Human Gene POLD2 (uc003tkf.5) Description and Page Index
  Description: Homo sapiens polymerase (DNA directed), delta 2, accessory subunit (POLD2), transcript variant 2, mRNA.
RefSeq Summary (NM_006230): This gene encodes the 50-kDa catalytic subunit of DNA polymerase delta. DNA polymerase delta possesses both polymerase and 3' to 5' exonuclease activity and plays a critical role in DNA replication and repair. The encoded protein is required for the stimulation of DNA polymerase delta activity by the processivity cofactor proliferating cell nuclear antigen (PCNA). Expression of this gene may be a marker for ovarian carcinomas. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 5. [provided by RefSeq, Mar 2012].
Transcript (Including UTRs)
   Position: hg19 chr7:44,154,279-44,163,169 Size: 8,891 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr7:44,154,384-44,163,158 Size: 8,775 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:44,154,279-44,163,169)mRNA (may differ from genome)Protein (504 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: DPOD2_HUMAN
DESCRIPTION: RecName: Full=DNA polymerase delta subunit 2; EC=2.7.7.7; AltName: Full=DNA polymerase delta subunit p50;
FUNCTION: The function of the small subunit is not yet clear.
CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
SUBUNIT: Heterotetramer composed of subunits of 125 kDa, 50 kDa, 66 kDa and 12 kDa. Interacts with KCTD10 (By similarity). Interacts with KCTD13/POLDIP1, POLDIP2 and POLDIP3. Interacts with WRNIP1. Interacts with POLD4.
INTERACTION: P28340:POLD1; NbExp=9; IntAct=EBI-372354, EBI-716569; Q15054:POLD3; NbExp=5; IntAct=EBI-372354, EBI-864956; Q9HCU8:POLD4; NbExp=3; IntAct=EBI-372354, EBI-864968;
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the DNA polymerase delta/II small subunit family.
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/pold2/";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): POLD2
CDC HuGE Published Literature: POLD2

-  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: 40.65 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1181.91 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
3' UTR -26.80105-0.255 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
IPR007185 - DNA_pol_alpha/epsilon_bsu
IPR024826 - DNA_pol_delta/II_ssu

Pfam Domains:
PF04042 - DNA polymerase alpha/epsilon subunit B

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3E0J
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P49005
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0005515 protein binding

Biological Process:
GO:0000723 telomere maintenance
GO:0006260 DNA replication
GO:0006271 DNA strand elongation involved in DNA replication
GO:0006281 DNA repair
GO:0006283 transcription-coupled nucleotide-excision repair
GO:0006296 nucleotide-excision repair, DNA incision, 5'-to lesion
GO:0006297 nucleotide-excision repair, DNA gap filling
GO:0006974 cellular response to DNA damage stimulus
GO:0019985 translesion synthesis
GO:0032201 telomere maintenance via semi-conservative replication
GO:0033683 nucleotide-excision repair, DNA incision
GO:0042769 DNA damage response, detection of DNA damage

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0043625 delta DNA polymerase complex


-  Descriptions from all associated GenBank mRNAs
  LF208991 - JP 2014500723-A/16494: Polycomb-Associated Non-Coding RNAs.
BC030001 - Homo sapiens polymerase (DNA directed), delta 2, regulatory subunit 50kDa, mRNA (cDNA clone IMAGE:5140179).
U21090 - Human DNA polymerase delta small subunit mRNA, complete cds.
BC000459 - Homo sapiens polymerase (DNA directed), delta 2, regulatory subunit 50kDa, mRNA (cDNA clone MGC:8498 IMAGE:2822169), complete cds.
AK298168 - Homo sapiens cDNA FLJ51260 complete cds, highly similar to DNA polymerase subunit delta 2 (EC 2.7.7.7).
AK292347 - Homo sapiens cDNA FLJ78293 complete cds, highly similar to Homo sapiens polymerase (DNA directed), delta 2, regulatory subunit 50kDa (POLD2), mRNA.
JD355234 - Sequence 336258 from Patent EP1572962.
JD382441 - Sequence 363465 from Patent EP1572962.
JD501516 - Sequence 482540 from Patent EP1572962.
JD245552 - Sequence 226576 from Patent EP1572962.
AK312294 - Homo sapiens cDNA, FLJ92598, highly similar to Homo sapiens polymerase (DNA directed), delta 2, regulatory subunit 50kDa (POLD2), mRNA.
KJ891841 - Synthetic construct Homo sapiens clone ccsbBroadEn_01235 POLD2 gene, encodes complete protein.
DQ891999 - Synthetic construct clone IMAGE:100004629; FLH182191.01X; RZPDo839D07138D polymerase (DNA directed), delta 2, regulatory subunit 50kDa (POLD2) gene, encodes complete protein.
DQ895189 - Synthetic construct Homo sapiens clone IMAGE:100009649; FLH182187.01L; RZPDo839D07137D polymerase (DNA directed), delta 2, regulatory subunit 50kDa (POLD2) gene, encodes complete protein.
AB463185 - Synthetic construct DNA, clone: pF1KB5275, Homo sapiens POLD2 gene for polymerase (DNA directed), delta 2, regulatory subunit 50kDa, without stop codon, in Flexi system.
JD032500 - Sequence 13524 from Patent EP1572962.
JD022230 - Sequence 3254 from Patent EP1572962.
JD024752 - Sequence 5776 from Patent EP1572962.
JD033203 - Sequence 14227 from Patent EP1572962.
MA444568 - JP 2018138019-A/16494: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00230 - Purine metabolism
hsa00240 - Pyrimidine metabolism
hsa01100 - Metabolic pathways
hsa03030 - DNA replication
hsa03410 - Base excision repair
hsa03420 - Nucleotide excision repair
hsa03430 - Mismatch repair
hsa03440 - Homologous recombination

Reactome (by CSHL, EBI, and GO)

Protein P49005 (Reactome details) participates in the following event(s):

R-HSA-69074 Formation of Processive Complex
R-HSA-174448 Formation of Processive Complex on the C-strand of the telomere
R-HSA-176702 Disassociation of Processive Complex and Completed Telomere End
R-HSA-69116 Formation of Okazaki fragments
R-HSA-174445 RPA binds to the Flap on the C-strand
R-HSA-174438 Formation of the Flap Intermediate on the C-strand
R-HSA-174456 Joining of adjacent Okazaki fragments of the C-strand
R-HSA-174446 Removal of remaining Flap from the C-strand
R-HSA-174444 Formation of C-strand Okazaki fragments
R-HSA-174441 Removal of RNA primer and dissociation of RPA and Dna2 from the C-strand
R-HSA-5653838 POLD,POLE binds deISGylated PCNA after TLS
R-HSA-5652009 RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA
R-HSA-5358579 DNA polymerase delta polymerizes DNA across single stranded gap
R-HSA-69127 Formation of the Flap Intermediate
R-HSA-69152 Removal of remaining Flap
R-HSA-69144 Removal of RNA primer and dissociation of RPA and Dna2
R-HSA-174451 Recruitment of Dna2 endonuclease to the C strand
R-HSA-110364 PCNA:POLD,POLE:RPA:RFC and FEN1 bind APEX1
R-HSA-5651992 PCNA-containing replication complex binds damaged dsDNA
R-HSA-5651809 LIG1, APEX1 and PCNA:POLD,POLE:RPA:RFC dissociate from repaired DNA
R-HSA-5653840 POLD,POLE complete replication of damaged DNA after TLS
R-HSA-5690213 DNA polymerases delta, epsilon or kappa bind the GG-NER site
R-HSA-6782211 DNA polymerases delta, epsilon or kappa bind the TC-NER site
R-HSA-69140 RPA binds to the Flap
R-HSA-110368 POLD,POLE-mediated DNA strand displacement synthesis
R-HSA-110371 LIG1 binds APEX1 and PCNA at SSB
R-HSA-110363 FEN1 bound to PCNA and APEX1 cleaves flap ssDNA
R-HSA-5651805 LIG1 bound to APEX1 and PCNA ligates SSB
R-HSA-5652005 RAD18:UBE2B or RBX1:CUL4:DDB1:DTL ubiquitin ligase complex binds PCNA:POLD,POLE:RPA:RFC associated with damaged dsDNA
R-HSA-69142 Recruitment of Dna2 endonuclease
R-HSA-5693593 D-loop extension by DNA polymerases
R-HSA-5690997 Ligation of newly synthesized repair patch to incised DNA in GG-NER
R-HSA-6782227 Ligation of newly synthesized repair patch to incised DNA in TC-NER
R-HSA-5690988 3'-incision of DNA by ERCC5 (XPG) in GG-NER
R-HSA-5691001 Repair DNA synthesis of ~27-30 bases long patch by POLD, POLE or POLK in GG-NER
R-HSA-6782224 3' incision by ERCC5 (XPG) in TC-NER
R-HSA-6782208 Repair DNA synthesis of ~27-30 bases long patch by POLD, POLE or POLK in TC-NER
R-HSA-69091 Polymerase switching
R-HSA-174411 Polymerase switching on the C-strand of the telomere
R-HSA-174417 Telomere C-strand (Lagging Strand) Synthesis
R-HSA-69183 Processive synthesis on the lagging strand
R-HSA-174437 Removal of the Flap Intermediate from the C-strand
R-HSA-174414 Processive synthesis on the C-strand of the telomere
R-HSA-5656169 Termination of translesion DNA synthesis
R-HSA-110314 Recognition of DNA damage by PCNA-containing replication complex
R-HSA-69109 Leading Strand Synthesis
R-HSA-69186 Lagging Strand Synthesis
R-HSA-180786 Extension of Telomeres
R-HSA-5358565 Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)
R-HSA-5358606 Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)
R-HSA-69166 Removal of the Flap Intermediate
R-HSA-5651801 PCNA-Dependent Long Patch Base Excision Repair
R-HSA-5696400 Dual Incision in GG-NER
R-HSA-6782135 Dual incision in TC-NER
R-HSA-110313 Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template
R-HSA-73893 DNA Damage Bypass
R-HSA-69190 DNA strand elongation
R-HSA-157579 Telomere Maintenance
R-HSA-5358508 Mismatch Repair
R-HSA-110373 Resolution of AP sites via the multiple-nucleotide patch replacement pathway
R-HSA-5696399 Global Genome Nucleotide Excision Repair (GG-NER)
R-HSA-6781827 Transcription-Coupled Nucleotide Excision Repair (TC-NER)
R-HSA-73894 DNA Repair
R-HSA-69239 Synthesis of DNA
R-HSA-73886 Chromosome Maintenance
R-HSA-5685942 HDR through Homologous Recombination (HRR)
R-HSA-73933 Resolution of Abasic Sites (AP sites)
R-HSA-5696397 Gap-filling DNA repair synthesis and ligation in GG-NER
R-HSA-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-HSA-5696398 Nucleotide Excision Repair
R-HSA-69242 S Phase
R-HSA-69306 DNA Replication
R-HSA-1640170 Cell Cycle
R-HSA-5693567 HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
R-HSA-73884 Base Excision Repair
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-5693538 Homology Directed Repair
R-HSA-5693532 DNA Double-Strand Break Repair

-  Other Names for This Gene
  Alternate Gene Symbols: DPOD2_HUMAN, NM_006230, NP_006221, P49005, uc003tkf.4
UCSC ID: uc003tkf.5
RefSeq Accession: NM_006230
Protein: P49005 (aka DPOD2_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006230.3
exon count: 11CDS single in 3' UTR: no RNA size: 1648
ORF size: 1515CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3230.00frame shift in genome: no % Coverage: 98.97
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.