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

Gene ID: 57661, updated on 27-Nov-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, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 9.2), spleen (RPKM 7.4) and 25 other tissues See more
Orthologs
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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: 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. 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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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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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

  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

  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

  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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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