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    POLDIP3 DNA polymerase delta interacting protein 3 [ Homo sapiens (human) ]

    Gene ID: 84271, updated on 28-Oct-2024

    Summary

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    Official Symbol
    POLDIP3provided by HGNC
    Official Full Name
    DNA polymerase delta interacting protein 3provided by HGNC
    Primary source
    HGNC:HGNC:23782
    See related
    Ensembl:ENSG00000100227 MIM:611520; AllianceGenome:HGNC:23782
    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
    SKAR; PDIP3; PDIP46
    Summary
    This gene encodes an RRM (RNA recognition motif)-containing protein that participates in the regulation of translation by recruiting ribosomal protein S6 kinase beta-1 to mRNAs. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
    Expression
    Ubiquitous expression in ovary (RPKM 49.2), bone marrow (RPKM 26.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See POLDIP3 in Genome Data Viewer
    Location:
    22q13.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (42583721..42614883, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (43064586..43095749, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (42979727..43010889, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene serine hydrolase like 2 Neighboring gene RNA, U6 small nuclear 513, pseudogene Neighboring gene ribosomal RNA processing 7 homolog B, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13831 Neighboring gene Sharpr-MPRA regulatory region 2357 Neighboring gene uncharacterized LOC124905127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43009109-43009652 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:43010197-43010740 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:43010741-43011284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43019599-43020153 Neighboring gene RNA, U12 small nuclear Neighboring gene cytochrome b5 reductase 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43027517-43028018 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43032221-43032758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43032759-43033294 Neighboring gene ATP synthase membrane subunit g like

    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 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. TDP-43 regulates global translational yield by splicing of exon junction complex component SKAR. Fiesel FC, et al. Nucleic Acids Res, 2012 Mar. PMID 22121224, Free PMC Article
    2. Human enhancer of rudimentary is a molecular partner of PDIP46/SKAR, a protein interacting with DNA polymerase delta and S6K1 and regulating cell growth. Smyk A, et al. FEBS J, 2006 Oct. PMID 16984396
    3. PDIP46 (DNA polymerase δ interacting protein 46) is an activating factor for human DNA polymerase δ. Wang X, et al. Oncotarget, 2016 Feb 2. PMID 26819372, Free PMC Article
    4. Human RTEL1 associates with Poldip3 to facilitate responses to replication stress and R-loop resolution. Björkman A, et al. Genes Dev, 2020 Aug 1. PMID 32561545, Free PMC Article
    5. Alteration of POLDIP3 splicing associated with loss of function of TDP-43 in tissues affected with ALS. Shiga A, et al. PLoS One, 2012. PMID 22900096, Free PMC Article

    See all (134) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Human RTEL1 associates with Poldip3 to facilitate responses to replication stress and R-loop resolution.
      Title: Human RTEL1 associates with Poldip3 to facilitate responses to replication stress and R-loop resolution.
    2. Altered expression of PDIP46 or its mutation may affect Pol delta functions in vivo, and thereby be a nexus for altered genomic stability.
      Title: PDIP46 (DNA polymerase δ interacting protein 46) is an activating factor for human DNA polymerase δ.
    3. hnRNP-U inhibits TDP-43-mediated alterations in splicing of POLDIP3 mRNA.
      Title: Nuclear TDP-43 causes neuronal toxicity by escaping from the inhibitory regulation by hnRNPs.
    4. PDIP3 and ZC11A associate with the human TREX complex in an ATP-dependent manner and function in mRNA export.
      Title: The proteins PDIP3 and ZC11A associate with the human TREX complex in an ATP-dependent manner and function in mRNA export.
    5. these findings establish critical and essential roles for SKAR in the regulation of mRNA translation of IFN-sensitive genes and induction of IFN-alpha biological responses.
      Title: Regulatory effects of SKAR in interferon α signaling and its role in the generation of type I IFN responses.
    6. Alteration of POLDIP3 splicing associated with loss of function of TDP-43 in tissues affected with amyotrophic lateral sclerosis (ALS) .
      Title: Alteration of POLDIP3 splicing associated with loss of function of TDP-43 in tissues affected with ALS.
    7. SKAR-mediated recruitment of activated S6K1 to newly processed mRNPs serves as a conduit between mTOR checkpoint signaling and the pioneer round of translation when cells exist in conditions supportive of protein synthesis.
      Title: SKAR links pre-mRNA splicing to mTOR/S6K1-mediated enhanced translation efficiency of spliced mRNAs.
    8. This study showed that PDIP46 aka SKAR, a protein possessing one RNA recognition motif (RRM) and being a protein partner of both the p50 subunit of DNA polymerase delta and p70 ribosomal protein S6 kinase 1 (S6K1).
      Title: Human enhancer of rudimentary is a molecular partner of PDIP46/SKAR, a protein interacting with DNA polymerase delta and S6K1 and regulating cell growth.
    9. SKAR is a specific target of S6K1 and regulates cell growth.
      Title: SKAR is a specific target of S6 kinase 1 in cell growth control.
    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

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1649

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in poly(A)+ mRNA export from nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in poly(A)+ mRNA export from nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of translation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in cytoplasmic ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nuclear speck IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    polymerase delta-interacting protein 3
    Names
    46 kDa DNA polymerase delta interaction protein
    RNA-binding protein P46
    S6K1 Aly/REF-like target
    polymerase (DNA) delta interacting protein 3
    polymerase (DNA-directed), delta interacting protein 3

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001278657.2 → NP_001265586.1  polymerase delta-interacting protein 3 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (3) is longer than isoform 1.
      Source sequence(s)
      AK303419, AL137743, DC368557
      Consensus CDS
      CCDS74873.1
      UniProtKB/TrEMBL
      B4E0L0, F6VRR5
      Related
      ENSP00000397927.3, ENST00000451060.6
      Conserved Domains (2) summary
      COG0724
      Location:301 → 424
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12681
      Location:297 → 365
      RRM_SKAR; RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

    2. NM_001363052.2 → NP_001349981.1  polymerase delta-interacting protein 3 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate exon in the 3' coding region, compared to variant 1. The encoded isoform (4) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL137743, Z93241
      UniProtKB/TrEMBL
      Q96DI9
      Conserved Domains (1) summary
      cd12681
      Location:280 → 341
      RRM_SKAR; RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

    3. NM_032311.5 → NP_115687.2  polymerase delta-interacting protein 3 isoform 1

      See identical proteins and their annotated locations for NP_115687.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AL160111, DC368557
      Consensus CDS
      CCDS14038.1
      UniProtKB/Swiss-Prot
      A8K6F8, A8K6V9, Q009A7, Q5H972, Q6PGN6, Q7Z6Z0, Q9BY77, Q9NSP5, Q9NSP6
      UniProtKB/TrEMBL
      Q96DI9
      Related
      ENSP00000252115.5, ENST00000252115.10
      Conserved Domains (2) summary
      COG0724
      Location:284 → 407
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12681
      Location:280 → 348
      RRM_SKAR; RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

    4. NM_178136.3 → NP_835237.1  polymerase delta-interacting protein 3 isoform 2

      See identical proteins and their annotated locations for NP_835237.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AL160112, DC368557
      Consensus CDS
      CCDS14039.1
      UniProtKB/TrEMBL
      Q96DI9
      Related
      ENSP00000252116.5, ENST00000348657.6
      Conserved Domains (2) summary
      COG0724
      Location:255 → 378
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12681
      Location:251 → 319
      RRM_SKAR; RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

    RNA

    1. NR_103820.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site at an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL137743, DC368557
      Related
      ENST00000445215.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      42583721..42614883 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      43064586..43095749 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BY77.2 GenPept UniProtKB/Swiss-Prot:Q9BY77

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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