Human Gene DCP1A (uc021wzi.1) Description and Page Index
  Description: Homo sapiens decapping mRNA 1A (DCP1A), mRNA.
RefSeq Summary (NM_018403): Decapping is a key step in general and regulated mRNA decay. The protein encoded by this gene is a decapping enzyme. This protein and another decapping enzyme form a decapping complex, which interacts with the nonsense-mediated decay factor hUpf1 and may be recruited to mRNAs containing premature termination codons. This protein also participates in the TGF-beta signaling pathway. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2014].
Transcript (Including UTRs)
   Position: hg19 chr3:53,317,445-53,381,654 Size: 64,210 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr3:53,321,598-53,381,544 Size: 59,947 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
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 (chr3:53,317,445-53,381,654)mRNA (may differ from genome)Protein (582 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: DCP1A_HUMAN
DESCRIPTION: RecName: Full=mRNA-decapping enzyme 1A; EC=3.-.-.-; AltName: Full=Smad4-interacting transcriptional co-activator; AltName: Full=Transcription factor SMIF;
FUNCTION: Necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7- methyl guanine cap structure from mRNA molecules, yielding a 5'- phosphorylated mRNA fragment and 7m-GDP. Contributes to the transactivation of target genes after stimulation by TGFB1.
SUBUNIT: Forms a complex with EDC3, DCP2, DDX6 and EDC4/HEDLS, within this complex directly interacts with EDC3. Binds DCP1B, UPF1 and SMAD4. Part of a cytoplasmic complex containing proteins involved in mRNA decay, including XRN1 and LSM1. Interacts with PNRC2. Interacts with DDX17 in an RNA-independent manner. Interacts with ZC3HAV1.
INTERACTION: Self; NbExp=4; IntAct=EBI-374238, EBI-374238; Q8IU60:DCP2; NbExp=6; IntAct=EBI-374238, EBI-521577; P26196:DDX6; NbExp=4; IntAct=EBI-374238, EBI-351257; Q92900:UPF1; NbExp=13; IntAct=EBI-374238, EBI-373471; P26651:ZFP36; NbExp=2; IntAct=EBI-374238, EBI-374248;
SUBCELLULAR LOCATION: Cytoplasm, P-body. Nucleus. Note=Co- localizes with NANOS3 in the processing bodies (By similarity). Predominantly cytoplasmic, in processing bodies (PB). Nuclear, after TGFB1 treatment. Translocation to the nucleus depends on interaction with SMAD4.
TISSUE SPECIFICITY: Detected in heart, brain, placenta, lung, skeletal muscle, liver, kidney and pancreas.
SIMILARITY: Belongs to the DCP1 family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DCP1A
CDC HuGE Published Literature: DCP1A
Positive Disease Associations: Angiography , Blood Pressure
Related Studies:
  1. Angiography
    Ramachandran S Vasan et al. BMC medical genetics 2007, Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study., BMC medical genetics. [PubMed 17903301]
    In hypothesis-generating GWAS of echocardiography, ETT and BA vascular function in a moderate-sized community-based sample, we identified several SNPs that are candidates for replication attempts and we provide a web-based GWAS resource for the research community.
  2. Blood Pressure
    Daniel Levy et al. BMC medical genetics 2007, Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness., BMC medical genetics. [PubMed 17903302]
    These results of genome-wide association testing for blood pressure and arterial stiffness phenotypes in an unselected community-based sample of adults may aid in the identification of the genetic basis of hypertension and arterial disease, help identify high risk individuals, and guide novel therapies for hypertension. Additional studies are needed to replicate any associations identified in these analyses.

-  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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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -43.60110-0.396 Picture PostScript Text
3' UTR -1239.094153-0.298 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
IPR010334 - DCP1

Pfam Domains:
PF06058 - Dcp1-like decapping family
PF16741 - mRNA-decapping enzyme C-terminus

SCOP Domains:
50729 - PH domain-like

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

2WX3
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9NPI6
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:0003729 mRNA binding
GO:0005515 protein binding
GO:0008047 enzyme activator activity
GO:0016787 hydrolase activity
GO:0019894 kinesin binding
GO:0030234 enzyme regulator activity
GO:0042802 identical protein binding

Biological Process:
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA
GO:0031087 deadenylation-independent decapping of nuclear-transcribed mRNA
GO:0043085 positive regulation of catalytic activity
GO:0043488 regulation of mRNA stability
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
GO:1903608 protein localization to cytoplasmic stress granule

Cellular Component:
GO:0000932 P-body
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0036464 cytoplasmic ribonucleoprotein granule


-  Descriptions from all associated GenBank mRNAs
  LF209983 - JP 2014500723-A/17486: Polycomb-Associated Non-Coding RNAs.
BC007439 - Homo sapiens DCP1 decapping enzyme homolog A (S. cerevisiae), mRNA (cDNA clone MGC:4252 IMAGE:3029175), complete cds.
AJ275986 - Homo sapiens mRNA for transcription factor (SMIF gene).
AB075507 - Homo sapiens neuroblastoma cDNA, clone:Nbla00360, full insert sequence.
AK295205 - Homo sapiens cDNA FLJ53884 complete cds, highly similar to mRNA decapping enzyme 1A (EC 3.-.-.-).
AK001969 - Homo sapiens cDNA FLJ11107 fis, clone PLACE1005803.
AY146651 - Homo sapiens decapping enzyme hDcp1a mRNA, complete cds.
KJ894264 - Synthetic construct Homo sapiens clone ccsbBroadEn_03658 DCP1A gene, encodes complete protein.
DQ893260 - Synthetic construct clone IMAGE:100005890; FLH195705.01X; RZPDo839F05152D DCP1 decapping enzyme homolog A (S. cerevisiae) (DCP1A) gene, encodes complete protein.
DQ896589 - Synthetic construct Homo sapiens clone IMAGE:100011049; FLH195701.01L; RZPDo839F05151D DCP1 decapping enzyme homolog A (S. cerevisiae) (DCP1A) gene, encodes complete protein.
AB590177 - Synthetic construct DNA, clone: pFN21AB9441, Homo sapiens DCP1A gene for DCP1 decapping enzyme homolog A, without stop codon, in Flexi system.
KU178716 - Homo sapiens DCP1 decapping enzyme-like protein A isoform 1 (DCP1A) mRNA, partial cds.
KU178717 - Homo sapiens DCP1 decapping enzyme-like protein A isoform 3 (DCP1A) mRNA, partial cds, alternatively spliced.
KU178718 - Homo sapiens DCP1 decapping enzyme-like protein A isoform 4 (DCP1A) mRNA, partial cds, alternatively spliced.
CU675659 - Synthetic construct Homo sapiens gateway clone IMAGE:100019905 5' read DCP1A mRNA.
MA445560 - JP 2018138019-A/17486: Polycomb-Associated Non-Coding RNAs.
AK025344 - Homo sapiens cDNA: FLJ21691 fis, clone COL09555.
LF333665 - JP 2014500723-A/141168: Polycomb-Associated Non-Coding RNAs.
BC016729 - Homo sapiens, clone IMAGE:4082361, mRNA.
DQ586254 - Homo sapiens piRNA piR-53366, complete sequence.
LF333664 - JP 2014500723-A/141167: Polycomb-Associated Non-Coding RNAs.
AK094470 - Homo sapiens cDNA FLJ37151 fis, clone BRACE2025710.
JD083010 - Sequence 64034 from Patent EP1572962.
JD387590 - Sequence 368614 from Patent EP1572962.
JD410306 - Sequence 391330 from Patent EP1572962.
JD313190 - Sequence 294214 from Patent EP1572962.
JD102869 - Sequence 83893 from Patent EP1572962.
LF333663 - JP 2014500723-A/141166: Polycomb-Associated Non-Coding RNAs.
LF333662 - JP 2014500723-A/141165: Polycomb-Associated Non-Coding RNAs.
LF333660 - JP 2014500723-A/141163: Polycomb-Associated Non-Coding RNAs.
LF333659 - JP 2014500723-A/141162: Polycomb-Associated Non-Coding RNAs.
LF333658 - JP 2014500723-A/141161: Polycomb-Associated Non-Coding RNAs.
LF333657 - JP 2014500723-A/141160: Polycomb-Associated Non-Coding RNAs.
LF333656 - JP 2014500723-A/141159: Polycomb-Associated Non-Coding RNAs.
LF333655 - JP 2014500723-A/141158: Polycomb-Associated Non-Coding RNAs.
MA569242 - JP 2018138019-A/141168: Polycomb-Associated Non-Coding RNAs.
MA569241 - JP 2018138019-A/141167: Polycomb-Associated Non-Coding RNAs.
MA569240 - JP 2018138019-A/141166: Polycomb-Associated Non-Coding RNAs.
MA569239 - JP 2018138019-A/141165: Polycomb-Associated Non-Coding RNAs.
MA569237 - JP 2018138019-A/141163: Polycomb-Associated Non-Coding RNAs.
MA569236 - JP 2018138019-A/141162: Polycomb-Associated Non-Coding RNAs.
MA569235 - JP 2018138019-A/141161: Polycomb-Associated Non-Coding RNAs.
MA569234 - JP 2018138019-A/141160: Polycomb-Associated Non-Coding RNAs.
MA569233 - JP 2018138019-A/141159: Polycomb-Associated Non-Coding RNAs.
MA569232 - JP 2018138019-A/141158: Polycomb-Associated Non-Coding RNAs.
LF333643 - JP 2014500723-A/141146: Polycomb-Associated Non-Coding RNAs.
JD226851 - Sequence 207875 from Patent EP1572962.
MA569220 - JP 2018138019-A/141146: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03018 - RNA degradation

Reactome (by CSHL, EBI, and GO)

Protein Q9NPI6 (Reactome details) participates in the following event(s):

R-HSA-450431 ZFP36 (TTP) recruits RNA degradation activities
R-HSA-450488 BRF1 Complex recruits RNA degradation activities
R-HSA-429860 DCP1-DCP2 complex decaps mRNA
R-HSA-450513 Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA
R-HSA-450385 Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-450531 Regulation of mRNA stability by proteins that bind AU-rich elements
R-HSA-927802 Nonsense-Mediated Decay (NMD)
R-HSA-430039 mRNA decay by 5' to 3' exoribonuclease
R-HSA-8953854 Metabolism of RNA
R-HSA-429914 Deadenylation-dependent mRNA decay

-  Other Names for This Gene
  Alternate Gene Symbols: DCP1A_HUMAN, NM_018403, NP_060873, Q9NPI6, SMIF
UCSC ID: uc021wzi.1
RefSeq Accession: NM_018403
Protein: Q9NPI6 (aka DCP1A_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018403.5
exon count: 10CDS single in 3' UTR: no RNA size: 6025
ORF size: 1749CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 3613.00frame shift in genome: no % Coverage: 99.78
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: 1
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.