Mouse Gene Phrf1 (ENSMUST00000106027.8) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus PHD and ring finger domains 1 (Phrf1), mRNA. (from RefSeq NM_001081118)
Gencode Transcript: ENSMUST00000106027.8
Gencode Gene: ENSMUSG00000038611.17
Transcript (Including UTRs)
   Position: mm10 chr7:141,228,789-141,262,626 Size: 33,838 Total Exon Count: 18 Strand: +
Coding Region
   Position: mm10 chr7:141,231,249-141,262,552 Size: 31,304 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:141,228,789-141,262,626)mRNA (may differ from genome)Protein (1682 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedSOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: PHRF1_MOUSE
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 (By similarity).
SIMILARITY: Contains 1 PHD-type zinc finger.
SIMILARITY: Contains 1 RING-type zinc finger.
SEQUENCE CAUTION: Sequence=BAC98197.1; Type=Miscellaneous discrepancy; Note=The sequence differs from that shown because it seems to be derived from a pre-mRNA;

-  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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -54.60125-0.437 Picture PostScript Text
3' UTR -27.4074-0.370 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
IPR002219 - Prot_Kinase_C-like_PE/DAG-bd
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 A6H619
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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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsemblEnsembl  
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  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


-  Descriptions from all associated GenBank mRNAs
  AK080286 - Mus musculus 3 days neonate thymus cDNA, RIKEN full-length enriched library, clone:A630030H21 product:unclassifiable, full insert sequence.
BC138446 - Mus musculus PHD and ring finger domains 1, mRNA (cDNA clone MGC:170071 IMAGE:8861466), complete cds.
BC145719 - Mus musculus PHD and ring finger domains 1, mRNA (cDNA clone MGC:175606 IMAGE:40131022), complete cds.
BC052534 - Mus musculus cDNA clone IMAGE:5256231, partial cds.
BC094566 - Mus musculus PHD and ring finger domains 1, mRNA (cDNA clone IMAGE:6836334), partial cds.
AK129387 - Mus musculus premature mRNA for mKIAA1542 protein.
AK134140 - Mus musculus adult male thymus cDNA, RIKEN full-length enriched library, clone:5830450H22 product:RA9 homolog [Rattus norvegicus], full insert sequence.
AK161749 - Mus musculus adult male thymus cDNA, RIKEN full-length enriched library, clone:5830449H02 product:RA9 homolog [Rattus norvegicus], full insert sequence.
AK164438 - Mus musculus 12 days embryo eyeball cDNA, RIKEN full-length enriched library, clone:D230026C23 product:hypothetical protein, full insert sequence.
AK164283 - Mus musculus 9 days embryo whole body cDNA, RIKEN full-length enriched library, clone:D030066F16 product:RA9 homolog [Rattus norvegicus], full insert sequence.
BC055395 - Mus musculus PHD and ring finger domains 1, mRNA (cDNA clone IMAGE:5709759), partial cds.
AK042050 - Mus musculus 3 days neonate thymus cDNA, RIKEN full-length enriched library, clone:A630054K02 product:hypothetical protein, full insert sequence.
BC039628 - Mus musculus PHD and ring finger domains 1, mRNA (cDNA clone IMAGE:5039965), with apparent retained intron.
AK137120 - Mus musculus 12 days embryo embryonic body between diaphragm region and neck cDNA, RIKEN full-length enriched library, clone:9430088O16 product:RA9 homolog [Rattus norvegicus], full insert sequence.
LF196690 - JP 2014500723-A/4193: Polycomb-Associated Non-Coding RNAs.
MA432267 - JP 2018138019-A/4193: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A6H619, Kiaa1542, NM_001081118, PHRF1_MOUSE, Q505G1, Q6ZPN4, uc009kkb.1, uc009kkb.2
UCSC ID: uc009kkb.2
RefSeq Accession: NM_001081118
Protein: A6H619 (aka PHRF1_MOUSE)
CCDS: CCDS52441.1

-  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.