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Aliases for PHRF1 Gene

Aliases for PHRF1 Gene

  • PHD And Ring Finger Domains 1 2 3 5
  • Protein Phosphatase 1, Regulatory Subunit 125 2 3
  • PHD And RING Finger Domain-Containing Protein 1 3
  • CTD Binding SR Like Protein RA9 2
  • CTD-Binding SR-Like Protein RA9 3
  • PPP1R125 3
  • KIAA1542 4
  • RNF221 3

External Ids for PHRF1 Gene

Previous HGNC Symbols for PHRF1 Gene

  • RNF221

Previous GeneCards Identifiers for PHRF1 Gene

  • GC11P000567
  • GC11P000371
  • GC11P000577
  • GC11P000578

Summaries for PHRF1 Gene

GeneCards Summary for PHRF1 Gene

PHRF1 (PHD And Ring Finger Domains 1) is a Protein Coding gene. GO annotations related to this gene include protein domain specific binding and RNA polymerase binding. An important paralog of this gene is SCAF1.

No data available for Entrez Gene Summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHRF1 Gene

Genomics for PHRF1 Gene

Regulatory Elements for PHRF1 Gene

Enhancers for PHRF1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11F000266 1.7 FANTOM5 Ensembl ENCODE 26.9 -306.2 -306168 6.8 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 SIN3A YY1 ZNF766 CBX5 ZNF143 RIC8A IFITM2 PHRF1 PSMD13 SNORA52 SIRT3 PGGHG ENSG00000255237 ENSG00000254559 ODF3
GH11F000311 1.4 FANTOM5 ENCODE 23.7 -261.4 -261352 7.0 HDGF ATF1 PKNOX1 ARNT CREB3L1 WRNIP1 SIN3A ARID4B ETS1 YY1 ENSG00000254910 IFITM3 PGGHG PHRF1 IFITM2 SNORA52 RIC8A ENSG00000251661 ENSG00000255026 NLRP6
GH11F000924 1.4 FANTOM5 ENCODE 19 +350.6 350585 5.0 ATF1 CREB3L1 ARID4B SIN3A ZNF48 GTF3C2 ZNF766 GLIS2 ELK1 ZNF207 PHRF1 SNORA52 ENSG00000255237 ENSG00000269915 RIC8A AP2A2 POLR2L LRRC56 BRSK2 CEND1
GH11F001335 1.5 FANTOM5 Ensembl ENCODE 15.8 +760.4 760401 2.8 TBP PKNOX1 YBX1 RAD21 ZNF48 CREM ZNF202 SMAD5 CEBPB ZEB2 PHRF1 SNORA52 ENSG00000255237 TOLLIP TSPAN4 TOLLIP-AS1 BRSK2 LOC105376513 GC11P001310
GH11F000803 1.1 ENCODE 19 +228.8 228767 3.2 HDGF PKNOX1 ARNT CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZNF143 RPLP2 PHRF1 SNORA52 ENSG00000255237 LOC171391 ENSG00000269915 RIC8A PIDD1 CRACR2B SLC25A22
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PHRF1 on UCSC Golden Path with GeneCards custom track

Promoters for PHRF1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for PHRF1 Gene

576,220 bp from pter
612,222 bp from pter
36,003 bases
Plus strand

Genomic View for PHRF1 Gene

Genes around PHRF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHRF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHRF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHRF1 Gene

Proteins for PHRF1 Gene

  • Protein details for PHRF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    PHD and RING finger domain-containing protein 1
    Protein Accession:
    Secondary Accessions:
    • A6H8W1
    • B7ZM64
    • B9EGP0
    • C9JS82
    • Q6PJP2
    • Q8IVY2
    • Q8N2Y7
    • Q9BSM2

    Protein attributes for PHRF1 Gene

    1649 amino acids
    Molecular mass:
    178666 Da
    Quaternary structure:
    • Interacts with POLR2A (via the C-terminal domain).
    • Sequence=BAA96066.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for PHRF1 Gene


neXtProt entry for PHRF1 Gene

Post-translational modifications for PHRF1 Gene

  • Ubiquitination at Lys 1579
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PHRF1 Gene

Domains & Families for PHRF1 Gene

Suggested Antigen Peptide Sequences for PHRF1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 PHD-type zinc finger.
  • Contains 1 PHD-type zinc finger.
  • Contains 1 RING-type zinc finger.
genes like me logo Genes that share domains with PHRF1: view

Function for PHRF1 Gene

Gene Ontology (GO) - Molecular Function for PHRF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008270 zinc ion binding IEA --
GO:0019904 protein domain specific binding IEA --
GO:0046872 metal ion binding IEA --
GO:0070063 RNA polymerase binding ISS --
genes like me logo Genes that share ontologies with PHRF1: view
genes like me logo Genes that share phenotypes with PHRF1: view

Animal Model Products

miRNA for PHRF1 Gene

Inhibitory RNA Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PHRF1 Gene

Localization for PHRF1 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHRF1 gene
Compartment Confidence
nucleus 4
cytosol 3

Gene Ontology (GO) - Cellular Components for PHRF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IDA 19946888
genes like me logo Genes that share ontologies with PHRF1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PHRF1 Gene

Pathways & Interactions for PHRF1 Gene

SuperPathways for PHRF1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PHRF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006366 transcription from RNA polymerase II promoter IEA --
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with PHRF1: view

No data available for Pathways by source and SIGNOR curated interactions for PHRF1 Gene

Transcripts for PHRF1 Gene

Unigene Clusters for PHRF1 Gene

PHD and ring finger domains 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHRF1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b
SP1: -
SP2: -
SP3: -
SP5: -

Relevant External Links for PHRF1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PHRF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PHRF1 Gene

Protein differential expression in normal tissues from HIPED for PHRF1 Gene

This gene is overexpressed in Breast (15.8), Cervix (10.6), Bone (8.0), and Peripheral blood mononuclear cells (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PHRF1 Gene

Protein tissue co-expression partners for PHRF1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PHRF1 Gene:


SOURCE GeneReport for Unigene cluster for PHRF1 Gene:

genes like me logo Genes that share expression patterns with PHRF1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PHRF1 Gene

Orthologs for PHRF1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PHRF1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PHRF1 34 35
  • 97.81 (n)
(Canis familiaris)
Mammalia PHRF1 34 35
  • 75.53 (n)
(Mus musculus)
Mammalia Phrf1 34 16 35
  • 72.89 (n)
(Rattus norvegicus)
Mammalia Phrf1 34
  • 72.73 (n)
(Bos Taurus)
Mammalia PHRF1 35
  • 60 (a)
(Monodelphis domestica)
Mammalia PHRF1 35
  • 49 (a)
(Gallus gallus)
Aves PHRF1 34 35
  • 61.36 (n)
(Anolis carolinensis)
Reptilia PHRF1 35
  • 45 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.3343 34
(Danio rerio)
Actinopterygii phrf1 35
  • 27 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG2926 35
  • 16 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 34 (a)
Species where no ortholog for PHRF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PHRF1 Gene

Gene Tree for PHRF1 (if available)
Gene Tree for PHRF1 (if available)

Paralogs for PHRF1 Gene

Paralogs for PHRF1 Gene

(3) SIMAP similar genes for PHRF1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with PHRF1: view

Variants for PHRF1 Gene

Sequence variations from dbSNP and Humsavar for PHRF1 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1055382 -- 612,182(+) TACCT(C/T)TGGCT downstream-variant-500B, utr-variant-3-prime
rs10736899 -- 579,256(+) CTCCT(A/C)CCCCC intron-variant
rs10902175 -- 578,996(+) CGCCA(C/T)GCCCG intron-variant
rs10902176 -- 585,026(+) agcca(A/C)cgcgc intron-variant
rs10902177 -- 591,083(+) GGCTC(A/G)CCGCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PHRF1 Gene

Variant ID Type Subtype PubMed ID
nsv951270 CNV deletion 24416366
nsv825681 CNV gain 20364138
nsv825680 CNV gain 20364138
nsv825679 CNV loss 20364138
nsv7633 CNV insertion 18451855
nsv552862 CNV loss 21841781
nsv552861 CNV loss 21841781
nsv552856 CNV gain 21841781
nsv552854 CNV loss 21841781
nsv528415 CNV loss 19592680
nsv527327 CNV loss 19592680
nsv518824 CNV loss 19592680
nsv476357 CNV novel sequence insertion 20440878
nsv469924 CNV gain 18288195
nsv469923 CNV loss 18288195
nsv467635 CNV loss 19166990
nsv467634 CNV loss 19166990
nsv1159791 CNV deletion 26073780
nsv1053964 CNV gain 25217958
nsv1039558 CNV gain 25217958
esv3625071 CNV loss 21293372
esv2762889 CNV loss 21179565
esv2759794 CNV loss 17122850
esv2743846 CNV deletion 23290073
esv2743845 CNV deletion 23290073
esv2663829 CNV deletion 23128226
esv24854 CNV loss 19812545
esv1760409 CNV insertion 17803354
esv1387942 CNV insertion 17803354
esv1008801 CNV insertion 20482838
dgv182e199 CNV deletion 23128226
dgv1524n54 CNV loss 21841781
dgv1523n54 CNV gain 21841781
dgv1522n54 CNV loss 21841781
dgv123e201 CNV deletion 23290073
dgv122e201 CNV deletion 23290073

Variation tolerance for PHRF1 Gene

Residual Variation Intolerance Score: 7.84% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.86; 79.41% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PHRF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHRF1 Gene

Disorders for PHRF1 Gene

Relevant External Links for PHRF1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for PHRF1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PHRF1 Gene

Publications for PHRF1 Gene

  1. Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. (PMID: 21408207) Chung S.A. … Criswell L.A. (PLoS Genet. 2011) 3 46 64
  2. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. (PMID: 18204446) Harley J.B. … Kelly J.A. (Nat. Genet. 2008) 3 46 64
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10997877) Nagase T. … Ohara O. (DNA Res. 2000) 3 4 64

Products for PHRF1 Gene

Sources for PHRF1 Gene

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