Human Gene PAN3 (uc001urz.3)
  Description: Homo sapiens PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae) (PAN3), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr13:28,712,643-28,869,475 Size: 156,833 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg19 chr13:28,712,795-28,866,659 Size: 153,865 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:28,712,643-28,869,475)mRNA (may differ from genome)Protein (887 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PAN3_HUMAN
DESCRIPTION: RecName: Full=PAB-dependent poly(A)-specific ribonuclease subunit 3; Short=hPan3;
FUNCTION: Functions in cytoplasmic mRNA decay. As part of the Pan nuclease complex, recruits polyadenylate-binding protein which in turn stimulates PAN2 nuclease activity.
SUBUNIT: Interacts with PAN2 to form the Pan nuclease complex. Mediates the interaction of the Pan nuclease complex with polyadenylate-binding protein.
SUBCELLULAR LOCATION: Cytoplasm.
DOMAIN: The protein kinase domain is predicted to be catalytically inactive.
SIMILARITY: Belongs to the protein kinase superfamily.
SIMILARITY: Contains 1 C3H1-type zinc finger.
SIMILARITY: Contains 1 protein kinase domain.
SEQUENCE CAUTION: Sequence=AAI28180.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=ABK41888.1; Type=Erroneous gene model prediction; Sequence=BAC03632.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAI12449.2; Type=Erroneous gene model prediction; Sequence=CAI12450.2; Type=Erroneous gene model prediction; Sequence=CAI14848.1; Type=Erroneous gene model prediction; Sequence=CAM20921.1; Type=Erroneous gene model prediction;
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/pan3/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PAN3
CDC HuGE Published Literature: PAN3
Positive Disease Associations: Stroke
Related Studies:
  1. Stroke
    , , . [PubMed 0]
  2. Stroke
    , , . [PubMed 0]

-  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: 19.98 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 471.48 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
5' UTR -68.70152-0.452 Picture PostScript Text
3' UTR -719.532816-0.256 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
IPR011009 - Kinase-like_dom
IPR000719 - Prot_kinase_cat_dom
IPR000571 - Znf_CCCH

Pfam Domains:
PF14608 - RNA-binding, Nab2-type zinc finger

SCOP Domains:
56112 - Protein kinase-like (PK-like)
90229 - CCCH zinc finger

ModBase Predicted Comparative 3D Structure on Q58A45
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:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0004672 protein kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0046872 metal ion binding
GO:0004535 poly(A)-specific ribonuclease activity

Biological Process:
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA
GO:0006397 mRNA processing
GO:0006468 protein phosphorylation
GO:0006605 protein targeting
GO:0010606 positive regulation of cytoplasmic mRNA processing body assembly
GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic

Cellular Component:
GO:0000932 P-body
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0031251 PAN complex


-  Descriptions from all associated GenBank mRNAs
  AK296435 - Homo sapiens cDNA FLJ54494 complete cds, highly similar to Homo sapiens PABP1-dependent poly A-specific ribonuclease subunit PAN3 (PAN3), mRNA.
LF384076 - JP 2014500723-A/191579: Polycomb-Associated Non-Coding RNAs.
AB107584 - Homo sapiens mRNA for PABP1-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3, complete cds.
AB109552 - Homo sapiens PAN3b mRNA for PABP1-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3b, complete cds.
BC128179 - Homo sapiens PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae), mRNA (cDNA clone MGC:149280 IMAGE:40113220), complete cds.
BC128180 - Homo sapiens PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae), mRNA (cDNA clone MGC:149281 IMAGE:40113222), complete cds.
KJ904079 - Synthetic construct Homo sapiens clone ccsbBroadEn_13473 PAN3 gene, encodes complete protein.
AK131556 - Homo sapiens cDNA FLJ16798 fis, clone TESTI2053667, weakly similar to PAB-dependent poly(A)-specific ribonuclease subunit PAN3 (EC 3.1.13.4).
BC024318 - Homo sapiens PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3915414), partial cds.
MA619653 - JP 2018138019-A/191579: Polycomb-Associated Non-Coding RNAs.
LF360190 - JP 2014500723-A/167693: Polycomb-Associated Non-Coding RNAs.
LF360215 - JP 2014500723-A/167718: Polycomb-Associated Non-Coding RNAs.
MA595767 - JP 2018138019-A/167693: Polycomb-Associated Non-Coding RNAs.
MA595792 - JP 2018138019-A/167718: Polycomb-Associated Non-Coding RNAs.
LF360220 - JP 2014500723-A/167723: Polycomb-Associated Non-Coding RNAs.
BX647740 - Homo sapiens mRNA; cDNA DKFZp686K19283 (from clone DKFZp686K19283).
AK091307 - Homo sapiens cDNA FLJ33988 fis, clone DFNES2006346, weakly similar to PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3 (EC 3.1.13.4).
AX746906 - Sequence 431 from Patent EP1308459.
LF360226 - JP 2014500723-A/167729: Polycomb-Associated Non-Coding RNAs.
LF360228 - JP 2014500723-A/167731: Polycomb-Associated Non-Coding RNAs.
JD371777 - Sequence 352801 from Patent EP1572962.
JD249026 - Sequence 230050 from Patent EP1572962.
LF360229 - JP 2014500723-A/167732: Polycomb-Associated Non-Coding RNAs.
JD479730 - Sequence 460754 from Patent EP1572962.
JD354753 - Sequence 335777 from Patent EP1572962.
JD316356 - Sequence 297380 from Patent EP1572962.
JD367902 - Sequence 348926 from Patent EP1572962.
JD565695 - Sequence 546719 from Patent EP1572962.
AY358261 - Homo sapiens clone DNA179649 KTIS8219 (UNQ8219) mRNA, complete cds.
JD307860 - Sequence 288884 from Patent EP1572962.
JD083047 - Sequence 64071 from Patent EP1572962.
JD564975 - Sequence 545999 from Patent EP1572962.
JD329998 - Sequence 311022 from Patent EP1572962.
LF360230 - JP 2014500723-A/167733: Polycomb-Associated Non-Coding RNAs.
JD299620 - Sequence 280644 from Patent EP1572962.
LF360231 - JP 2014500723-A/167734: Polycomb-Associated Non-Coding RNAs.
JD041998 - Sequence 23022 from Patent EP1572962.
JD287810 - Sequence 268834 from Patent EP1572962.
JD530694 - Sequence 511718 from Patent EP1572962.
JD435566 - Sequence 416590 from Patent EP1572962.
JD488800 - Sequence 469824 from Patent EP1572962.
LF360232 - JP 2014500723-A/167735: Polycomb-Associated Non-Coding RNAs.
JD331428 - Sequence 312452 from Patent EP1572962.
JD428732 - Sequence 409756 from Patent EP1572962.
JD504973 - Sequence 485997 from Patent EP1572962.
MA595797 - JP 2018138019-A/167723: Polycomb-Associated Non-Coding RNAs.
MA595803 - JP 2018138019-A/167729: Polycomb-Associated Non-Coding RNAs.
MA595805 - JP 2018138019-A/167731: Polycomb-Associated Non-Coding RNAs.
MA595806 - JP 2018138019-A/167732: Polycomb-Associated Non-Coding RNAs.
MA595807 - JP 2018138019-A/167733: Polycomb-Associated Non-Coding RNAs.
MA595808 - JP 2018138019-A/167734: Polycomb-Associated Non-Coding RNAs.
MA595809 - JP 2018138019-A/167735: Polycomb-Associated Non-Coding RNAs.

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

Protein Q58A45 (Reactome details) participates in the following event(s):

R-HSA-430021 PAN2-PAN3 complex partially deadenylates mRNA
R-HSA-429947 Deadenylation of mRNA
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A0N0X1, A1A4Y8, A1A4Y9, B1ALF1, B7Z3W7, NM_175854, NP_787050, PAN3_HUMAN, Q0D2P2, Q58A45, Q5HYG6, Q5T515, Q5T516, Q5TBA0, Q76E13, Q8NBA6
UCSC ID: uc001urz.3
RefSeq Accession: NM_175854
Protein: Q58A45 (aka PAN3_HUMAN)
CCDS: CCDS9329.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_175854.7
exon count: 19CDS single in 3' UTR: no RNA size: 5643
ORF size: 2664CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5469.00frame shift in genome: no % Coverage: 99.81
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.