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    DCP2 decapping mRNA 2 [ Homo sapiens (human) ]

    Gene ID: 167227, updated on 10-Dec-2024

    Summary

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    Official Symbol
    DCP2provided by HGNC
    Official Full Name
    decapping mRNA 2provided by HGNC
    Primary source
    HGNC:HGNC:24452
    See related
    Ensembl:ENSG00000172795 MIM:609844; AllianceGenome:HGNC:24452
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NUDT20
    Summary
    The protein encoded by this gene is a key component of an mRNA-decapping complex required for degradation of mRNAs, both in normal mRNA turnover, and in nonsense-mediated mRNA decay (NMD). It removes the 7-methyl guanine cap structure from mRNA, prior to its degradation from the 5' end. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Jun 2011]
    Expression
    Ubiquitous expression in lymph node (RPKM 7.7), placenta (RPKM 6.8) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DCP2 in Genome Data Viewer
    Location:
    5q22.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (112976798..113022195)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (113487331..113532745)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (112312495..112357892)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22913 Neighboring gene MPRA-validated peak5421 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16241 Neighboring gene Sharpr-MPRA regulatory region 12983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22914 Neighboring gene uncharacterized LOC105379126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22916 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:112312161-112312920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:112317139-112317674 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:112369970-112370528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:112379403-112379941 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:112404856-112405632 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:112405633-112406407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:112409037-112409538 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:112416605-112417526 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:112417522-112418721 Neighboring gene MCC regulator of WNT signaling pathway Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:112454694-112455201 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:112502443-112503642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:112538908-112539449 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:112571092-112572066 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:112580307-112581082 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16242 Neighboring gene uncharacterized LOC124901045 Neighboring gene MPRA-validated peak5422 silencer Neighboring gene uncharacterized LOC107986366 Neighboring gene testis specific serine kinase 1B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Competition between Decapping Complex Formation and Ubiquitin-Mediated Proteasomal Degradation Controls Human Dcp2 Decapping Activity. Erickson SL, et al. Mol Cell Biol, 2015 Jun. PMID 25870104, Free PMC Article
    2. Decapping enzyme 2 is a novel immune-related biomarker that predicts poor prognosis in glioma. Mei Y, et al. Biotechnol Genet Eng Rev, 2024 Dec. PMID 37191010
    3. The hDcp2 protein is a mammalian mRNA decapping enzyme. Wang Z, et al. Proc Natl Acad Sci U S A, 2002 Oct 1. PMID 12218187, Free PMC Article
    4. Transcript-specific decapping and regulated stability by the human Dcp2 decapping protein. Li Y, et al. Mol Cell Biol, 2008 Feb. PMID 18039849, Free PMC Article
    5. Visualizing an mRNA destruction line. Grzymski EC. Nat Struct Biol, 2003 Jun. PMID 12768200

    See all (72) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Decapping enzyme 2 is a novel immune-related biomarker that predicts poor prognosis in glioma.
      Title: Decapping enzyme 2 is a novel immune-related biomarker that predicts poor prognosis in glioma.
    2. MOV10 recruits DCP2 to decap human LINE-1 RNA by forming large cytoplasmic granules with phase separation properties.
      Title: MOV10 recruits DCP2 to decap human LINE-1 RNA by forming large cytoplasmic granules with phase separation properties.
    3. Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA.
      Title: Intrinsically disordered regions of tristetraprolin and DCP2 directly interact to mediate decay of ARE-mRNA.
    4. Human MARF1 is an endoribonuclease that interacts with the DCP1:DCP2 decapping complex and degrades target mRNAs.
      Title: Human MARF1 is an endoribonuclease that interacts with the DCP1:2 decapping complex and degrades target mRNAs.
    5. Human Dcp2 levels and activity are controlled by a competition between decapping complex assembly and Dcp2 degradation.
      Title: Competition between Decapping Complex Formation and Ubiquitin-Mediated Proteasomal Degradation Controls Human Dcp2 Decapping Activity.
    6. The data indicates that DCP2 activation by DCP1 occurs preferentially on the EDC4 scaffold, which may serve to couple DCP2 activation by DCP1 with 5'-to-3' mRNA degradation by XRN1 in human cells.
      Title: The activation of the decapping enzyme DCP2 by DCP1 occurs on the EDC4 scaffold and involves a conserved loop in DCP1.
    7. Data show that Y14 interacts directly with the decapping factor Dcp2 and the 5' cap structure of mRNAs via different but overlapping domains.
      Title: The RNA-binding protein Y14 inhibits mRNA decapping and modulates processing body formation.
    8. PNRC2 acts in synergy with Dcp1a to stimulate the decapping activity of Dcp2 by bridging the interaction between Dcp1a and Dcp2.
      Title: Structural basis of the PNRC2-mediated link between mrna surveillance and decapping.
    9. Like Dcp2, Nudt16 also regulates the stability of a subset of mRNAs including a member of the motin family of proteins involved in angiogenesis.
      Title: Multiple mRNA decapping enzymes in mammalian cells.
    10. These data support the novel notion of the association between Ro52 with hDCP2 protein in cytoplasmic p-bodies, playing a role in mRNA metabolism in response to cellular stimulation.
      Title: SSA/Ro52 autoantigen interacts with Dcp2 to enhance its decapping activity.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of DCP2 decapping enzyme homolog (S. cerevisiae, DCP2) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag The efficiency of incorporation of Mov10, A3G, and A3F into viral particles, which contains both HIV-1 Gag and genomic RNA, is much higher than that of the other P-body proteins AGO2, DCP1a, DCP2, and DDX6 PubMed
    gag DCP2 is associated with HIV-1 Gag and ABCE1 by immunoprecipitation analysis PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ33245

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 5'-3' RNA exonuclease activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables RNA exonuclease activity, producing 5'-phosphomonoesters TAS
    Traceable Author Statement
    more info
    		  
    enables manganese ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables telomerase RNA binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in deadenylation-dependent decapping of nuclear-transcribed mRNA IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in histone mRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mRNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of telomere maintenance via telomerase IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay TAS
    Traceable Author Statement
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of mRNA stability IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of telomerase RNA localization to Cajal body IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in P-body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of RISC complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cell junction IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasmic ribonucleoprotein granule IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    m7GpppN-mRNA hydrolase
    Names
    DCP2 decapping enzyme homolog
    hDpc
    mRNA-decapping enzyme 2
    nudix (nucleoside diphosphate linked moiety X)-type motif 20
    NP_001229306.1
    NP_689837.2
    XP_047272821.1
    XP_047272822.1
    XP_047272823.1
    XP_054207882.1
    XP_054207883.1
    XP_054207884.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_029929.2 RefSeqGene

      Range
      5089..50486
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001242377.2 → NP_001229306.1  m7GpppN-mRNA hydrolase isoform 2

      See identical proteins and their annotated locations for NP_001229306.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame coding exon compared to variant 1. This results in a shorter isoform (2) missing an internal protein segment compared to isoform 1.
      Source sequence(s)
      AA837315, AC008536, AL135390, AY135173, AY146650, BC045596, BC064593, BX537716, BX648838, CF994730, DB146225
      Consensus CDS
      CCDS56377.1
      UniProtKB/Swiss-Prot
      Q8IU60
      Related
      ENSP00000425770.1, ENST00000515408.5
      Conserved Domains (2) summary
      cd03672
      Location:97 → 246
      Dcp2p; mRNA decapping enzyme 2 (Dcp2p), the catalytic subunit, and Dcp1p are the two components of the decapping enzyme complex. Decapping is a key step in both general and nonsense-mediated 5'->3' mRNA-decay pathways. Dcp2p contains an all-alpha helical ...
      pfam05026
      Location:12 → 93
      DCP2; Dcp2, box A domain

    2. NM_152624.6 → NP_689837.2  m7GpppN-mRNA hydrolase isoform 1

      See identical proteins and their annotated locations for NP_689837.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript, and encodes the longer isoform (1).
      Source sequence(s)
      AA837315, AC008536, AK090564, AL135390, AY135173, AY146650, BC045596, BX537716, BX648838, CF994730, DB146225
      Consensus CDS
      CCDS34210.1
      UniProtKB/Swiss-Prot
      C9J778, Q6P2D4, Q7Z5W5, Q8IU60, Q8NBG5
      Related
      ENSP00000373715.2, ENST00000389063.3
      Conserved Domains (2) summary
      cd03672
      Location:97 → 246
      Dcp2p; mRNA decapping enzyme 2 (Dcp2p), the catalytic subunit, and Dcp1p are the two components of the decapping enzyme complex. Decapping is a key step in both general and nonsense-mediated 5'->3' mRNA-decay pathways. Dcp2p contains an all-alpha helical ...
      pfam05026
      Location:12 → 93
      DCP2; Dcp2, box A domain

    RNA

    1. NR_038352.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two consecutive exons compared to variant 1. It is represented as non-coding because the use of the 5'-most translational start codon (with a strong Kozak signal), as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA837315, AC008536, AK090564, AL135390, AY135173, AY146650, BC045596, BX537716, BX648838, CF994730, DB146225

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      112976798..113022195
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416866.1 → XP_047272822.1  m7GpppN-mRNA hydrolase isoform X2

    2. XM_047416867.1 → XP_047272823.1  m7GpppN-mRNA hydrolase isoform X3

    3. XM_047416865.1 → XP_047272821.1  m7GpppN-mRNA hydrolase isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      113487331..113532745
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351908.1 → XP_054207883.1  m7GpppN-mRNA hydrolase isoform X2

    2. XM_054351909.1 → XP_054207884.1  m7GpppN-mRNA hydrolase isoform X3

    3. XM_054351907.1 → XP_054207882.1  m7GpppN-mRNA hydrolase isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IU60.3 GenPept UniProtKB/Swiss-Prot:Q8IU60

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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