Human Gene PHACTR3 (ENST00000371015.6) from GENCODE V44
  Description: Homo sapiens phosphatase and actin regulator 3 (PHACTR3), transcript variant 1, mRNA. (from RefSeq NM_080672)
RefSeq Summary (NM_080672): This gene encodes a member of the phosphatase and actin regulator protein family. The encoded protein is associated with the nuclear scaffold in proliferating cells, and binds to actin and the catalytic subunit of protein phosphatase-1, suggesting that it functions as a regulatory subunit of protein phosphatase-1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013].
Gencode Transcript: ENST00000371015.6
Gencode Gene: ENSG00000087495.17
Transcript (Including UTRs)
   Position: hg38 chr20:59,604,540-59,847,711 Size: 243,172 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg38 chr20:59,605,015-59,847,130 Size: 242,116 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr20:59,604,540-59,847,711)mRNA (may differ from genome)Protein (559 aa)
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-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Phosphatase and actin regulator 3; AltName: Full=Scaffold-associated PP1-inhibiting protein; Short=Scapinin;
SUBUNIT: Binds actin and PPP1CA; thus inhibiting the protein phosphatase 1 (PP1) activity.
SUBCELLULAR LOCATION: Nucleus matrix. Note=Localized to the nuclear matrix-intermediate filament scaffold. Isoform 2 is also found in some cytoplasmic extensions.
TISSUE SPECIFICITY: Abundantly expressed in brain. Also found in several tumors such as lung carcinomas, nervous tumors and HL-60 leukemia cells. Isoform 3 is the major form in U-937, GOTO and HL- 60 leukemia cells.
INDUCTION: Down-regulated in HL-60 leukemia cells by RA, PMA and dimethyl sulfoxide.
SIMILARITY: Belongs to the phosphatase and actin regulator family.
SIMILARITY: Contains 4 RPEL repeats.
SEQUENCE CAUTION: Sequence=CAC67489.2; Type=Erroneous initiation;

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 33.32 RPKM in Brain - Amygdala
Total median expression: 338.92 RPKM

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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -155.70475-0.328 Picture PostScript Text
3' UTR -141.80581-0.244 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
IPR004018 - RPEL_repeat

Pfam Domains:
PF02755 - RPEL repeat

ModBase Predicted Comparative 3D Structure on Q96KR7
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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0004864 protein phosphatase inhibitor activity
GO:0008157 protein phosphatase 1 binding
GO:0019888 protein phosphatase regulator activity

Biological Process:
GO:0032515 negative regulation of phosphoprotein phosphatase activity
GO:0043666 regulation of phosphoprotein phosphatase activity

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016363 nuclear matrix

-  Descriptions from all associated GenBank mRNAs
  AK098788 - Homo sapiens cDNA FLJ25922 fis, clone CBR05032.
BC108303 - Homo sapiens phosphatase and actin regulator 3, mRNA (cDNA clone MGC:117178 IMAGE:4179728), complete cds.
AJ311122 - Homo sapiens mRNA for scapinin 1B (SCAPIN1 gene).
BC117362 - Homo sapiens phosphatase and actin regulator 3, mRNA (cDNA clone MGC:150971 IMAGE:40125913), complete cds.
BC117364 - Homo sapiens phosphatase and actin regulator 3, mRNA (cDNA clone MGC:150973 IMAGE:40125915), complete cds.
AK314493 - Homo sapiens cDNA, FLJ95307, Homo sapiens Q9H4T4 like (H17739), mRNA.
AK091632 - Homo sapiens cDNA FLJ34313 fis, clone FEBRA2008266, highly similar to Phosphatase and actin regulator 3.
AX747102 - Sequence 627 from Patent EP1308459.
AB590898 - Synthetic construct DNA, clone: pFN21AE1983, Homo sapiens PHACTR3 gene for phosphatase and actin regulator 3, without stop codon, in Flexi system.
HQ258286 - Synthetic construct Homo sapiens clone IMAGE:100072595 phosphatase and actin regulator 3 (PHACTR3) gene, encodes complete protein.
KJ895303 - Synthetic construct Homo sapiens clone ccsbBroadEn_04697 PHACTR3 gene, encodes complete protein.
AK295459 - Homo sapiens cDNA FLJ53995 complete cds, highly similar to Phosphatase and actin regulator 3.
AJ617581 - Homo sapiens mRNA for scapinin 1C (SCAPIN1 gene).
AK316047 - Homo sapiens cDNA, FLJ78946 complete cds, highly similar to Phosphatase and actin regulator 3.
AB098521 - Homo sapiens SCAPIN1 mRNA for scapinin, complete cds.
AB098522 - Homo sapiens SCAPIN1 mRNA for scapinin S, complete cds.
JD390663 - Sequence 371687 from Patent EP1572962.
BC036834 - Homo sapiens phosphatase and actin regulator 3, mRNA (cDNA clone IMAGE:4538175), with apparent retained intron.
AK090812 - Homo sapiens cDNA FLJ33493 fis, clone BRAMY2003893.
JD239394 - Sequence 220418 from Patent EP1572962.
JD235155 - Sequence 216179 from Patent EP1572962.
JD563123 - Sequence 544147 from Patent EP1572962.
JD212541 - Sequence 193565 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B1AN68, B1AN69, B2RB46, C20orf101, ENST00000371015.1, ENST00000371015.2, ENST00000371015.3, ENST00000371015.4, ENST00000371015.5, NM_080672, PHAR3_HUMAN, Q32P33, Q707P6, Q96KR7, Q9H4T4, SCAPIN1, uc002yau.1, uc002yau.2, uc002yau.3, uc002yau.4, uc002yau.5, uc002yau.6
UCSC ID: ENST00000371015.6
RefSeq Accession: NM_080672
Protein: Q96KR7 (aka PHAR3_HUMAN or PHR3_HUMAN)
CCDS: CCDS13480.1

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