Human Gene PHRF1 (ENST00000264555.10_8) from GENCODE V47lift37
  Description: PHD and ring finger domains 1, transcript variant 1 (from RefSeq NM_001286581.2)
Gencode Transcript: ENST00000264555.10_8
Gencode Gene: ENSG00000070047.13_13
Transcript (Including UTRs)
   Position: hg19 chr11:576,470-612,222 Size: 35,753 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr11:581,513-611,777 Size: 30,265 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:576,470-612,222)mRNA (may differ from genome)Protein (1649 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PHRF1_HUMAN
DESCRIPTION: RecName: Full=PHD and RING finger domain-containing protein 1;
SUBUNIT: Interacts with POLR2A (via the C-terminal domain) (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 1 PHD-type zinc finger.
SIMILARITY: Contains 1 RING-type zinc finger.
SEQUENCE CAUTION: Sequence=BAA96066.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.58 RPKM in Testis
Total median expression: 591.27 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -71.20144-0.494 Picture PostScript Text
3' UTR -163.70445-0.368 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00097 - Zinc finger, C3HC4 type (RING finger)
PF00628 - PHD-finger
PF13445 - RING-type zinc-finger
PF13639 - Ring finger domain
PF13923 - Zinc finger, C3HC4 type (RING finger)

SCOP Domains:
57850 - RING/U-box
57889 - Cysteine-rich domain
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q9P1Y6
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0019904 protein domain specific binding
GO:0046872 metal ion binding
GO:0070063 RNA polymerase binding

Biological Process:
GO:0006366 transcription from RNA polymerase II promoter
GO:0006397 mRNA processing

Cellular Component:
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AB040975 - Homo sapiens KIAA1542 mRNA for KIAA1542 protein.
BC146771 - Homo sapiens PHD and ring finger domains 1, mRNA (cDNA clone MGC:166848 IMAGE:9007218), complete cds.
JD452352 - Sequence 433376 from Patent EP1572962.
JD057738 - Sequence 38762 from Patent EP1572962.
AK308541 - Homo sapiens cDNA, FLJ98582.
BC136615 - Homo sapiens PHD and ring finger domains 1, mRNA (cDNA clone MGC:168228 IMAGE:9020605), complete cds.
BC144293 - Homo sapiens PHD and ring finger domains 1, mRNA (cDNA clone MGC:177830 IMAGE:9052813), complete cds.
BC144294 - Homo sapiens PHD and ring finger domains 1, mRNA (cDNA clone MGC:177831 IMAGE:9052814), complete cds.
BC144295 - Homo sapiens PHD and ring finger domains 1, mRNA (cDNA clone MGC:177832 IMAGE:9052815), complete cds.
BC112931 - Homo sapiens cDNA clone IMAGE:6188410.
AB384232 - Synthetic construct DNA, clone: pF1KSDA1542, Homo sapiens KIAA1542 gene for RING and PHD-finger domain-containing protein KIAA1542, complete cds, without stop codon, in Flexi system.
DQ581107 - Homo sapiens piRNA piR-49219, complete sequence.
BC029651 - Homo sapiens PHD and ring finger domains 1, mRNA (cDNA clone IMAGE:4339078), partial cds.
BC041631 - Homo sapiens PHD and ring finger domains 1, mRNA (cDNA clone IMAGE:4135284), partial cds.
BC013381 - Homo sapiens PHD and ring finger domains 1, mRNA (cDNA clone IMAGE:4079893), partial cds.
BC004950 - Homo sapiens PHD and ring finger domains 1, mRNA (cDNA clone IMAGE:3619689), partial cds.
BC127876 - Homo sapiens cDNA clone IMAGE:40133758, partial cds.
LF207966 - JP 2014500723-A/15469: Polycomb-Associated Non-Coding RNAs.
JD199066 - Sequence 180090 from Patent EP1572962.
JD552871 - Sequence 533895 from Patent EP1572962.
MA443543 - JP 2018138019-A/15469: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A6H8W1, B7ZM64, B9EGP0, C9JS82, ENST00000264555.1, ENST00000264555.2, ENST00000264555.3, ENST00000264555.4, ENST00000264555.5, ENST00000264555.6, ENST00000264555.7, ENST00000264555.8, ENST00000264555.9, KIAA1542, NM_001286581, PHRF1_HUMAN, Q6PJP2, Q8IVY2, Q8N2Y7, Q9BSM2, Q9P1Y6, uc317htg.1, uc317htg.2
UCSC ID: ENST00000264555.10_8
RefSeq Accession: NM_001286581.2
Protein: Q9P1Y6 (aka PHRF1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.