Human Gene EDC4 (ENST00000358933.10_4) from GENCODE V47lift37
  Description: enhancer of mRNA decapping 4 (from RefSeq NM_014329.5)
Gencode Transcript: ENST00000358933.10_4
Gencode Gene: ENSG00000038358.15_8
Transcript (Including UTRs)
   Position: hg19 chr16:67,906,955-67,918,402 Size: 11,448 Total Exon Count: 29 Strand: +
Coding Region
   Position: hg19 chr16:67,907,165-67,918,051 Size: 10,887 Coding Exon Count: 29 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:67,906,955-67,918,402)mRNA (may differ from genome)Protein (1401 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: EDC4_HUMAN
DESCRIPTION: RecName: Full=Enhancer of mRNA-decapping protein 4; AltName: Full=Autoantigen Ge-1; AltName: Full=Autoantigen RCD-8; AltName: Full=Human enhancer of decapping large subunit; Short=Hedls;
FUNCTION: In the process of mRNA degradation, seems to play a role in mRNA decapping. Component of a complex containing DCP2 and DCP1A which functions in decapping of ARE-containing mRNAs. Promotes complex formation between DCP1A and DCP2. Enhances the catalytic activity of DCP2 (in vitro).
SUBUNIT: Part of a decapping complex consisting of DCP1A, DCP2, EDC3, EDC4 and probably DDX6. Part of a complex consisting of DCP1A, EDC3, EDC4 and DDX6. Part of a complex consisting of DCP1B, EDC3, EDC4 and DDX6. Interacts with DCP2.
INTERACTION: Q8IU60:DCP2; NbExp=4; IntAct=EBI-1006038, EBI-521577; P19525:EIF2AK2; NbExp=2; IntAct=EBI-1006038, EBI-640775;
SUBCELLULAR LOCATION: Cytoplasm, P-body. Nucleus.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the WD repeat EDC4 family.
SIMILARITY: Contains 4 WD repeats.
SEQUENCE CAUTION: Sequence=AAA21833.1; Type=Frameshift; Positions=1189; Sequence=AAB51444.1; Type=Erroneous initiation; Sequence=AAH53598.1; Type=Erroneous initiation;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: EDC4
Diseases sorted by gene-association score: griscelli syndrome, type 1 (1), focal hand dystonia (1)

-  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: 32.97 RPKM in Brain - Cerebellum
Total median expression: 757.82 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 -106.20210-0.506 Picture PostScript Text
3' UTR -135.80351-0.387 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
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat
PF16529 - WD40 region of Ge1, enhancer of mRNA-decapping protein

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
117289 - Nucleoporin domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Peptidase/esterase 'gauge' domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like

ModBase Predicted Comparative 3D Structure on Q6P2E9
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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 orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0008150 biological_process
GO:0031087 deadenylation-independent decapping of nuclear-transcribed mRNA
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay

Cellular Component:
GO:0000932 P-body
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0036464 cytoplasmic ribonucleoprotein granule


-  Descriptions from all associated GenBank mRNAs
  AK128582 - Homo sapiens cDNA FLJ46741 fis, clone TRACH3021373.
BC043616 - Homo sapiens enhancer of mRNA decapping 4, mRNA (cDNA clone MGC:50940 IMAGE:6065418), complete cds.
BC064567 - Homo sapiens enhancer of mRNA decapping 4, mRNA (cDNA clone MGC:70559 IMAGE:5575195), complete cds.
L26339 - Human autoantigen mRNA, complete cds.
AK291049 - Homo sapiens cDNA FLJ76807 complete cds, highly similar to Homo sapiens autoantigen (RCD-8), mRNA.
AK302563 - Homo sapiens cDNA FLJ53245 complete cds, highly similar to Homo sapiens autoantigen (RCD-8), mRNA.
BC053598 - Homo sapiens enhancer of mRNA decapping 4, mRNA (cDNA clone IMAGE:5741107), partial cds.
U17474 - Human autoantigen mRNA, complete cds.
U93216 - Homo sapiens clone DT1P1D1 mRNA, CAG repeat region.
AK125818 - Homo sapiens cDNA FLJ43830 fis, clone TESTI4004887, weakly similar to Homo sapiens autoantigen (RCD-8).
JD483244 - Sequence 464268 from Patent EP1572962.
JD221630 - Sequence 202654 from Patent EP1572962.
JD542082 - Sequence 523106 from Patent EP1572962.
JD450187 - Sequence 431211 from Patent EP1572962.
JD110668 - Sequence 91692 from Patent EP1572962.
JD195326 - Sequence 176350 from Patent EP1572962.
JD199129 - Sequence 180153 from Patent EP1572962.
JD322367 - Sequence 303391 from Patent EP1572962.
JD055745 - Sequence 36769 from Patent EP1572962.
JD418382 - Sequence 399406 from Patent EP1572962.
JD297690 - Sequence 278714 from Patent EP1572962.
JD554989 - Sequence 536013 from Patent EP1572962.
JD085553 - Sequence 66577 from Patent EP1572962.
JD071793 - Sequence 52817 from Patent EP1572962.
JD420483 - Sequence 401507 from Patent EP1572962.
JD098760 - Sequence 79784 from Patent EP1572962.
JD222210 - Sequence 203234 from Patent EP1572962.
JD413943 - Sequence 394967 from Patent EP1572962.
JD247844 - Sequence 228868 from Patent EP1572962.
JD416848 - Sequence 397872 from Patent EP1572962.
JD423006 - Sequence 404030 from Patent EP1572962.
JD223080 - Sequence 204104 from Patent EP1572962.
JD400014 - Sequence 381038 from Patent EP1572962.
JD177198 - Sequence 158222 from Patent EP1572962.
JD367983 - Sequence 349007 from Patent EP1572962.
JD248031 - Sequence 229055 from Patent EP1572962.

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

Protein Q6P2E9 (Reactome details) participates in the following event(s):

R-HSA-429860 DCP1-DCP2 complex decaps mRNA
R-HSA-430039 mRNA decay by 5' to 3' exoribonuclease
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A6NGM1, A8K4T4, EDC4_HUMAN, ENST00000358933.1, ENST00000358933.2, ENST00000358933.3, ENST00000358933.4, ENST00000358933.5, ENST00000358933.6, ENST00000358933.7, ENST00000358933.8, ENST00000358933.9, HEDLS, NM_014329, Q13025, Q13826, Q6P2E9, Q6ZR12, Q7Z6H7, uc318auu.1, uc318auu.2
UCSC ID: ENST00000358933.10_4
RefSeq Accession: NM_014329.5
Protein: Q6P2E9 (aka EDC4_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.