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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PHRF1 Gene

protein-coding   GIFtS: 49
GCID: GC11P000567

PHD And Ring Finger Domains 1


(Previous symbol: RNF221)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
PHD And Ring Finger Domains 11 2
RNF2211 2
CTD Binding SR Like Protein RA91 2
KIAA15423 5
CTD-Binding SR-Like Protein RA92
PHD And RING Finger Domain-Containing Protein 12

External Ids:    HGNC: 243511   Entrez Gene: 576612   Ensembl: ENSG000000700477   OMIM: 6117805   UniProtKB: Q9P1Y63   

Export aliases for PHRF1 gene to outside databases

Previous GC identifer: GC11P000371


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for PHRF1 Gene: 
PHRF1 (PHD and ring finger domains 1) is a protein-coding gene. Diseases associated with PHRF1 include systemic lupus erythematosus, and lupus erythematosus. GO annotations related to this gene include RNA polymerase binding and protein domain specific binding. An important paralog of this gene is SCAF1.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000011.9  NT_009237.18  NC_018922.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PHRF1 gene promoter:
         ER-alpha   E2F-4   E2F-3a   E2F-5   E2F-2   Arnt   E2F   E2F-1   HSF2   HOXA5   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPHRF1 promoter sequence
   Search SABiosciences Chromatin IP Primers for PHRF1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PHRF1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11p15.5   Ensembl cytogenetic band:  11p15.5   HGNC cytogenetic band: 11p15.5

PHRF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PHRF1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P000567:  view genomic region     (about GC identifiers)

Start:
576,483 bp from pter      End:
612,222 bp from pter
Size:
35,740 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: PHRF1_HUMAN, Q9P1Y6 (See protein sequence)
Recommended Name: PHD and RING finger domain-containing protein 1  
Size: 1649 amino acids; 178666 Da
Subunit: Interacts with POLR2A (via the C-terminal domain) (By similarity)
Sequence caution: Sequence=BAA96066.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: A6H8W1 B7ZM64 B9EGP0 C9JS82 Q6PJP2 Q8IVY2 Q8N2Y7 Q9BSM2
Alternative splicing: 3 isoforms:  Q9P1Y6-1   Q9P1Y6-2   Q9P1Y6-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PHRF1: NX_Q9P1Y6

Explore proteomics data for PHRF1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9P1Y6

  • PHRF1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PHRF1 Protein Expression
    REFSEQ proteins: NP_065952.2  
    ENSEMBL proteins: 
     ENSP00000435360   ENSP00000264555   ENSP00000431870   ENSP00000388589   ENSP00000410626  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    RNF: RING-type (C3HC4) zinc fingers
    PHF: Zinc fingers, PHD-type

    5/6 InterPro protein domains (see all 6):
     IPR001841 Znf_RING
     IPR001965 Znf_PHD
     IPR013083 Znf_RING/FYVE/PHD
     IPR017907 Znf_RING_CS
     IPR011011 Znf_FYVE_PHD

    Graphical View of Domain Structure for InterPro Entry Q9P1Y6

    ProtoNet protein and cluster: Q9P1Y6

    1 Blocks protein domain: IPB001841 Zn-finger

    UniProtKB/Swiss-Prot: PHRF1_HUMAN, Q9P1Y6
    Similarity: Contains 1 PHD-type zinc finger
    Similarity: Contains 1 RING-type zinc finger


    PHRF1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 5 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
    GO:0019904protein domain specific binding IEA--
    GO:0046872metal ion binding ----
    GO:0070063RNA polymerase binding ISS--
         
    PHRF1 for ontologies           About GeneDecksing


    Animal Models:
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    SwitchGear 3'UTR luciferase reporter plasmidPHRF1 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PHRF1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    5/6 Interacting proteins for PHRF1 (ENSP000004106264) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    JMJD6ENSP000003940854STRING: ENSP00000394085
    PPP1CAENSP000003260314STRING: ENSP00000326031
    SIRT7ENSP000003294664STRING: ENSP00000329466
    UBCENSP000003448184STRING: ENSP00000344818
    AGPAT2ENSP000003607614STRING: ENSP00000360761
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006366transcription from RNA polymerase II promoter IEA--
    GO:0006397mRNA processing IEA--

    PHRF1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PHRF1

    Search CenterWatch for drugs/clinical trials and news about PHRF1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PHRF1 gene: 
    NM_020901.2  

    Unigene Cluster for PHRF1:

    PHD and ring finger domains 1
    Hs.325838  [show with all ESTs]
    Unigene Representative Sequence: BC112931
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000534320 ENST00000264555(uc010qwc.2 uc010qwd.2 uc001lqe.3 uc010qwe.2 uc009yca.2)
    ENST00000533464 ENST00000413872 ENST00000416188 ENST00000532550
    miRNA
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    8/13 QIAGEN miScript miRNA Assays for microRNAs that regulate PHRF1 (see all 13):
    hsa-miR-576-5p hsa-miR-3688-3p hsa-miR-374b hsa-miR-4263 hsa-miR-374a hsa-miR-764 hsa-miR-3914 hsa-miR-3161
    SwitchGear 3'UTR luciferase reporter plasmidPHRF1 3' UTR sequence
    Inhib. RNA
    Products:
         
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    Additional mRNA sequence: 

    AB040975.1 AK308541.1 BC004950.1 BC013381.2 BC029651.1 BC041631.1 BC112931.1 BC127876.1 
    BC136615.1 BC144293.1 BC144294.1 BC144295.1 BC146771.1 

    9 DOTS entries:

    DT.444396  DT.100029364  DT.100029363  DT.108108  DT.95233840  DT.100785104  DT.120715005  DT.320147 
    DT.95361384 

    24/167 AceView cDNA sequences (see all 167):

    AI521741 AW450796 CD722462 BU193065 BC029651 BQ214393 BU168453 AW294435 
    BU429663 BQ058681 BQ683015 BI115565 BQ691436 BQ686458 BU179446 BQ684753 
    BQ877998 BQ440287 BC041631 BQ070156 BX280648 BQ888704 BC004950 AA309560 

    GeneLoc Exon Structure

    5/8 Alternative Splicing Database (ASD) splice patterns (SP) for PHRF1 (see all 8)    About this scheme

    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:                                                                          -                                                         


    ECgene alternative splicing isoforms for PHRF1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PHRF1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCTGCCGTCG
    PHRF1 Expression
    About this image


    See PHRF1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PHRF1

    SOURCE GeneReport for Unigene cluster: Hs.325838
        SABiosciences Expression via Pathway-Focused PCR Array including PHRF1: 
              Ubiquitin Ligases in human mouse rat

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for PHRF1 gene from 6/12 species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Phrf11 , 5 PHD and ring finger domains 11, 5 74.93(n)1
    71.64(a)1
      7 (86.53 cM)5
    1014711  NM_001081118.11  NP_001074587.11 
     1412287845 
    chicken
    (Gallus gallus)
    Aves PHRF11 PHD and ring finger domains 1 68(n)
    68.57(a)
      426102  XM_423776.3  XP_423776.3 
    lizard
    (Anolis carolinensis)
    Reptilia PHRF16
    Uncharacterized protein
    44(a)
    1 ↔ 1
    1(74445250-74474246)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.33432 Transcribed sequence with weak similarity to protein more 82.93(n)    142003632 
    zebrafish
    (Danio rerio)
    Actinopterygii phrf11 PHD and ring finger domains 1 48.99(n)
    46.22(a)
      321905  XM_002666868.1  XP_002666914.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG29266
    --
    13(a)
    1 → many
    3R(1405023-1414097)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PHRF1 gene
    SCAF12  SCAF112  
    3 SIMAP similar genes for PHRF1 using alignment to 5 protein entries:     PHRF1_HUMAN (see all proteins):
    PHF21A    SCAF11    AIRE

    PHRF1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1723 SNPs in PHRF1 are shown (see all 1723)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1172146141,2
    C,F--369246(+) GGGGGG/ATGGTC 1 -- us2k11Minor allele frequency- A:0.02NA 120
    rs1841569841,2
    --369286(+) TGCTAA/GAATTG 1 -- us2k10--------
    rs1128156891,2
    F--369301(+) TGGCCG/AAGGGG 1 -- us2k12Minor allele frequency- A:0.07CSA WA 120
    rs1897036231,2
    --369321(+) GAGCTC/GCGAGT 1 -- us2k10--------
    rs112461841,2
    C,A,H--369343(+) TTGCCG/AGCCCC 1 -- us2k16Minor allele frequency- A:0.47NA WA EA 364
    rs1157545531,2
    F--369360(+) AGAGCC/TACCTC 1 -- us2k11Minor allele frequency- T:0.01WA 118
    rs1483625961,2
    --369396(+) AGCTGC/TTCGCC 1 -- us2k10--------
    rs1415222081,2
    --369434(+) CTCCCA/GTCTCC 1 -- us2k10--------
    rs122776111,2
    C,F,A,H--369482(+) CCCGTC/TCCCTC 1 -- us2k117Minor allele frequency- T:0.44NS EA NA CSA WA 2112
    rs1930734501,2
    --369554(+) TGCGGG/TTTACT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for PHRF1 (576483 - 612222 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/40 variations for PHRF1 (see all 40):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2743846CNV Deletion23290073
    esv2743845CNV Deletion23290073
    esv2663829CNV Deletion23128226
    dgv142e201CNV Deletion23290073
    dgv141e201CNV Deletion23290073
    dgv182e199CNV Deletion23128226
    esv1387942CNV Insertion17803354
    esv1008801CNV Insertion20482838
    esv1760409CNV Insertion17803354
    nsv7633CNV Insertion18451855

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 611780    OMIM disorders: --

    4 diseases for PHRF1:    About MalaCards
    systemic lupus erythematosus    lupus erythematosus    rheumatoid arthritis    arthritis

    1 disease from the University of Copenhagen DISEASES database for PHRF1:
    Systemic lupus erythematosus

    PHRF1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PHRF1
    Human Genome Epidemiology (HuGE) Navigator: PHRF1 (0 documents)

    Export disorders for PHRF1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for PHRF1 gene, integrated from 9 sources (see all 31):
    (articles sorted by number of sources associating them with PHRF1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. (PubMed id 21408207)1, 4 Chung S.A....Criswell L.A. (2011)
    2. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. (PubMed id 18204446)1, 4 Harley J.B.... Kelly J.A. (2008)
    3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    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. (PubMed id 10997877)1, 2 Nagase T.... Ohara O. (2000)
    6. Interlaboratory reproducibility of large-scale human p rotein-complex analysis by standardized AP-MS. (PubMed id 23455922)1 Varjosalo M....Superti-Furga G. (2013)
    7. Association of PHRF1-IRF7 region polymorphism with cli nical manifestations of systemic lupus erythematosus in a Japanese population. (PubMed id 22433914)1 Kawasaki A....Tsuchiya N. (2012)
    8. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (2012)
    9. Functional proteomics establishes the interaction of S IRT7 with chromatin remodeling complexes and expands its role in regulation of R NA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C....Cristea I.M. (2012)
    10. Early disease onset is predicted by a higher genetic risk for lupus and is associated with a more severe phenotype in lupus patients . (PubMed id 20881011)1 Webb R....Sawalha A.H. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 57661 HGNC: 24351 AceView: KIAA1542 Ensembl:ENSG00000070047 euGenes: HUgn57661
    ECgene: PHRF1 H-InvDB: PHRF1

    (According to HUGE)
    About This Section
    HUGE: KIAA1542

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for PHRF1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PHRF1 gene:
    Search GeneIP for patents involving PHRF1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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