Human Gene POLDIP3 (uc003bcu.3) Description and Page Index
  Description: Homo sapiens polymerase (DNA-directed), delta interacting protein 3 (POLDIP3), transcript variant 1, mRNA.
RefSeq Summary (NM_032311): 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].
Transcript (Including UTRs)
   Position: hg19 chr22:42,979,727-43,010,962 Size: 31,236 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr22:42,981,797-43,010,863 Size: 29,067 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:42,979,727-43,010,962)mRNA (may differ from genome)Protein (421 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PDIP3_HUMAN
DESCRIPTION: RecName: Full=Polymerase delta-interacting protein 3; AltName: Full=46 kDa DNA polymerase delta interaction protein; Short=p46; AltName: Full=S6K1 Aly/REF-like target; Short=SKAR;
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.
SUBUNIT: Interacts with POLD2. Interacts with NCBP1 and EIF4A3. Associates with the multiprotein exon junction complex (EJC). Interacts with RPS6KB1 (activated). Interacts with ERH.
INTERACTION: Q09161:NCBP1; NbExp=3; IntAct=EBI-1776152, EBI-464743;
SUBCELLULAR LOCATION: Nucleus. Nucleus speckle. Cytoplasm. Note=Nucleocytoplasmic shuttling protein.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR. Phosphorylated at Ser-383 and Ser-385 by RPS6KB1.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SEQUENCE CAUTION: Sequence=BAB33368.2; Type=Erroneous initiation;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 58.91 RPKM in Ovary
Total median expression: 1337.21 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -52.8099-0.533 Picture PostScript Text
3' UTR -863.992070-0.417 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
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q9BY77
FrontTopSide
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
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0006405 RNA export from nucleus
GO:0006406 mRNA export from nucleus
GO:0006417 regulation of translation
GO:0016973 poly(A)+ mRNA export from nucleus
GO:0031124 mRNA 3'-end processing
GO:0045727 positive regulation of translation
GO:0051028 mRNA transport

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016607 nuclear speck
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:0000346 transcription export complex
GO:0035145 exon-exon junction complex


-  Descriptions from all associated GenBank mRNAs
  BC001488 - Homo sapiens polymerase (DNA-directed), delta interacting protein 3, mRNA (cDNA clone IMAGE:2967216), partial cds.
BC056912 - Homo sapiens polymerase (DNA-directed), delta interacting protein 3, mRNA (cDNA clone MGC:65170 IMAGE:4941153), complete cds.
AL137743 - Homo sapiens mRNA; cDNA DKFZp434G0310 (from clone DKFZp434G0310).
BC049840 - Homo sapiens polymerase (DNA-directed), delta interacting protein 3, mRNA (cDNA clone MGC:54310 IMAGE:4937781), complete cds.
AL160111 - Isoform 1 of a novel human mRNA from chromosome 22.
AL160112 - Isoform 2 of a novel human mRNA from chromosome 22.
AK024626 - Homo sapiens cDNA: FLJ20973 fis, clone ADSU01580, highly similar to HS222E13A Isoform 1 of a novel human mRNA from chromosome 22.
BC019643 - Homo sapiens polymerase (DNA-directed), delta interacting protein 3, mRNA (cDNA clone MGC:24943 IMAGE:4933145), complete cds.
AB055760 - Homo sapiens KIAA1649 mRNA for KIAA1649 protein.
BC095411 - Homo sapiens polymerase (DNA-directed), delta interacting protein 3, mRNA (cDNA clone MGC:110911 IMAGE:30341984), complete cds.
KJ903406 - Synthetic construct Homo sapiens clone ccsbBroadEn_12800 POLDIP3 gene, encodes complete protein.
AY506562 - Homo sapiens polymerase delta interacting protein 46 (PDIP46) mRNA, complete cds, alternatively spliced.
CU676456 - Synthetic construct Homo sapiens gateway clone IMAGE:100016824 5' read POLDIP3 mRNA.
AK291623 - Homo sapiens cDNA FLJ75715 complete cds, highly similar to Homo sapiens polymerase (DNA-directed), delta interacting protein 3 (POLDIP3), transcript variant 2, mRNA.
AK297532 - Homo sapiens cDNA FLJ52566 complete cds, highly similar to Polymerase delta-interacting protein 3.
AK299751 - Homo sapiens cDNA FLJ60857 complete cds, highly similar to Polymerase delta-interacting protein 3.
AK291774 - Homo sapiens cDNA FLJ78506 complete cds.
CR456456 - Homo sapiens dJ222E13.3 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.dJ222E13.3).
AK303419 - Homo sapiens cDNA FLJ54030 complete cds, highly similar to Polymerase delta-interacting protein 3.
DQ887818 - Homo sapiens POLDIP3 (POLDIP3) mRNA, partial cds.
CU013006 - Homo sapiens POLDIP3, mRNA (cDNA clone IMAGE:100000169), complete cds, with stop codon, in Gateway system.
AB385492 - Synthetic construct DNA, clone: pF1KA1649, Homo sapiens POLDIP3 gene for polymerase delta-interacting protein 3, complete cds, without stop codon, in Flexi system.
CU013294 - Homo sapiens POLDIP3, mRNA (cDNA clone IMAGE:100000073), complete cds, without stop codon, in Gateway system.
AL080227 - Homo sapiens mRNA; cDNA DKFZp434D048 (from clone DKFZp434D048).
BC007397 - Homo sapiens polymerase (DNA-directed), delta interacting protein 3, mRNA (cDNA clone IMAGE:3835492), partial cds.
JD045751 - Sequence 26775 from Patent EP1572962.
JD162296 - Sequence 143320 from Patent EP1572962.
JD525985 - Sequence 507009 from Patent EP1572962.
JD547413 - Sequence 528437 from Patent EP1572962.
JD232553 - Sequence 213577 from Patent EP1572962.
JD256225 - Sequence 237249 from Patent EP1572962.
JD172754 - Sequence 153778 from Patent EP1572962.
JD187968 - Sequence 168992 from Patent EP1572962.
JD485029 - Sequence 466053 from Patent EP1572962.
JD396001 - Sequence 377025 from Patent EP1572962.
JD299841 - Sequence 280865 from Patent EP1572962.
JD097945 - Sequence 78969 from Patent EP1572962.
JD361698 - Sequence 342722 from Patent EP1572962.
JD380832 - Sequence 361856 from Patent EP1572962.
JD281839 - Sequence 262863 from Patent EP1572962.
JD470482 - Sequence 451506 from Patent EP1572962.
JD339140 - Sequence 320164 from Patent EP1572962.
JD106739 - Sequence 87763 from Patent EP1572962.
JD319029 - Sequence 300053 from Patent EP1572962.
JD026931 - Sequence 7955 from Patent EP1572962.
JD029722 - Sequence 10746 from Patent EP1572962.
JD480106 - Sequence 461130 from Patent EP1572962.
JD180827 - Sequence 161851 from Patent EP1572962.
JD294297 - Sequence 275321 from Patent EP1572962.
JD279712 - Sequence 260736 from Patent EP1572962.
JD075075 - Sequence 56099 from Patent EP1572962.
JD340511 - Sequence 321535 from Patent EP1572962.
JD432235 - Sequence 413259 from Patent EP1572962.
JD255248 - Sequence 236272 from Patent EP1572962.
JD382580 - Sequence 363604 from Patent EP1572962.
JD385903 - Sequence 366927 from Patent EP1572962.
JD326307 - Sequence 307331 from Patent EP1572962.
JD454450 - Sequence 435474 from Patent EP1572962.
JD479138 - Sequence 460162 from Patent EP1572962.
JD221216 - Sequence 202240 from Patent EP1572962.
DQ599081 - Homo sapiens piRNA piR-37147, complete sequence.
JD167455 - Sequence 148479 from Patent EP1572962.
JD387806 - Sequence 368830 from Patent EP1572962.
JD291914 - Sequence 272938 from Patent EP1572962.
JD320823 - Sequence 301847 from Patent EP1572962.
JD144851 - Sequence 125875 from Patent EP1572962.
JD237157 - Sequence 218181 from Patent EP1572962.
JD193505 - Sequence 174529 from Patent EP1572962.
JD194534 - Sequence 175558 from Patent EP1572962.
JD498073 - Sequence 479097 from Patent EP1572962.
JD545422 - Sequence 526446 from Patent EP1572962.
JD138599 - Sequence 119623 from Patent EP1572962.
JD215122 - Sequence 196146 from Patent EP1572962.
JD482103 - Sequence 463127 from Patent EP1572962.
JD108510 - Sequence 89534 from Patent EP1572962.
JD384116 - Sequence 365140 from Patent EP1572962.
JD282934 - Sequence 263958 from Patent EP1572962.
DQ576038 - Homo sapiens piRNA piR-44150, complete sequence.
JD024964 - Sequence 5988 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9BY77 (Reactome details) participates in the following event(s):

R-HSA-8849157 TREX complex binds spliced, capped mRNA:CBC:EJC cotranscriptionally
R-HSA-75098 mRNP complex dissociates from cytosolic face of NPC
R-HSA-75096 Docking of the TAP:EJC Complex with the NPC
R-HSA-72185 mRNA polyadenylation
R-HSA-72180 Cleavage of mRNA at the 3'-end
R-HSA-159101 NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)
R-HSA-72187 mRNA 3'-end processing
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-72202 Transport of Mature Transcript to Cytoplasm
R-HSA-109688 Cleavage of Growing Transcript in the Termination Region
R-HSA-8953854 Metabolism of RNA
R-HSA-73856 RNA Polymerase II Transcription Termination
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A8K6F8, A8K6V9, KIAA1649, NM_032311, NP_115687, PDIP3_HUMAN, PDIP46, Q009A7, Q5H972, Q6PGN6, Q7Z6Z0, Q9BY77, Q9NSP5, Q9NSP6
UCSC ID: uc003bcu.3
RefSeq Accession: NM_032311
Protein: Q9BY77 (aka PDIP3_HUMAN or PDP3_HUMAN)
CCDS: CCDS14038.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_032311.3
exon count: 9CDS single in 3' UTR: no RNA size: 3435
ORF size: 1266CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2732.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.