Human Gene PAPD4 (uc003kgb.2) Description and Page Index
  Description: Homo sapiens PAP associated domain containing 4 (PAPD4), transcript variant 3, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:78,908,243-78,982,471 Size: 74,229 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr5:78,915,472-78,981,096 Size: 65,625 Coding Exon Count: 14 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:78,908,243-78,982,471)mRNA (may differ from genome)Protein (484 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
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H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: GLD2_HUMAN
DESCRIPTION: RecName: Full=Poly(A) RNA polymerase GLD2; Short=hGLD-2; EC=2.7.7.19; AltName: Full=PAP-associated domain-containing protein 4; AltName: Full=Terminal uridylyltransferase 2; Short=TUTase 2;
FUNCTION: Cytoplasmic poly(A) RNA polymerase that adds successive AMP monomers to the 3'-end of specific RNAs, forming a poly(A) tail. In contrast to the canonical nuclear poly(A) RNA polymerase, it only adds poly(A) to selected cytoplasmic mRNAs. Does not play a role in replication-dependent histone mRNA degradation.
CATALYTIC ACTIVITY: ATP + RNA(n) = diphosphate + RNA(n+1).
COFACTOR: Magnesium or manganese (By similarity).
SUBUNIT: Interacts with CPEB1, CPEB2, CPSF1 and PABPC1 (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity).
TISSUE SPECIFICITY: Expressed in brain. Within brain, it is expressed in cerebellum, hippocampus and medulla.
SIMILARITY: Belongs to the DNA polymerase type-B-like family. GLD2 subfamily.
SIMILARITY: Contains 1 PAP-associated domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PAPD4
CDC HuGE Published Literature: PAPD4
Positive Disease Associations: Hemoglobin A, Glycosylated
Related Studies:
  1. Hemoglobin A, Glycosylated
    James B Meigs et al. BMC medical genetics 2007, Genome-wide association with diabetes-related traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903298]
    Framingham 100K SNP data is a resource for association tests of known and novel genes with diabetes and related traits posted at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite. Framingham 100K data replicate the TCF7L2 association with diabetes.

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 23.96 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 525.52 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 -168.81452-0.373 Picture PostScript Text
3' UTR -315.621375-0.230 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
IPR002058 - PAP_assoc

Pfam Domains:
PF03828 - Cid1 family poly A polymerase

SCOP Domains:
81631 - PAP/OAS1 substrate-binding domain
81301 - Nucleotidyltransferase

ModBase Predicted Comparative 3D Structure on Q6PIY7
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004652 polynucleotide adenylyltransferase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0046872 metal ion binding

Biological Process:
GO:0002244 hematopoietic progenitor cell differentiation
GO:0006397 mRNA processing
GO:0021766 hippocampus development
GO:0030182 neuron differentiation
GO:0043631 RNA polyadenylation
GO:0060041 retina development in camera-type eye
GO:0071044 histone mRNA catabolic process
GO:1990603 dark adaptation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0031380 nuclear RNA-directed RNA polymerase complex


-  Descriptions from all associated GenBank mRNAs
  AL833136 - Homo sapiens mRNA; cDNA DKFZp313N0932 (from clone DKFZp313N0932).
BC047581 - Homo sapiens PAP associated domain containing 4, mRNA (cDNA clone MGC:48402 IMAGE:4824607), complete cds.
BC026061 - Homo sapiens PAP associated domain containing 4, mRNA (cDNA clone MGC:16201 IMAGE:3640197), complete cds.
AK095818 - Homo sapiens cDNA FLJ38499 fis, clone HCASM1000050.
JD561212 - Sequence 542236 from Patent EP1572962.
JD297221 - Sequence 278245 from Patent EP1572962.
JD091386 - Sequence 72410 from Patent EP1572962.
JD289712 - Sequence 270736 from Patent EP1572962.
JD087253 - Sequence 68277 from Patent EP1572962.
JD245988 - Sequence 227012 from Patent EP1572962.
JD425176 - Sequence 406200 from Patent EP1572962.
JD282465 - Sequence 263489 from Patent EP1572962.
JD548895 - Sequence 529919 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: GLD2, GLD2_HUMAN, NM_173797, NP_776158, Q6PIY7, Q86WZ2, Q8N927
UCSC ID: uc003kgb.2
RefSeq Accession: NM_173797
Protein: Q6PIY7 (aka GLD2_HUMAN)
CCDS: CCDS4048.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_173797.3
exon count: 16CDS single in 3' UTR: no RNA size: 3282
ORF size: 1455CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3067.50frame 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.