Human Gene EDC3 (ENST00000315127.9_8) from GENCODE V47lift37
  Description: enhancer of mRNA decapping 3, transcript variant 3 (from RefSeq NM_025083.5)
Gencode Transcript: ENST00000315127.9_8
Gencode Gene: ENSG00000179151.13_12
Transcript (Including UTRs)
   Position: hg19 chr15:74,922,899-74,988,365 Size: 65,467 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr15:74,924,953-74,967,465 Size: 42,513 Coding Exon Count: 6 

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 (chr15:74,922,899-74,988,365)mRNA (may differ from genome)Protein (508 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: EDC3_HUMAN
DESCRIPTION: RecName: Full=Enhancer of mRNA-decapping protein 3; AltName: Full=LSM16 homolog; AltName: Full=YjeF N-terminal domain-containing protein 2; Short=YjeF_N2; Short=hYjeF_N2; AltName: Full=YjeF domain-containing protein 1;
FUNCTION: Binds single-stranded RNA. In the process of mRNA degradation, may play a role in mRNA decapping. May play a role in spermiogenesis and oogenesis.
SUBUNIT: Homodimer (via YjeF N-terminal domain). Forms a complex with DCP1A, DCP2, DDX6 and EDC4/HEDLS, within this complex directly interacts with DCP1A and DDX6. Interacts with ZFP36.
INTERACTION: Self; NbExp=2; IntAct=EBI-997311, EBI-997311; P26196:DDX6; NbExp=2; IntAct=EBI-997311, EBI-351257; P26651:ZFP36; NbExp=2; IntAct=EBI-997311, EBI-374248;
SUBCELLULAR LOCATION: Cytoplasm, P-body. Note=Processing bodies (PB).
TISSUE SPECIFICITY: Expressed in theca and granulosa cells in ovary, and in spermatids of the meiotic division part II and apical membrane of Sertoli cells in testis (at protein level). Also expressed in brain and mammary gland.
DOMAIN: The DFDF domain is unstructured by itself. It assumes a helical fold upon interaction with DDX6.
SIMILARITY: Belongs to the EDC3 family.
SIMILARITY: Contains 1 DFDF domain.
SIMILARITY: Contains 1 YjeF N-terminal domain.

-  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: EDC3
Diseases sorted by gene-association score: mental retardation, autosomal recessive 50* (1279), autosomal recessive non-syndromic intellectual disability* (97), intellectual disability (6), syringomyelia (6), gliosarcoma (1)
* = Manually curated disease association

-  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: 21.32 RPKM in Testis
Total median expression: 355.40 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 -72.50163-0.445 Picture PostScript Text
3' UTR -785.602054-0.382 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
IPR025762 - DFDF
IPR019050 - FDF_dom
IPR025609 - Lsm14_N
IPR004443 - YjeF_N_dom

Pfam Domains:
PF03853 - YjeF-related protein N-terminus
PF09532 - FDF domain
PF12701 - Scd6-like Sm domain
PF16598 - Linker region of enhancer of mRNA-decapping protein 3

SCOP Domains:
64153 - YjeF N-terminal domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2VC8 - X-ray MuPIT 2WAX - X-ray MuPIT 2WAY - X-ray MuPIT 3D3J - X-ray MuPIT 3D3K - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q96F86
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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 SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0042802 identical protein binding
GO:1990174 phosphodiesterase decapping endonuclease activity

Biological Process:
GO:0031087 deadenylation-independent decapping of nuclear-transcribed mRNA
GO:0033962 cytoplasmic mRNA processing body assembly
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic

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


-  Descriptions from all associated GenBank mRNAs
  BC011534 - Homo sapiens enhancer of mRNA decapping 3 homolog (S. cerevisiae), mRNA (cDNA clone MGC:9943 IMAGE:3875364), complete cds.
AK056339 - Homo sapiens cDNA FLJ31777 fis, clone NT2RI2008171, highly similar to YjeF domain-containing protein 1.
BC021271 - Homo sapiens enhancer of mRNA decapping 3 homolog (S. cerevisiae), mRNA (cDNA clone MGC:29460 IMAGE:4811016), complete cds.
AK024781 - Homo sapiens cDNA: FLJ21128 fis, clone CAS06258.
AK225099 - Homo sapiens mRNA for hypothetical protein LOC80153 variant, clone: CAS06258.
AF193058 - Homo sapiens PP844 mRNA, complete cds.
AL133447 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 30872.
JD163593 - Sequence 144617 from Patent EP1572962.
JD474164 - Sequence 455188 from Patent EP1572962.
JD206492 - Sequence 187516 from Patent EP1572962.
JD071453 - Sequence 52477 from Patent EP1572962.
JD174779 - Sequence 155803 from Patent EP1572962.
JD260376 - Sequence 241400 from Patent EP1572962.
JD358400 - Sequence 339424 from Patent EP1572962.
JD159277 - Sequence 140301 from Patent EP1572962.
JD486454 - Sequence 467478 from Patent EP1572962.
JD109180 - Sequence 90204 from Patent EP1572962.
JD068173 - Sequence 49197 from Patent EP1572962.
JD450035 - Sequence 431059 from Patent EP1572962.
JD283800 - Sequence 264824 from Patent EP1572962.
JD467984 - Sequence 449008 from Patent EP1572962.
JD070968 - Sequence 51992 from Patent EP1572962.
JD424876 - Sequence 405900 from Patent EP1572962.
JD206949 - Sequence 187973 from Patent EP1572962.
JD040154 - Sequence 21178 from Patent EP1572962.
JD449481 - Sequence 430505 from Patent EP1572962.
JD220946 - Sequence 201970 from Patent EP1572962.
JD088240 - Sequence 69264 from Patent EP1572962.
JD378117 - Sequence 359141 from Patent EP1572962.
JD546512 - Sequence 527536 from Patent EP1572962.
JD532519 - Sequence 513543 from Patent EP1572962.
JD269823 - Sequence 250847 from Patent EP1572962.
JD375761 - Sequence 356785 from Patent EP1572962.
JD051727 - Sequence 32751 from Patent EP1572962.
JD499427 - Sequence 480451 from Patent EP1572962.
JD399146 - Sequence 380170 from Patent EP1572962.
JD103206 - Sequence 84230 from Patent EP1572962.
JD493446 - Sequence 474470 from Patent EP1572962.
JD516340 - Sequence 497364 from Patent EP1572962.
JD527449 - Sequence 508473 from Patent EP1572962.
JD276636 - Sequence 257660 from Patent EP1572962.
JD317409 - Sequence 298433 from Patent EP1572962.
JD235246 - Sequence 216270 from Patent EP1572962.
JD297145 - Sequence 278169 from Patent EP1572962.
JD475122 - Sequence 456146 from Patent EP1572962.
JD074837 - Sequence 55861 from Patent EP1572962.
JD085821 - Sequence 66845 from Patent EP1572962.
JD510317 - Sequence 491341 from Patent EP1572962.
JD552960 - Sequence 533984 from Patent EP1572962.
JD499446 - Sequence 480470 from Patent EP1572962.
JD549566 - Sequence 530590 from Patent EP1572962.
JD561904 - Sequence 542928 from Patent EP1572962.
KJ894784 - Synthetic construct Homo sapiens clone ccsbBroadEn_04178 EDC3 gene, encodes complete protein.
JD527984 - Sequence 509008 from Patent EP1572962.
JD217774 - Sequence 198798 from Patent EP1572962.

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

Protein Q96F86 (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: B3KPH0, D3DW61, EDC3_HUMAN, ENST00000315127.1, ENST00000315127.2, ENST00000315127.3, ENST00000315127.4, ENST00000315127.5, ENST00000315127.6, ENST00000315127.7, ENST00000315127.8, LSM16, NM_025083, PP844, Q96F86, Q9H797, uc317pth.1, uc317pth.2, YJDC, YJEFN2
UCSC ID: ENST00000315127.9_8
RefSeq Accession: NM_025083.5
Protein: Q96F86 (aka EDC3_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.