EIF2D Gene (Protein Coding)

Eukaryotic Translation Initiation Factor 2D

GC01M206571
GIFtS:
33
This gene encodes a translation initiation factor involved in the recruitment and delivery of aminoacyl-tRNAs to the P-site of the eukaryotic ribosome in a GTP-independent manner. This gene was previously referred to as ligatin, but is now known to localize to the cytoplasm and localize and function with translation factors. Multiple transcript variants encoding different isofo... See more...

Aliases for EIF2D Gene

Aliases for EIF2D Gene

  • Eukaryotic Translation Initiation Factor 2D 2 3 4 5
  • LGTN 2 3 4
  • Hepatocellular Carcinoma-Associated Antigen 56 3 4
  • Ligatin 3 4
  • HCA56 3 4
  • EIF2D 5
  • EIF2d 4

External Ids for EIF2D Gene

Previous GeneCards Identifiers for EIF2D Gene

  • GC01M206745

Summaries for EIF2D Gene

Entrez Gene Summary for EIF2D Gene

  • This gene encodes a translation initiation factor involved in the recruitment and delivery of aminoacyl-tRNAs to the P-site of the eukaryotic ribosome in a GTP-independent manner. This gene was previously referred to as ligatin, but is now known to localize to the cytoplasm and localize and function with translation factors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2011]

GeneCards Summary for EIF2D Gene

EIF2D (Eukaryotic Translation Initiation Factor 2D) is a Protein Coding gene. Diseases associated with EIF2D include Hepatocellular Carcinoma. Gene Ontology (GO) annotations related to this gene include RNA binding and translation initiation factor activity.

UniProtKB/Swiss-Prot Summary for EIF2D Gene

  • Translation initiation factor that is able to deliver tRNA to the P-site of the eukaryotic ribosome in a GTP-independent manner. The binding of Met-tRNA(I) occurs after the AUG codon finds its position in the P-site of 40S ribosomes, the situation that takes place during initiation complex formation on some specific RNAs. Its activity in tRNA binding with 40S subunits does not require the presence of the aminoacyl moiety. Possesses the unique ability to deliver non-Met (elongator) tRNAs into the P-site of the 40S subunit. In addition to its role in initiation, can promote release of deacylated tRNA and mRNA from recycled 40S subunits following ABCE1-mediated dissociation of post-termination ribosomal complexes into subunits.

Gene Wiki entry for EIF2D Gene

Additional gene information for EIF2D Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for EIF2D Gene

Genomics for EIF2D Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for EIF2D Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EIF2D on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for EIF2D

Genomic Locations for EIF2D Gene

Genomic Locations for EIF2D Gene
chr1:206,571,292-206,612,551
(GRCh38/hg38)
Size:
41,260 bases
Orientation:
Minus strand
chr1:206,744,620-206,785,904
(GRCh37/hg19)
Size:
41,285 bases
Orientation:
Minus strand

Genomic View for EIF2D Gene

Genes around EIF2D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EIF2D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EIF2D Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for EIF2D Gene

Proteins for EIF2D Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for EIF2D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P41214-EIF2D_HUMAN
    Recommended name:
    Eukaryotic translation initiation factor 2D
    Protein Accession:
    P41214
    Secondary Accessions:
    • Q5SY40
    • Q8IXV3
    • Q96DG3
    • Q96TG7
    • Q9NR27
    • Q9NSN0
    • Q9NV18
    • Q9NZ21

    Protein attributes for EIF2D Gene

    Size:
    584 amino acids
    Molecular mass:
    64706 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for EIF2D Gene

    Alternative splice isoforms for EIF2D Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EIF2D Gene

Protein Expression for EIF2D Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for EIF2D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for EIF2D Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for EIF2D
  • Santa Cruz Biotechnology (SCBT) Antibodies for EIF2D

No data available for DME Specific Peptides for EIF2D Gene

Domains & Families for EIF2D Gene

Gene Families for EIF2D Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for EIF2D Gene

InterPro:
Blocks:
  • Translation initiation factor SUI1
ProtoNet:

Suggested Antigen Peptide Sequences for EIF2D Gene

GenScript: Design optimal peptide antigens:
  • Ligatin (EIF2D_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P41214

UniProtKB/Swiss-Prot:

EIF2D_HUMAN :
  • Belongs to the eIF2D family.
Family:
  • Belongs to the eIF2D family.
genes like me logo Genes that share domains with EIF2D: view

Function for EIF2D Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for EIF2D Gene

UniProtKB/Swiss-Prot Function:
Translation initiation factor that is able to deliver tRNA to the P-site of the eukaryotic ribosome in a GTP-independent manner. The binding of Met-tRNA(I) occurs after the AUG codon finds its position in the P-site of 40S ribosomes, the situation that takes place during initiation complex formation on some specific RNAs. Its activity in tRNA binding with 40S subunits does not require the presence of the aminoacyl moiety. Possesses the unique ability to deliver non-Met (elongator) tRNAs into the P-site of the 40S subunit. In addition to its role in initiation, can promote release of deacylated tRNA and mRNA from recycled 40S subunits following ABCE1-mediated dissociation of post-termination ribosomal complexes into subunits.

Phenotypes From GWAS Catalog for EIF2D Gene

Gene Ontology (GO) - Molecular Function for EIF2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0003743 translation initiation factor activity IEA,IDA 20566627
GO:0038023 signaling receptor activity TAS --
genes like me logo Genes that share ontologies with EIF2D: view
genes like me logo Genes that share phenotypes with EIF2D: view

Animal Model Products

CRISPR Products

miRNA for EIF2D Gene

miRTarBase miRNAs that target EIF2D

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EIF2D

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for EIF2D Gene

Localization for EIF2D Gene

Subcellular locations from UniProtKB/Swiss-Prot for EIF2D Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for EIF2D gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nuclear bodies (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for EIF2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm TAS,IDA 20566627
GO:0005829 cytosol IDA --
GO:0016604 nuclear body IDA --
GO:0022627 colocalizes_with cytosolic small ribosomal subunit IBA,IDA 20713520
genes like me logo Genes that share ontologies with EIF2D: view

Pathways & Interactions for EIF2D Gene

PathCards logo

SuperPathways for EIF2D Gene

No Data Available

Gene Ontology (GO) - Biological Process for EIF2D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001731 formation of translation preinitiation complex IEA,IDA 20713520
GO:0006412 translation IEA --
GO:0006413 translational initiation IEA --
GO:0006886 intracellular protein transport TAS --
GO:0032790 ribosome disassembly IDA 20713520
genes like me logo Genes that share ontologies with EIF2D: view

No data available for Pathways by source and SIGNOR curated interactions for EIF2D Gene

Drugs & Compounds for EIF2D Gene

Products:

  1. Drug

(1) Drugs for EIF2D Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for EIF2D Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with EIF2D: view

Transcripts for EIF2D Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for EIF2D Gene

2 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for EIF2D

Alternative Splicing Database (ASD) splice patterns (SP) for EIF2D Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17
SP1: - - - -
SP2: - - - - - -
SP3: - - - - - - -
SP4: - - -
SP5: - - - -
SP6: - - -
SP7: - - -
SP8:
SP9:

Relevant External Links for EIF2D Gene

GeneLoc Exon Structure for
EIF2D

Expression for EIF2D Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for EIF2D Gene

mRNA expression in normal human tissues for EIF2D Gene
mRNA expression by GTEx for EIF2D GenemRNA expression by BioGPS for EIF2D Gene

Protein differential expression in normal tissues from HIPED for EIF2D Gene

This gene is overexpressed in Breast (24.6) and Esophagus (9.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for EIF2D Gene



Protein tissue co-expression partners for EIF2D Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for EIF2D

SOURCE GeneReport for Unigene cluster for EIF2D Gene:

Hs.497581

Evidence on tissue expression from TISSUES for EIF2D Gene

  • Nervous system(3.1)
  • Blood(2.1)
  • Skin(2)
genes like me logo Genes that share expression patterns with EIF2D: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for EIF2D Gene

Orthologs for EIF2D Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for EIF2D Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia EIF2D 30 31
  • 99.6 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia EIF2D 30 31
  • 89.06 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia EIF2D 30 31
  • 89.02 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Eif2d 30
  • 85.91 (n)
Mouse
(Mus musculus)
 Mammalia Eif2d 30 17 31
  • 85.61 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia EIF2D 31
  • 69 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia EIF2D 31
  • 59 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves EIF2D 30 31
  • 66.9 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia EIF2D 31
  • 59 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia eif2d 30
  • 62.41 (n)
MGC76058 30
Zebrafish
(Danio rerio)
 Actinopterygii eif2d 30 31
  • 60.71 (n)
 OneToOne
zgc63669 30
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.13929 30
Fruit Fly
(Drosophila melanogaster)
 Insecta ligatin 30 31
  • 47.88 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP011804 30
  • 45.57 (n)
Worm
(Caenorhabditis elegans)
 Secernentea CELE_C25H3.4 30
  • 44.47 (n)
C25H3.4 31
  • 30 (a)
 OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes TMA64 31 33
  • 24 (a)
 OneToOne
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons AT1G71350 30
  • 46.21 (n)
Rice
(Oryza sativa)
 Liliopsida Os02g0557600 30
  • 44.72 (n)
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 36 (a)
 OneToOne
Species where no ortholog for EIF2D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for EIF2D Gene

ENSEMBL:
Gene Tree for EIF2D (if available)
TreeFam:
Gene Tree for EIF2D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for EIF2D: view image

Paralogs for EIF2D Gene

No data available for Paralogs for EIF2D Gene

Variants for EIF2D Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for EIF2D Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs35252702 - p.Thr210Ile

Additional dbSNP identifiers (rs#s) for EIF2D Gene

Variation tolerance for EIF2D Gene

Residual Variation Intolerance Score: 20.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.57; 56.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EIF2D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
EIF2D

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for EIF2D Gene

Disorders for EIF2D Gene

MalaCards: The human disease database

(1) MalaCards diseases for EIF2D Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
hepatocellular carcinoma
  • hcc
- elite association - COSMIC cancer census association via MalaCards
Search EIF2D in MalaCards View complete list of genes associated with diseases

Additional Disease Information for EIF2D

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with EIF2D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for EIF2D Gene

Publications for EIF2D Gene

  1. GTP-independent tRNA delivery to the ribosomal P-site by a novel eukaryotic translation factor. (PMID: 20566627) Dmitriev SE … Shatsky IN (The Journal of biological chemistry 2010) 2 3 4
  2. Activities of Ligatin and MCT-1/DENR in eukaryotic translation initiation and ribosomal recycling. (PMID: 20713520) Skabkin MA … Pestova TV (Genes & development 2010) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Large scale identification of human hepatocellular carcinoma-associated antigens by autoantibodies. (PMID: 12097419) Wang Y … Chen WF (Journal of immunology (Baltimore, Md. : 1950) 2002) 3 4
  5. ATG5 is required for B cell polarization and presentation of particulate antigens. (PMID: 30196744) Arbogast F … Gros F (Autophagy 2019) 3

ExternalLinks

View latest publications for EIF2D gene in Mastermind

Products for EIF2D Gene

Sources for EIF2D Gene