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] See more...

Aliases for POLDIP3 Gene

Aliases for POLDIP3 Gene

  • DNA Polymerase Delta Interacting Protein 3 2 3 5
  • S6K1 Aly/REF-Like Target 2 3 4
  • PDIP46 2 3 4
  • SKAR 2 3 4
  • Polymerase (DNA-Directed), Delta Interacting Protein 3 2 3
  • 46 KDa DNA Polymerase Delta Interaction Protein 3 4
  • Polymerase Delta-Interacting Protein 3 3 4
  • KIAA1649 2 4
  • PDIP3 2 3
  • Polymerase (DNA) Delta Interacting Protein 3 3
  • RNA-Binding Protein P46 3
  • POLDIP3 5
  • P46 4

External Ids for POLDIP3 Gene

Previous GeneCards Identifiers for POLDIP3 Gene

  • GC22M041211
  • GC22M041212
  • GC22M041304
  • GC22M042979
  • GC22M025940

Summaries for POLDIP3 Gene

Entrez Gene Summary for POLDIP3 Gene

  • 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]

GeneCards Summary for POLDIP3 Gene

POLDIP3 (DNA Polymerase Delta Interacting Protein 3) is a Protein Coding gene. Diseases associated with POLDIP3 include Methylmalonic Aciduria, Cblb Type. Among its related pathways are Tat-mediated elongation of the HIV-1 transcript and Transport of Mature Transcript to Cytoplasm. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is ALYREF.

UniProtKB/Swiss-Prot Summary for POLDIP3 Gene

  • Is involved in regulation of translation. Is preferentially associated with CBC-bound spliced mRNA-protein complexes during the pioneer round of mRNA translation. Contributes to enhanced translational efficiency of spliced over nonspliced mRNAs. Recruits activated ribosomal protein S6 kinase beta-1 I/RPS6KB1 to newly synthesized mRNA. Involved in nuclear mRNA export; probably mediated by association with the TREX complex.

Gene Wiki entry for POLDIP3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for POLDIP3 Gene

Genomics for POLDIP3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for POLDIP3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around POLDIP3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for POLDIP3

Top Transcription factor binding sites by QIAGEN in the POLDIP3 gene promoter:
  • AML1a
  • ATF6
  • CREB
  • deltaCREB
  • Elk-1
  • LUN-1
  • MZF-1
  • Pax-6
  • SRF
  • SRF (504 AA)

Genomic Locations for POLDIP3 Gene

Latest Assembly
chr22:42,583,721-42,614,962
(GRCh38/hg38)
Size:
31,242 bases
Orientation:
Minus strand

Previous Assembly
chr22:42,979,727-43,010,889
(GRCh37/hg19 by Entrez Gene)
Size:
31,163 bases
Orientation:
Minus strand

chr22:42,979,727-43,010,968
(GRCh37/hg19 by Ensembl)
Size:
31,242 bases
Orientation:
Minus strand

Genomic View for POLDIP3 Gene

Genes around POLDIP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
POLDIP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for POLDIP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for POLDIP3 Gene

Proteins for POLDIP3 Gene

  • Protein details for POLDIP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BY77-PDIP3_HUMAN
    Recommended name:
    Polymerase delta-interacting protein 3
    Protein Accession:
    Q9BY77
    Secondary Accessions:
    • A8K6F8
    • A8K6V9
    • Q009A7
    • Q5H972
    • Q6PGN6
    • Q7Z6Z0
    • Q9NSP5
    • Q9NSP6

    Protein attributes for POLDIP3 Gene

    Size:
    421 amino acids
    Molecular mass:
    46089 Da
    Quaternary structure:
    • Interacts with POLD2. Interacts with NCBP1 and EIF4A3. Associates with the multiprotein exon junction complex (EJC). Interacts with RPS6KB1 (activated). Interacts with ERH. Interacts with THOC2, DDX39B and ZC3H11A; the interactions are ATP-dependent and indicative for an association with the TREX complex.
    SequenceCaution:
    • Sequence=BAB33368.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for POLDIP3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for POLDIP3 Gene

Post-translational modifications for POLDIP3 Gene

  • Phosphorylated at Ser-383 and Ser-385 by RPS6KB1.
  • Ubiquitination at Lys197, Lys178, Lys218, Lys223, Lys229, and Lys418
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for POLDIP3 Gene

Domains & Families for POLDIP3 Gene

Gene Families for POLDIP3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for POLDIP3 Gene

InterPro:
Blocks:
  • RNA-binding region RNP-1 (RNA recognition motif)

Suggested Antigen Peptide Sequences for POLDIP3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ52566, highly similar to Polymerase delta-interacting protein 3 (B4DMM2_HUMAN)
  • cDNA FLJ60857, highly similar to Polymerase delta-interacting protein 3 (B4DSH9_HUMAN)
  • S6K1 Aly/REF-like target (PDIP3_HUMAN)
  • POLDIP3 protein (Q8WUT1_HUMAN)
  • POLDIP3 protein (Q96DI9_HUMAN)
genes like me logo Genes that share domains with POLDIP3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for POLDIP3 Gene

Function for POLDIP3 Gene

Molecular function for POLDIP3 Gene

UniProtKB/Swiss-Prot Function:
Is involved in regulation of translation. Is preferentially associated with CBC-bound spliced mRNA-protein complexes during the pioneer round of mRNA translation. Contributes to enhanced translational efficiency of spliced over nonspliced mRNAs. Recruits activated ribosomal protein S6 kinase beta-1 I/RPS6KB1 to newly synthesized mRNA. Involved in nuclear mRNA export; probably mediated by association with the TREX complex.

Phenotypes From GWAS Catalog for POLDIP3 Gene

Gene Ontology (GO) - Molecular Function for POLDIP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,HDA 22658674
GO:0005515 protein binding IPI 18423201
GO:0044877 protein-containing complex binding IPI 18423201
genes like me logo Genes that share ontologies with POLDIP3: view
genes like me logo Genes that share phenotypes with POLDIP3: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for POLDIP3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for POLDIP3 Gene

Localization for POLDIP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for POLDIP3 Gene

Nucleus. Nucleus speckle. Cytoplasm. Note=Nucleocytoplasmic shuttling protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for POLDIP3 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (4)
  • Cytoplasmic bodies (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for POLDIP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm TAS 18423201
GO:0005829 cytosol TAS --
GO:0016607 nuclear speck IDA 18423201
genes like me logo Genes that share ontologies with POLDIP3: view

Pathways & Interactions for POLDIP3 Gene

genes like me logo Genes that share pathways with POLDIP3: view

Pathways by source for POLDIP3 Gene

SIGNOR curated interactions for POLDIP3 Gene

Other effect:

Gene Ontology (GO) - Biological Process for POLDIP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006405 RNA export from nucleus TAS --
GO:0006406 mRNA export from nucleus TAS --
GO:0006417 regulation of translation IEA --
GO:0016973 poly(A)+ mRNA export from nucleus IEA,IDA 22928037
GO:0031124 mRNA 3'-end processing TAS --
genes like me logo Genes that share ontologies with POLDIP3: view

Drugs & Compounds for POLDIP3 Gene

No Compound Related Data Available

Transcripts for POLDIP3 Gene

mRNA/cDNA for POLDIP3 Gene

4 REFSEQ mRNAs :
22 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for POLDIP3

Alternative Splicing Database (ASD) splice patterns (SP) for POLDIP3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12a · 12b · 12c · 12d ^ 13 ^
SP1: - - - - - -
SP2: - - - - - - -
SP3: - -
SP4: -
SP5: - - -
SP6: -
SP7: -
SP8: -
SP9: - - - - - - - - - - - - - - - - - -
SP10:
SP11: - -
SP12:

ExUns: 14 ^ 15a · 15b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for POLDIP3 Gene

GeneLoc Exon Structure for
POLDIP3

Expression for POLDIP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for POLDIP3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for POLDIP3 Gene

This gene is overexpressed in Breast (14.2), Peripheral blood mononuclear cells (8.0), and Fetal testis (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for POLDIP3 Gene



Protein tissue co-expression partners for POLDIP3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for POLDIP3

SOURCE GeneReport for Unigene cluster for POLDIP3 Gene:

Hs.505802

Evidence on tissue expression from TISSUES for POLDIP3 Gene

  • Nervous system(5)
  • Liver(4.3)
  • Skin(3.4)
  • Lung(2.5)
  • Muscle(2.2)
  • Kidney(2.1)
  • Blood(2)
genes like me logo Genes that share expression patterns with POLDIP3: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for POLDIP3 Gene

Orthologs for POLDIP3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for POLDIP3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia POLDIP3 29 30
  • 99.52 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia POLDIP3 29 30
  • 91.05 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia POLDIP3 29 30
  • 89.63 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Poldip3 29
  • 88.81 (n)
Mouse
(Mus musculus)
Mammalia Poldip3 29 16 30
  • 87.94 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia POLDIP3 30
  • 71 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia POLDIP3 30
  • 45 (a)
OneToOne
Chicken
(Gallus gallus)
Aves POLDIP3 29 30
  • 73.46 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia POLDIP3 30
  • 72 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia poldip3 29
  • 66.67 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.2649 29
Zebrafish
(Danio rerio)
Actinopterygii POLDIP3 30
  • 30 (a)
OneToOne
Dr.26582 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10311 29
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.2373 30
  • 21 (a)
OneToOne
Species where no ortholog for POLDIP3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for POLDIP3 Gene

ENSEMBL:
Gene Tree for POLDIP3 (if available)
TreeFam:
Gene Tree for POLDIP3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for POLDIP3: view image
Alliance of Genome Resources:
Additional Orthologs for POLDIP3

Paralogs for POLDIP3 Gene

Paralogs for POLDIP3 Gene

(2) SIMAP similar genes for POLDIP3 Gene using alignment to 6 proteins:

  • PDIP3_HUMAN
  • B4DMM2_HUMAN
  • F8WCX5_HUMAN
  • F8WEE2_HUMAN
  • Q8WUT1_HUMAN
  • Q96DI9_HUMAN
genes like me logo Genes that share paralogs with POLDIP3: view

Variants for POLDIP3 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for POLDIP3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for POLDIP3 Gene

Variant ID Type Subtype PubMed ID
dgv101e203 CNV gain+loss 21179565
dgv1323e212 CNV loss 25503493
dgv4578n100 CNV gain 25217958
dgv4585n100 CNV gain 25217958
esv2758839 CNV gain+loss 17122850
esv28197 CNV gain 19812545
esv3568423 CNV loss 25503493
nsv1136683 CNV deletion 24896259
nsv428391 CNV gain 18775914
nsv524028 CNV loss 19592680
nsv9912 CNV gain+loss 18304495

Variation tolerance for POLDIP3 Gene

Residual Variation Intolerance Score: 11.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.70; 73.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for POLDIP3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
POLDIP3
Leiden Open Variation Database (LOVD)
POLDIP3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for POLDIP3 Gene

Disorders for POLDIP3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for POLDIP3 Gene - From: COP

Disorder Aliases PubMed IDs
methylmalonic aciduria, cblb type
  • methylmalonic acidemia, cblb type
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for POLDIP3

genes like me logo Genes that share disorders with POLDIP3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for POLDIP3 Gene

Publications for POLDIP3 Gene

  1. Human enhancer of rudimentary is a molecular partner of PDIP46/SKAR, a protein interacting with DNA polymerase delta and S6K1 and regulating cell growth. (PMID: 16984396) Smyk A … Kozlowski P (The FEBS journal 2006) 3 4 22
  2. Identification of a novel protein, PDIP38, that interacts with the p50 subunit of DNA polymerase delta and proliferating cell nuclear antigen. (PMID: 12522211) Liu L … Lee MY (The Journal of biological chemistry 2003) 2 3 4
  3. The proteins PDIP3 and ZC11A associate with the human TREX complex in an ATP-dependent manner and function in mRNA export. (PMID: 22928037) Folco EG … Reed R (PloS one 2012) 3 4
  4. ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex. (PMID: 20844015) Dufu K … Reed R (Genes & development 2010) 3 4
  5. SKAR links pre-mRNA splicing to mTOR/S6K1-mediated enhanced translation efficiency of spliced mRNAs. (PMID: 18423201) Ma XM … Blenis J (Cell 2008) 3 4

Products for POLDIP3 Gene

Sources for POLDIP3 Gene