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    PHACTR3 phosphatase and actin regulator 3 [ Homo sapiens (human) ]

    Gene ID: 116154, updated on 3-Apr-2024

    Summary

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    Official Symbol
    PHACTR3provided by HGNC
    Official Full Name
    phosphatase and actin regulator 3provided by HGNC
    Primary source
    HGNC:HGNC:15833
    See related
    Ensembl:ENSG00000087495 MIM:608725; AllianceGenome:HGNC:15833
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    H17739; SCAPIN1; PPP1R123; SCAPININ; C20orf101
    Summary
    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]
    Expression
    Biased expression in brain (RPKM 9.3), spleen (RPKM 1.0) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    20q13.32-q13.33
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (59577509..59847711)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (61361726..61631999)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (58152564..58422766)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57893004-57893504 Neighboring gene Sharpr-MPRA regulatory region 9189 Neighboring gene endothelin 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57950919-57951420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57979490-57979990 Neighboring gene NANOG hESC enhancer GRCh37_chr20:58013205-58013760 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:58051005-58051166 Neighboring gene piezo type mechanosensitive ion channel component 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:58070963-58071463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:58089356-58090192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:58090193-58091028 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:58133017-58133222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:58143003-58143837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:58147145-58147686 Neighboring gene MPRA-validated peak4290 silencer Neighboring gene PHACTR3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:58325659-58326160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18191 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:58345121-58346320 Neighboring gene RNA, U7 small nuclear 141 pseudogene Neighboring gene synaptonemal complex protein 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. DNA methylation of phosphatase and actin regulator 3 detects colorectal cancer in stool and complements FIT. Bosch LJ, et al. Cancer Prev Res (Phila), 2012 Mar. PMID 22135045
    2. Scapinin, the protein phosphatase 1 binding protein, enhances cell spreading and motility by interacting with the actin cytoskeleton. Sagara J, et al. PLoS One, 2009. PMID 19158953, Free PMC Article
    3. Scapinin-induced inhibition of axon elongation is attenuated by phosphorylation and translocation to the cytoplasm. Farghaian H, et al. J Biol Chem, 2011 Jun 3. PMID 21487013, Free PMC Article
    4. Genomic organization and expression pattern of scapinin (PHACTR3) in mouse and human. Worch S, et al. Cytogenet Genome Res, 2006. PMID 16974080
    5. Scapinin, a putative protein phosphatase-1 regulatory subunit associated with the nuclear nonchromatin structure. Sagara J, et al. J Biol Chem, 2003 Nov 14. PMID 12925532

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DNA methylation of phosphatase and actin regulator 3 is associated with colorectal cancer.
      Title: DNA methylation of phosphatase and actin regulator 3 detects colorectal cancer in stool and complements FIT.
    2. Because its expression is highest in relatively plastic regions of the adult brain (cortex, hippocampus), scapinin is a new regulator of neurite outgrowth and neuroplasticity in the brain.
      Title: Scapinin-induced inhibition of axon elongation is attenuated by phosphorylation and translocation to the cytoplasm.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    6. E2F4, PHACTR3, PRAME family member and CDH12 most probably play important role in non-small-cell lung cancer geneses
      Title: Identification of genes associated with non-small-cell lung cancer promotion and progression.
    7. scapinin enhances cell spreading and motility through direct interaction with actin and PP1 plays a regulatory role in scapinin-induced morphological changes
      Title: Scapinin, the protein phosphatase 1 binding protein, enhances cell spreading and motility by interacting with the actin cytoskeleton.
    8. scapinin is a putative regulatory subunit of PP1 and is involved in transformed or immature phenotypes of HL-60 cells
      Title: Scapinin, a putative protein phosphatase-1 regulatory subunit associated with the nuclear nonchromatin structure.
    9. a highly conserved complex genomic organization with four different leader exons; Alternative splicing of exon 5 was found to be limited to human vs. mouse; expression seems to occur predominantly in the brain
      Title: Genomic organization and expression pattern of scapinin (PHACTR3) in mouse and human.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association analysis implicates the involvement of eight loci with response to tocilizumab for the treatment of rheumatoid arthritis.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC117178

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein phosphatase inhibitor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    phosphatase and actin regulator 3
    Names
    protein phosphatase 1, regulatory subunit 123
    scaffold-associated PP1-inhibiting protein

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_029537.2 RefSeqGene

      Range
      32032..275203
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001199505.1 → NP_001186434.1  phosphatase and actin regulator 3 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (4) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AB098521, AJ311122, AK098788
      Consensus CDS
      CCDS56202.1
      UniProtKB/TrEMBL
      B7Z339
      Related
      ENSP00000353002.3, ENST00000359926.7
      Conserved Domains (1) summary
      smart00707
      Location:437 → 461
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2

    2. NM_001199506.2 → NP_001186435.1  phosphatase and actin regulator 3 isoform 2

      See identical proteins and their annotated locations for NP_001186435.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate 5'-terminal exon and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2, also known as scapinin-L) has a shorter N-terminus, compared to isoform 1. Variants 2, 5, and 6 encode the same isoform.
      Source sequence(s)
      AB098521, AJ311122, AJ617581
      Consensus CDS
      CCDS42895.1
      UniProtKB/TrEMBL
      B7Z339
      Related
      ENSP00000347866.4, ENST00000355648.8
      Conserved Domains (1) summary
      smart00707
      Location:399 → 423
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2

    3. NM_001281507.2 → NP_001268436.1  phosphatase and actin regulator 3 isoform 2

      See identical proteins and their annotated locations for NP_001268436.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate 5'-terminal exon and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2, also known as scapinin-L) has a shorter N-terminus, compared to isoform 1. Variants 2, 5, and 6 encode the same isoform.
      Source sequence(s)
      AB098521, AJ311122, AK295459
      Consensus CDS
      CCDS42895.1
      UniProtKB/TrEMBL
      B7Z339
      Related
      ENSP00000442483.1, ENST00000541461.5
      Conserved Domains (1) summary
      smart00707
      Location:399 → 423
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2

    4. NM_080672.5 → NP_542403.1  phosphatase and actin regulator 3 isoform 1

      See identical proteins and their annotated locations for NP_542403.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB098521, AL121908, BC108303
      Consensus CDS
      CCDS13480.1
      UniProtKB/Swiss-Prot
      B1AKX0, B1AN68, B1AN69, B2RB46, Q32P33, Q707P6, Q96KR7, Q9H4T4
      UniProtKB/TrEMBL
      B3KRI3
      Related
      ENSP00000360054.1, ENST00000371015.6
      Conserved Domains (2) summary
      smart00707
      Location:440 → 464
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2
      cl26511
      Location:292 → 551
      Neuromodulin_N; Gap junction protein N-terminal region

    5. NM_183244.2 → NP_899067.1  phosphatase and actin regulator 3 isoform 2

      See identical proteins and their annotated locations for NP_899067.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate 5'-terminal exon and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2, also known as scapinin-L) has a shorter N-terminus, compared to isoform 1. Variants 2, 5, and 6 encode the same isoform.
      Source sequence(s)
      AB098521, BC108303
      Consensus CDS
      CCDS42895.1
      UniProtKB/TrEMBL
      B7Z339
      Related
      ENSP00000378998.2, ENST00000395636.6
      Conserved Domains (1) summary
      smart00707
      Location:399 → 423
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2

    6. NM_183246.2 → NP_899069.1  phosphatase and actin regulator 3 isoform 3

      See identical proteins and their annotated locations for NP_899069.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate 5'-terminal exon, lacks an in-frame exon in the central coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3, also known as scapinin-S) is shorter, compared to isoform 1.
      Source sequence(s)
      AB098521, AB098522, BC108303
      Consensus CDS
      CCDS13481.1
      UniProtKB/TrEMBL
      B7Z339
      Related
      ENSP00000354555.4, ENST00000361300.4
      Conserved Domains (1) summary
      smart00707
      Location:329 → 353
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      59577509..59847711
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017027628.2 → XP_016883117.1  phosphatase and actin regulator 3 isoform X3

      UniProtKB/TrEMBL
      B7Z339

    2. XM_017027626.3 → XP_016883115.1  phosphatase and actin regulator 3 isoform X1

      UniProtKB/TrEMBL
      B7Z339
      Conserved Domains (1) summary
      smart00707
      Location:399 → 423
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2

    3. XM_017027630.2 → XP_016883119.1  phosphatase and actin regulator 3 isoform X4

      UniProtKB/TrEMBL
      B7Z339
      Conserved Domains (1) summary
      smart00707
      Location:329 → 353
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2

    4. XM_011528525.3 → XP_011526827.1  phosphatase and actin regulator 3 isoform X1

      See identical proteins and their annotated locations for XP_011526827.1

      UniProtKB/TrEMBL
      B7Z339
      Conserved Domains (1) summary
      smart00707
      Location:399 → 423
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2

    5. XM_011528526.3 → XP_011526828.1  phosphatase and actin regulator 3 isoform X2

      UniProtKB/TrEMBL
      B3KRI3
      Conserved Domains (1) summary
      pfam17380
      Location:324 → 477
      DUF5401; Family of unknown function (DUF5401)

    6. XM_017027631.2 → XP_016883120.1  phosphatase and actin regulator 3 isoform X1

      UniProtKB/TrEMBL
      B7Z339
      Conserved Domains (1) summary
      smart00707
      Location:399 → 423
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2

    7. XM_017027627.3 → XP_016883116.1  phosphatase and actin regulator 3 isoform X1

      UniProtKB/TrEMBL
      B7Z339
      Conserved Domains (1) summary
      smart00707
      Location:399 → 423
      RPEL; Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      61361726..61631999
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322927.1 → XP_054178902.1  phosphatase and actin regulator 3 isoform X3

    2. XM_054322924.1 → XP_054178899.1  phosphatase and actin regulator 3 isoform X1

    3. XM_054322928.1 → XP_054178903.1  phosphatase and actin regulator 3 isoform X4

    4. XM_054322923.1 → XP_054178898.1  phosphatase and actin regulator 3 isoform X1

    5. XM_054322926.1 → XP_054178901.1  phosphatase and actin regulator 3 isoform X2

    6. XM_054322929.1 → XP_054178904.1  phosphatase and actin regulator 3 isoform X1

    7. XM_054322925.1 → XP_054178900.1  phosphatase and actin regulator 3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96KR7.1 GenPept UniProtKB/Swiss-Prot:Q96KR7

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