Human Gene DCP1A (ENST00000610213.6_8) from GENCODE V47lift37
  Description: decapping mRNA 1A, transcript variant 1 (from RefSeq NM_018403.7)
Gencode Transcript: ENST00000610213.6_8
Gencode Gene: ENSG00000272886.6_14
Transcript (Including UTRs)
   Position: hg19 chr3:53,317,449-53,381,570 Size: 64,122 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 CommentsPrimersCTDGene Alleles
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:53,317,449-53,381,570)mRNA (may differ from genome)Protein (584 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  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.

-  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


-  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 -3.7026-0.142 Picture PostScript Text
3' UTR -1187.604149-0.286 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
56399 - ADP-ribosylation

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2WX3 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9NPI6
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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 orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGDEnsembl WormBase 
    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.
MA569220 - JP 2018138019-A/141146: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  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: B4DHN9, DCP1A_HUMAN, ENST00000610213.1, ENST00000610213.2, ENST00000610213.3, ENST00000610213.4, ENST00000610213.5, NM_018403, Q9NPI6, SMIF, U3KQM8, uc327mpx.1, uc327mpx.2
UCSC ID: ENST00000610213.6_8
RefSeq Accession: NM_018403.7
Protein: Q9NPI6 (aka DCP1A_HUMAN)

-  Gene Model Information
  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.