146771, DA656880
      Consensus CDS
      CCDS44507.1
      UniProtKB/TrEMBL
      A0A0J9YWD5
      Related
      ENSP00000410626.2, ENST00000416188.3
      Conserved Domains (3) summary
      cd15536
      Location:185 → 230
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam12678
      Location:92 → 149
      zf-rbx1; RING-H2 zinc finger
      pfam13639
      Location:106 → 149
      zf-RING_2; Ring finger domain

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      576470..612222
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011520236.4 → XP_011518538.1  PHD and RING finger domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A0J9YWD5
      Conserved Domains (3) summary
      cd15536
      Location:185 → 230
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam12678
      Location:92 → 149
      zf-rbx1; RING-H2 zinc finger
      pfam13639
      Location:106 → 149
      zf-RING_2; Ring finger domain

    2. XM_047427343.1 → XP_047283299.1  PHD and RING finger domain-containing protein 1 isoform X5

      UniProtKB/TrEMBL
      A0A0J9YWD5

    3. XM_005253025.6 → XP_005253082.1  PHD and RING finger domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0J9YYB5, B7ZM66
      Conserved Domains (3) summary
      cd15536
      Location:184 → 229
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam12678
      Location:91 → 148
      zf-rbx1; RING-H2 zinc finger
      pfam13639
      Location:105 → 148
      zf-RING_2; Ring finger domain

    4. XM_047427342.1 → XP_047283298.1  PHD and RING finger domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A0J9YYB5, B7ZM66

    5. XM_011520237.4 → XP_011518539.1  PHD and RING finger domain-containing protein 1 isoform X10

      UniProtKB/TrEMBL
      A0A0J9YYB5, B7ZM66
      Conserved Domains (3) summary
      cd15536
      Location:145 → 190
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam12678
      Location:52 → 109
      zf-rbx1; RING-H2 zinc finger
      pfam13639
      Location:66 → 109
      zf-RING_2; Ring finger domain

    6. XM_047427348.1 → XP_047283304.1  PHD and RING finger domain-containing protein 1 isoform X11

      UniProtKB/TrEMBL
      A0A0J9YYB5, B7ZM66

    7. XM_005253027.4 → XP_005253084.1  PHD and RING finger domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      B7ZM65
      Conserved Domains (3) summary
      cd15536
      Location:182 → 227
      PHD_PHRF1; PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1)
      pfam12678
      Location:89 → 146
      zf-rbx1; RING-H2 zinc finger
      pfam13639
      Location:103 → 146
      zf-RING_2; Ring finger domain

    8. XM_047427344.1 → XP_047283300.1  PHD and RING finger domain-containing protein 1 isoform X6

      UniProtKB/TrEMBL
      B7ZM65

    9. XM_047427345.1 → XP_047283301.1  PHD and RING finger domain-containing protein 1 isoform X7

      UniProtKB/TrEMBL
      B7ZM65

    10. XM_047427346.1 → XP_047283302.1  PHD and RING finger domain-containing protein 1 isoform X8

      UniProtKB/TrEMBL
      B7ZM65

    11. XM_047427347.1 → XP_047283303.1  PHD and RING finger domain-containing protein 1 isoform X9

      UniProtKB/TrEMBL
      B7ZM65

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187586.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      106126..142115
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328910.1 → XP_054184885.1  PHD and RING finger domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A0J9YWD5

    2. XM_054328913.1 → XP_054184888.1  PHD and RING finger domain-containing protein 1 isoform X5

      UniProtKB/TrEMBL
      A0A0J9YWD5

    3. XM_054328909.1 → XP_054184884.1  PHD and RING finger domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0J9YYB5

    4. XM_054328912.1 → XP_054184887.1  PHD and RING finger domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A0J9YYB5

    5. XM_054328915.1 → XP_054184890.1  PHD and RING finger domain-containing protein 1 isoform X12

      UniProtKB/TrEMBL
      A0A0J9YYB5

    6. XM_054328920.1 → XP_054184895.1  PHD and RING finger domain-containing protein 1 isoform X10

      UniProtKB/TrEMBL
      A0A0J9YYB5

    7. XM_054328921.1 → XP_054184896.1  PHD and RING finger domain-containing protein 1 isoform X11

      UniProtKB/TrEMBL
      A0A0J9YYB5

    8. XM_054328922.1 → XP_054184897.1  PHD and RING finger domain-containing protein 1 isoform X15

      UniProtKB/TrEMBL
      A0A0J9YYB5

    9. XM_054328911.1 → XP_054184886.1  PHD and RING finger domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      B7ZM65

    10. XM_054328914.1 → XP_054184889.1  PHD and RING finger domain-containing protein 1 isoform X6

      UniProtKB/TrEMBL
      B7ZM65

    11. XM_054328916.1 → XP_054184891.1  PHD and RING finger domain-containing protein 1 isoform X7

      UniProtKB/TrEMBL
      B7ZM65

    12. XM_054328919.1 → XP_054184894.1  PHD and RING finger domain-containing protein 1 isoform X14

      UniProtKB/TrEMBL
      B7ZM65

    13. XM_054328917.1 → XP_054184892.1  PHD and RING finger domain-containing protein 1 isoform X13

      UniProtKB/TrEMBL
      B7ZM65

    14. XM_054328918.1 → XP_054184893.1  PHD and RING finger domain-containing protein 1 isoform X8

      UniProtKB/TrEMBL
      B7ZM65

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      619076..660868
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369490.1 → XP_054225465.1  PHD and RING finger domain-containing protein 1 isoform X16

      UniProtKB/TrEMBL
      A0A0J9YWD5

    2. XM_054369492.1 → XP_054225467.1  PHD and RING finger domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A0J9YWD5

    3. XM_054369495.1 → XP_054225470.1  PHD and RING finger domain-containing protein 1 isoform X5

      UniProtKB/TrEMBL
      A0A0J9YWD5

    4. XM_054369491.1 → XP_054225466.1  PHD and RING finger domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0J9YYB5

    5. XM_054369494.1 → XP_054225469.1  PHD and RING finger domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A0J9YYB5

    6. XM_054369497.1 → XP_054225472.1  PHD and RING finger domain-containing protein 1 isoform X17

      UniProtKB/TrEMBL
      A0A0J9YYB5

    7. XM_054369503.1 → XP_054225478.1  PHD and RING finger domain-containing protein 1 isoform X10

      UniProtKB/TrEMBL
      A0A0J9YYB5

    8. XM_054369504.1 → XP_054225479.1  PHD and RING finger domain-containing protein 1 isoform X11

      UniProtKB/TrEMBL
      A0A0J9YYB5

    9. XM_054369505.1 → XP_054225480.1  PHD and RING finger domain-containing protein 1 isoform X20

      UniProtKB/TrEMBL
      A0A0J9YYB5

    10. XM_054369493.1 → XP_054225468.1  PHD and RING finger domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      B7ZM65

    11. XM_054369496.1 → XP_054225471.1  PHD and RING finger domain-containing protein 1 isoform X6

      UniProtKB/TrEMBL
      B7ZM65

    12. XM_054369498.1 → XP_054225473.1  PHD and RING finger domain-containing protein 1 isoform X7

      UniProtKB/TrEMBL
      B7ZM65

    13. XM_054369501.1 → XP_054225476.1  PHD and RING finger domain-containing protein 1 isoform X19

      UniProtKB/TrEMBL
      B7ZM65

    14. XM_054369499.1 → XP_054225474.1  PHD and RING finger domain-containing protein 1 isoform X18

      UniProtKB/TrEMBL
      B7ZM65

    15. XM_054369500.1 → XP_054225475.1  PHD and RING finger domain-containing protein 1 isoform X8

      UniProtKB/TrEMBL
      B7ZM65

    16. XM_054369502.1 → XP_054225477.1  PHD and RING finger domain-containing protein 1 isoform X9

      UniProtKB/TrEMBL
      B7ZM65
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P1Y6.3 GenPept UniProtKB/Swiss-Prot:Q9P1Y6

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