Free for academic non-profit institutions. Other users need a Commercial license

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. Gene Ontology (GO) annotations related to this gene include protein domain specific binding and RNA polymerase binding. An important paralog of this gene is SCAF1.

Additional gene information for PHRF1 Gene

No data available for Entrez Gene Summary , CIViC 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

GeneHancer (GH) Regulatory Elements for PHRF1 Gene

Promoters and enhancers for PHRF1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I000574 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 578.2 +2.2 2161 6.9 HDGF PKNOX1 FOXA2 SMAD1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 PHRF1 TMEM80 SNORA52 ENSG00000255237 BET1L TSPAN4 PSMD13 RIC8A RPLP2 HRAS
GH11I000575 Enhancer 0.7 ENCODE 550.8 -1.9 -1864 0.1 HDGF LEF1 ZNF335 LCORL ZNF316 FOXK2 CBFA2T2 MAFK SMARCE1 ZNF639 GC11P000582 PHRF1 LOC143666 GC11M000578
GH11I000807 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 29.3 +234.8 234767 6.2 HDGF PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 RPLP2 SNORA52 PIDD1 GC11P000825 GC11P000813 GC11P000812 ENSG00000255108 TMEM80 PHRF1 BET1L
GH11I000303 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 23.8 -263.6 -263605 17.8 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A YY1 POLR2B ZNF766 IFITM2 IFITM3 ENSG00000254910 IFITM1 PGGHG TMEM80 PHRF1 ENSG00000270030 BET1L RIC8A
GH11I000443 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 14.4 -128.5 -128474 8.2 MLX ZFP64 DMAP1 IRF4 YY1 ZNF213 ZNF143 ZNF548 SP3 NFYC PTDSS2 RNH1 LRRC56 TSPAN4 SNORA52 PHRF1 ENSG00000255237 ANO9 HRAS RIC8A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PHRF1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PHRF1 gene promoter:

Genomic Locations for PHRF1 Gene

Genomic Locations for PHRF1 Gene
chr11:576,220-612,222
(GRCh38/hg38)
Size:
36,003 bases
Orientation:
Plus strand
chr11:576,483-612,222
(GRCh37/hg19)

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:
    Q9P1Y6-PHRF1_HUMAN
    Recommended name:
    PHD and RING finger domain-containing protein 1
    Protein Accession:
    Q9P1Y6
    Secondary Accessions:
    • A6H8W1
    • B7ZM64
    • B9EGP0
    • C9JS82
    • Q6PJP2
    • Q8IVY2
    • Q8N2Y7
    • Q9BSM2

    Protein attributes for PHRF1 Gene

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

    Alternative splice isoforms for PHRF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PHRF1 Gene

Post-translational modifications for PHRF1 Gene

  • Ubiquitination at Lys1579
  • 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

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

No data available for UniProtKB/Swiss-Prot for PHRF1 Gene

Function for PHRF1 Gene

Phenotypes From GWAS Catalog for PHRF1 Gene

Gene Ontology (GO) - Molecular Function for PHRF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
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

CRISPR Products

miRNA for PHRF1 Gene

Inhibitory RNA 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

COMPARTMENTS
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 HDA,IDA 19946888
genes like me logo Genes that share ontologies with PHRF1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) 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 by RNA polymerase II 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

Drugs & Compounds for PHRF1 Gene

No Compound Related Data Available

Transcripts for PHRF1 Gene

Unigene Clusters for PHRF1 Gene

PHD and ring finger domains 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA 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: -
SP4:
SP5: -
SP6:
SP7:
SP8:

Relevant External Links for PHRF1 Gene

GeneLoc Exon Structure for
PHRF1
ECgene alternative splicing isoforms for
PHRF1

Expression for PHRF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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:

PHRF1

SOURCE GeneReport for Unigene cluster for PHRF1 Gene:

Hs.325838

Evidence on tissue expression from TISSUES for PHRF1 Gene

  • Liver(4.2)
  • Nervous system(4.2)
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 , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia PHRF1 33 34
  • 97.81 (n)
dog
(Canis familiaris)
Mammalia PHRF1 33 34
  • 75.53 (n)
mouse
(Mus musculus)
Mammalia Phrf1 33 16 34
  • 72.89 (n)
rat
(Rattus norvegicus)
Mammalia Phrf1 33
  • 72.73 (n)
cow
(Bos Taurus)
Mammalia PHRF1 34
  • 60 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PHRF1 34
  • 49 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHRF1 33 34
  • 61.36 (n)
lizard
(Anolis carolinensis)
Reptilia PHRF1 34
  • 45 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.3343 33
zebrafish
(Danio rerio)
Actinopterygii phrf1 34
  • 27 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG2926 34
  • 16 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 34 (a)
OneToMany
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

ENSEMBL:
Gene Tree for PHRF1 (if available)
TreeFam:
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 Variation AA Info Type
rs1000036067 -- 612,527(+) A/G downstream_transcript_variant
rs1000077051 -- 592,863(+) C/T intron_variant
rs1000317201 -- 589,326(+) C/G intron_variant
rs1000394613 -- 612,502(+) C/G downstream_transcript_variant
rs1000422060 -- 579,505(+) C/T intron_variant

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

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

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)

Additional Variant Information for PHRF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHRF1

SNP Genotyping and Copy Number Assay Products

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

Disorders for PHRF1 Gene

Additional Disease Information for PHRF1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 SA … Criswell LA (PLoS genetics 2011) 3 44 58
  2. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. (PMID: 18204446) International Consortium for Systemic Lupus Erythematosus Genetics (SLEGEN) … Kelly JA (Nature genetics 2008) 3 44 58
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  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 research : an international journal for rapid publication of reports on genes and genomes 2000) 3 4 58

Products for PHRF1 Gene

Sources for PHRF1 Gene

Content
Loading form....