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EEF1DP3 (Eukaryotic translation elongation factor 1 delta pseudogene 3)

Written2019-06Luigi Cristiano
Aesthetic and medical biotechnologies research unit, Prestige, Terranuova Bracciolini, Italy. prestige.infomed@gmail.com - luigicristiano@libero.it

Abstract Eukaryotic translation elongation factor 1 delta pseudogene 3, alias EEF1DP3, is a pseudogene. This review collects the data about its DNA/RNA and on the diseases where it is involved.

Keywords EEF1DP3; eukaryotic translation elongation factor 1 delta pseudogene 3; ankylosing spondylitis; cancer; oncogenesis

(Note : for Links provided by Atlas : click)

Identity

Alias (NCBI)EEF1DP3-201
MGC149669
MGC149670
Putative Elongation Factor 1-Delta-Like Protein
Putative EF-1-Delta-Like Pseudogene 3 Protein
HGNC (Hugo) EEF1DP3
LocusID (NCBI) 196549
Atlas_Id 62732
Location 13q13.1  [Link to chromosome band 13q13]
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
EEF1DP3/BLVRBEEF1DP3/FRYEEF1DP3/CLDN10
EEF1DP3/N4BP2L1EEF1DP3/TEX26

DNA/RNA

 
  Figure. 1. EEF1DP3 gene. The figure shows the locus on chromosome 13 of the EEF1DP3 gene (reworked from https://www.ncbi.nlm.nih.gov/gene; http://grch37.ensembl.org; www.genecards.org)
Description EEF1DP3, alias eukaryotic translation elongation factor 1 delta pseudogene 3, is a pseudogene and it is located on chromosome 13 that is known to bring some putative oncogenes involved in cancer including the breast cancer type 2 (BRCA2) and the retinoblastoma (RB1) genes (Dunham et al., 2004). The related functional gene is the "eukaryotic translation elongation factor 1 delta" (EEF1D) that is located on chromosome 8 (8q24.3).
EEF1DP3 starts at 31,846,783 nt and ends at 31,959,584 from pter. It has a length of 112,802 bp and the current reference sequence is NC_000013.11 (Dunham et al., 2004). It is proximal to the 'relaxin family peptide receptor 2' (RXFP2) gene and FRY microtubule binding protein (FRY) gene. Curiously, closer to the genomic sequence of EEF1DP3 there is a promoter element that is located at -0.1 kb. This promoter element exercises its influence also on genes closer to EEF1DP3, i.e. FRY and RXFP2.
EEF1DP3 is classified as a transcribed unprocessed pseudogene. In the genomic sequence there are 4 non-coding exons.
Transcription EEF1DP3 pseudogene is transcribed and produces a long non-coding RNA (lncRNA) of 575 nt (Kimura et al., 2006) with a reference sequence NR_027062.1. It is still unknown if it is subjected to post-transcriptional modifications, such as 5'-capping, 3'-polyadenylation or splicing. However, other alternative transcripts are reported: EEF1DP3-001, a processed transcript of 1309 nt, EEF1DP3-002, a retained intron of 3283 nt and EEF1DP3-003, a transcribed unprocessed pseudogene of 782 nt (http://phase3browser.1000genomes.org). It seems that EEF1DP3 is overexpressed in heart, in particular in the left ventricle (https://www.genecards.org) and also expressed in normal trachea, liver, testis, kidney, bladder and brain (http://source-search.princeton.edu/). On the contrary, a low expression is detected in adrenal gland, colon and pituitary gland (https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3). It is known that lncRNAs, as pseudogenes as well as the others ncRNAs, may modulate the gene expression both at the transcriptional level, interacting with the promotor of parental gene o other genes, and post-transcriptional level, acting as microRNA decoys and so they may play key roles in cellular biological processes (Chan and Tay, 2018; Hu et al., 2018; Kovalenko and Patrushev, 2018). Nowadays, is still unknown the exact role of EEF1DP3 in healthy tissues.

Protein

Note EEF1DP3 seems to be able to produce a lncRNA but there are no proofs about the existence of a codified protein. However, is reported in some databases (UniProtKB; InterPro) a protein product also for this pseudogene, called "putative elongation factor 1-delta-like protein", alias EF1DL (accession number: Q658K8).
Until recently, it was believed that pseudogenes were not able to encode a protein, but recent transcriptomic and proteomic analyses seem to demonstrate not only the presence of pseudogene-derived transcripts but also of pseudogene-derived proteins (Chan and Tay, 2018; Kim et al., 2014; Djebali et al., 2012). Although it is still unclear if the protein EF1DL can be displayed or not, its presence should be not excluded. This protein should be 133 amino acids long and should have a molecular weight of 14,137 kDa and a theoretical pI of 5.94. Curiously, EF1DL shows 90% of identity with an uncharacterized protein (H2NJJ9_PONAB) of similar mass and length present in Sumatran orangutan (Pongo pygmaeus abelii) and linked to its chromosome 13.
Bioinformatic analysis of the comparison between EF1DL protein and eEF1D isoforms (pblast) revealed that there is an 85% of identity between EF1DL (1-90 aa) and a fragment of the long isoform of eEF1D (367-458 aa) and that is included a little portion of the second leucine-zipper domain of eEF1D. A similar result is obtained between EF1DL (1-90 aa) and the short form of eEF1D (1-92 aa) with the inclusion of a little portion of the unique leucine-zipper domain of the short form of eEF1D.
EF1DL could take a significant aspect in relation to cellular alterations observed in cancer that frequently juxtapose genomic elements next to strong promotor elements to produce unusual proteins that contribute to its malignant behavior and its aggressiveness. In fact, it is reported the involvement of EEF1DP3 in some genomic rearrangements and although there are no sufficient data yet to clarify these phenomena it cannot be excluded that EEF1DP3 can bring to a protein product after significative genomic alterations.

Mutations

Note Have been discovered a large number of mutations and alterations in the genomic sequence for EEF1DP3. The genomic alterations observed include copy number variations, translocations and interchromosomal translocations with the formation of novel fusion genes. However, there are no sufficient experimental data yet to understand the repercussions on cellular behavior of these fusion genes.
 
  Figure.2 Circos plot for fusion events involving EEF1DP3. The picture summarizes all fusion events concerning EEF1DP3 and its fusion partners (from https://fusionhub.persistent.co.in/search_genewise.html).

Implicated in

Note It is known that the aberrant expression of lncRNAs, as pseudogenes as well as the others ncRNAs, could have an important role in cancer development and progression (Chan and Tay, 2018; An et al., 2017). EEF1DP3 was found highly expressed in some healthy tissue types and also in many cancer types and this suggests that it could act as a positive regulator of gene expression, with high probability for its parental gene EEF1D and maybe also for other genes. In fact, it is known that the pseudogenes may act as positive regulators or negative regulators of gene expression (Hu et al., 2008). However, its role is still to be determined.
Name5' end3' endLoc1Loc2DescriptionTypeDiseaseOrganCodeRef.<
APC/EEF1DP3APCEEF1DP3 5q22.213q13.1t(5;13)(q22;q13) Translocation(?)---
EEF1DP3/BLVRBEEF1DP3BLVRB13q13.119q13.2t(13;19)(q13;q13) TranslocationSarcomaSoft tissueSARC-
EEF1DP3/CLDN10EEF1DP3CLDN1013q13.113q32.1t(13;13)(q13;q32) Fusion geneAdenocarcinomaBreastBRCAAlaei-Mahabadi et al., 2016
 EEF1DP3/FRY EEF1DP3 FRY13q13.113q13.1Readthrough transcriptionFusion geneAdenocarcinomaBreastBRCAKim et al., 2015
Burkitt lymphomaBloodBL-
AdenocarcinomaLungLUAD-
Malignant melanomaSkinSKCM-
Nonneoplastic epithelial disorder/lesion Adrenal gland-Babiceanu et al., 2016
Nonneoplastic epithelial disorder/lesionBladder-
-Bone marrow-
-Embryonic stem cells (cell line)ESC
Nonneoplastic mesenchymal disorder/lesionHeart-
Nonneoplastic epithelial disorder/lesionSkin-
Nonneoplastic epithelial disorder/lesion Stomach-
Nonneoplastic epithelial disorder/lesion Testis-
Nonneoplastic epithelial disorder/lesion Thyroid-
EEF1DP3/N4BP2L1EEF1DP3N4BP2L113q13.113q13.1t(13;13)(q13;q13) Fusion geneAdenocarcinomaBreastBRCA-
EEF1DP3/TEX26EEF1DP3TEX2613q13.113q12.3t(13;13)(q13;q12) Fusion geneAdenocarcinomaBreastBRCA-
EEF1DP3/TLK1EEF1DP3TLK113q13.1 2q31.1t(2;13)(q31;q13) TranslocationBurkitt lymphomaBloodBL-
NCL/EEF1DP3NCL EEF1DP3 13q13.113q13.1t(13;13)(q13;q13) Fusion gene(?)---

Table.1 EEF1DP3 rearrangements: translocations and fusion genes (reworked from https://cgap.nci.nih.gov/Chromosomes; http://atlasgeneticsoncology.org//Bands/13q13.html#REFERENCES; https://fusionhub.persistent.co.in/home.html; https://ccsm.uth.edu/FusionGDB/index.html)[ (?) ] unknown;  [ - ] no reference
  
Entity EEF1DP3/FRY read-through fusion
Note EEF1DP3/FRY is a recurrent read-through fusion transcript that is found in some types of nonneoplastic disorders and in some types of tumors such as malignant melanoma, Burkitt lymphoma, lung cancer and breast cancer (Babiceanu et al., 2016; Kim et al., 2015; Kim et al., 2011; https://fusionhub.persistent.co.in/home.html; https://ccsm.uth.edu/FusionGDB/index.html). The off-frame fusion of these two adjacent genes brings to the formation of a novel transcript formed by the 1 and 2 exons of EEF1DP3 joined with the exons from 2 to 61 of FRY. This results in an insertion of a stop codon in the nucleotidic sequence with an early truncation with loss-of-function of the FRY gene (Kim et al., 2015).
  
  
Entity Adrenal carcinoma
Note EEF1DP3 is reported to be highly expressed inadrenocortical carcinoma (ACC) and pheochromocytoma and other paraganglioma (PCPG) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3).
  
  
Entity Ankylosing Spondylitis
Note EEF1DP3 seems to be involved in some variants associated with ankylosing spondylitis (AS), a chronic and complex autoimmune disorder. In particular, it was found a loss in EEF1DP3 due to its deletion and this has been associated with an increased risk and predisposition for AS (Shahba et al., 2018; Yim et al., 2015; Jung et al., 2014).
  
  
Entity Brain and central nervous system (CNS) cancers
Note EEF1DP3 is reported to be highly expressed in brain lower grade glioma (LGG) (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3).
  
  
Entity Breast Cancer
Note Some fusion genes caused by intrachromosomal translocations were reported for EEFDP3 in breast cancer (Alaei-Mahabadi et al., 2016; Babiceanu et al., 2016; Kim et al., 2015; https://fusionhub.persistent.co.in/home.html).
Hybrid/Mutated Gene All fusion genes reported until now between EEF1DP3 and other partner genes are due to intrachromosomal translocations except the more known fusion gene EEF1DP3/FRY that is the result of a fusion between EEF1DP3 at 5'-end and "FRY microtubule binding protein" ( FRY) gene at 3'-end (Kim et al., 2015) and it is due to a readthrough transcription. This fusion gene was found also in nonneoplastic epithelial disorders or in healthy tissues, so its presence in the cell seems to be not only linked with neoplastic transformation. Its biological significance needs to be clarified as well as its role in the cells and in cancer cells.
Other fusion genes are reported such as EEF1DP3/CLDN10 that is originated by fusion of EEF1DP3 at 5'-end with "claudin 10" ( CLDN10) gene at 3'-end (Alaei-Mahabadi et al., 2016), EEF1DP3/N4BP2L1 that is originated by fusion of EEF1DP3 at 5'-end with "NEDD4 binding protein 2 like 1" ( N4BP2L1) gene at 3'-end and finally EEF1DP3/TEX26 that is originated by fusion of EEF1DP3 at 5'-end with "testis expressed 26" ( TEX26) gene at 3'-end. The significance of these genomic alterations is still poorly understood.
  
  
Entity Colorectal cancer
Note EEF1DP3 is reported to be highly expressed in rectum adenocarcinoma (READ) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3).
  
  
Entity Gynaecological cancers
Note EEF1DP3 is reported to be highly expressed in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) samples and also in uterine carcinosarcoma (UCS) (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3).
  
  
Entity Head and neck squamous cell carcinoma (HNSC)
Note EEF1DP3 is reported to be highly expressed in head and neck squamous cell carcinoma (HNSC) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3).
  
  
Entity Liver cancer
Note EEF1DP3 is reported to be highly expressed in liver hepatocellular carcinoma samples (LIHC) (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3).
  
  
Entity Lung cancer
Note EEF1DP3 is reported to be highly expressed in lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC) and mesothelioma (MESO) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3).
  
  
Entity Lymphoma, leukaemia and other blood cancers
Note EEF1DP3 is reported to be highly expressed in acute myeloid leukemia (AML) and lymphoid neoplasm diffuse large B-cell lymphoma (DLBC) (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3) and are reported the fusion gene EEF1DP3 /FRY and the translocation t(2;13)(q31;q13) EEF1DP3/TLK1 in Burkitt lymphoma (https://fusionhub.persistent.co.in/home.html).
Hybrid/Mutated Gene The t(2;13)(q31;q13) EEF1DP3/TLK1 and EEF1DP3/FRY fusion gene were found in Burkitt lymphoma. The first rearrangement is originated by the fusion of EEF1D gene at 5'-end with "tousled like kinase 1" (TLK1) gene at 3' end while the EEF1DP3/FRY fusion gene is originated by the fusion of EEF1D gene at 5'-end with "FRY microtubule binding protein" (FRY) gene at 3' end and it is probably due to readthrough transcription. In fact, EEF1D and FRY are two neighboring genes on the same chromosome. There are no data about the chimeric transcripts or proteins and the role of these genomic alterations are still unknown.
  
  
Entity Melanoma
Note EEF1DP3 is reported to be highly expressed in skin cutaneous melanoma (SKCM) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3).
  
  
Entity Neurodegenerative disorders
Note EEF1DP3 seems to be related to various neurodegenerative disorders as synucleinopathy and Parkinson's disease (https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3).
  
  
Entity Pancreatic cancer
Note EEF1DP3 is reported to be highly expressed in pancreatic adenocarcinoma (PAAD) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3).
  
  
Entity Prostate Cancer
Note Erho and colleagues found that EEF1DP3 is differentially expressed between normal prostate tissues and primary and metastatic prostate cancer samples (Erho et al., 2012) and other authors confirm this overexpression in prostate adenocarcinoma (PRAD) (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3).
  
  
Entity Sarcoma
Note EEF1DP3 is revealed to be highly expressed in sarcoma (SARC) samples (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3) and was reported the translocation t(13;19)(q13;q13) EEF1DP3/BLVRB (https://fusionhub.persistent.co.in/home.html).
Hybrid/Mutated Gene The t(13;19)(q13;q13) EEF1DP3/BLVRB was found in sarcoma. This rearrangement is originated by the fusion of EEF1D gene at 5'-end with 'biliverdin reductase B' (BLVRB) gene at 3' end. There are no data about the respective chimeric transcript or protein and the role of this genomic alteration is unknown.
  
  
Entity Urinary tract cancers
Note EEF1DP3 is reported to be highly expressed in bladder urothelial carcinoma (BLCA) samples and also in chromophobe renal cell carcinoma (KICH), clear cell renal cell carcinoma (KIRC) and papillary renal cell carcinoma (KIRP) (Cancer Genome Atlas Research Network et al., 2013; https://amp.pharm.mssm.edu/Harmonizome/gene/EEF1DP3).
  

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Citation

This paper should be referenced as such :
Luigi Cristiano
EEF1DP3 (Eukaryotic translation elongation factor 1 delta pseudogene 3)
Atlas Genet Cytogenet Oncol Haematol. 2020;24(4):164-169.
Free journal version : [ pdf ]   [ DOI ]

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(13;13)(q13;q13) EEF1DP3/FRY
t(13;13)(q13;q13) EEF1DP3/FRY

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 8 ]
  EEF1DP3/FRY (13q13)
EEF1DP3/FRY (13q13)
EEF1DP3/FRY (13q13)
EEF1DP3/FRY (13q13)
EEF1DP3/FRY (13q13)
EEF1DP3/FRY (13q13)
EEF1DP3/FRY (13q13)
EEF1DP3/FRY (13q13)

External links

Nomenclature
HGNC (Hugo)EEF1DP3   30486
Cards
AtlasEEF1DP3ID62732ch13q13
Entrez_Gene (NCBI)EEF1DP3    eukaryotic translation elongation factor 1 delta pseudogene 3
Aliases
GeneCards (Weizmann)EEF1DP3
Ensembl hg19 (Hinxton) [Gene_View]
Ensembl hg38 (Hinxton) [Gene_View]   [Sequence]  - [Contig_View]  EEF1DP3 [Vega]
TCGA cBioPortalEEF1DP3
AceView (NCBI)EEF1DP3
Genatlas (Paris)EEF1DP3
SOURCE (Princeton)EEF1DP3
Genetics Home Reference (NIH)EEF1DP3
Genomic and cartography
GoldenPath hg38 (UCSC)EEF1DP3  -  
GoldenPath hg19 (UCSC)EEF1DP3  -  
GoldenPathEEF1DP3 - [CytoView hg19]  EEF1DP3 - [CytoView hg38]
genome Data Viewer NCBIEEF1DP3 [Mapview hg19]  
Gene and transcription
Genbank (Entrez)AL833768 BC021729 BC125059 BC125060 DA657873
RefSeq transcript (Entrez)NM_145293
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)EEF1DP3
Gene ExpressionEEF1DP3 [ NCBI-GEO ]   EEF1DP3 [ EBI - ARRAY_EXPRESS ]   EEF1DP3 [ SEEK ]   EEF1DP3 [ MEM ]
Gene Expression Viewer (FireBrowse)EEF1DP3 [ Firebrowse - Broad ]
GenevisibleExpression of EEF1DP3 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)196549
GTEX Portal (Tissue expression)EEF1DP3
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ658K8   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ658K8  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ658K8
Splice isoforms : SwissVarQ658K8
PhosPhoSitePlusQ658K8
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)EEF1DP3
Blocks (Seattle)EEF1DP3
SuperfamilyQ658K8
Peptide AtlasQ658K8
HPRD08314
IPIIPI00103194   
Protein Interaction databases
DIP (DOE-UCLA)Q658K8
IntAct (EBI)Q658K8
BioGRIDEEF1DP3
STRING (EMBL)EEF1DP3
ZODIACEEF1DP3
Ontologies - Pathways
QuickGOQ658K8
Ontology : AmiGO
Ontology : EGO-EBI
NDEx NetworkEEF1DP3
Atlas of Cancer Signalling NetworkEEF1DP3
Wikipedia pathwaysEEF1DP3
Orthology - Evolution
OrthoDB196549
Phylogenetic Trees/Animal Genes : TreeFamEEF1DP3
HOGENOMQ658K8
Homologs : HomoloGeneEEF1DP3
Homology/Alignments : Family Browser (UCSC)EEF1DP3
Gene fusions - Rearrangements
Fusion : Fusion_HubAPC--EEF1DP3    EEF1DP3--CLDN10    EEF1DP3--FRY    EEF1DP3--TLK1    NCL--EEF1DP3   
Fusion : QuiverEEF1DP3
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerEEF1DP3 [hg38]
dbVarEEF1DP3
ClinVarEEF1DP3
MonarchEEF1DP3
1000_GenomesEEF1DP3 
Exome Variant ServerEEF1DP3
Varsome BrowserEEF1DP3
Genomic Variants (DGV)EEF1DP3 [DGVbeta]
DECIPHEREEF1DP3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisEEF1DP3 
Mutations
ICGC Data PortalEEF1DP3 
TCGA Data PortalEEF1DP3 
Broad Tumor PortalEEF1DP3
OASIS PortalEEF1DP3 [ Somatic mutations - Copy number]
Mutations and Diseases : HGMDEEF1DP3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch EEF1DP3
DgiDB (Drug Gene Interaction Database)EEF1DP3
DoCM (Curated mutations)EEF1DP3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)EEF1DP3 (select a term)
intoGenEEF1DP3
Cancer3DEEF1DP3(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM
Orphanet
DisGeNETEEF1DP3
MedgenEEF1DP3
Genetic Testing Registry EEF1DP3
NextProtQ658K8 [Medical]
GENETestsEEF1DP3
Target ValidationEEF1DP3
Huge Navigator EEF1DP3 [HugePedia]
ClinGenEEF1DP3
Clinical trials, drugs, therapy
MyCancerGenomeEEF1DP3
Protein Interactions : CTD
PharosQ658K8
Clinical trialEEF1DP3
Miscellaneous
canSAR (ICR)EEF1DP3 (select the gene name)
HarmonizomeEEF1DP3
DataMed IndexEEF1DP3
Probes
Litterature
PubMed4 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXEEF1DP3
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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