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EIF2D eukaryotic translation initiation factor 2D [ Homo sapiens (human) ]

Gene ID: 1939, updated on 3-Nov-2024

Summary

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Official Symbol
EIF2Dprovided by HGNC
Official Full Name
eukaryotic translation initiation factor 2Dprovided by HGNC
Primary source
HGNC:HGNC:6583
See related
Ensembl:ENSG00000143486 MIM:613709; AllianceGenome:HGNC:6583
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
LGTN; HCA56
Summary
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]
Annotation information
Note: The name of this locus was changed from ligatin to eukaryotic translation initiation factor 2D based on the gene characterization reported in PMID:20566627. [18 Aug 2011]
Expression
Ubiquitous expression in ovary (RPKM 12.2), thyroid (RPKM 9.1) and 25 other tissues See more
Orthologs
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Genomic context

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See EIF2D in Genome Data Viewer
Location:
1q32.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (206569146..206612465, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (205827369..205876640, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (206764974..206785818, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Ras association domain family member 5 Neighboring gene ribosomal protein L7a pseudogene 20 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:206717516-206718060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:206718061-206718603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1756 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1757 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:206730813-206731313 Neighboring gene uncharacterized LOC124904494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:206761431-206761931 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:206775241-206776440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2411 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1759 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1760 Neighboring gene DYRK3 antisense RNA 1 Neighboring gene dual specificity tyrosine phosphorylation regulated kinase 3 Neighboring gene uncharacterized LOC124904496 Neighboring gene Sharpr-MPRA regulatory region 10950 Neighboring gene uncharacterized LOC124904495

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Time dependent expression of the blood biomarkers EIF2D and TOX in patients with schizophrenia. Gilabert-Juan J, et al. Brain Behav Immun, 2019 Aug. PMID 31078689
  2. Translation of Sindbis Subgenomic mRNA is Independent of eIF2, eIF2A and eIF2D. Sanz MA, et al. Sci Rep, 2017 Feb 27. PMID 28240315, Free PMC Article
  3. The enterovirus genome can be translated in an IRES-independent manner that requires the initiation factors eIF2A/eIF2D. Kim H, et al. PLoS Biol, 2023 Jan. PMID 36689548, Free PMC Article
  4. A novel uORF-based regulatory mechanism controls translation of the human MDM2 and eIF2D mRNAs during stress. Akulich KA, et al. Biochimie, 2019 Feb. PMID 30419262
  5. Possible role of differentially expressing novel protein markers (ligatin and fibulin-7) in human aqueous humor and trabecular meshwork tissue in glaucoma progression. Basu K, et al. Cell Biol Int, 2019 Jul. PMID 30958601

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. To initiate or not to initiate: A critical assessment of eIF2A, eIF2D, and MCT-1.DENR to deliver initiator tRNA to ribosomes.
    Title: To initiate or not to initiate: A critical assessment of eIF2A, eIF2D, and MCT-1·DENR to deliver initiator tRNA to ribosomes.
  2. The enterovirus genome can be translated in an IRES-independent manner that requires the initiation factors eIF2A/eIF2D.
    Title: The enterovirus genome can be translated in an IRES-independent manner that requires the initiation factors eIF2A/eIF2D.
  3. We observed a positive correlation trend between EIF2D mRNA levels and years of schizophrenia (SZ) disease (p=0.0794; r=0.35). We found a trend of an increase in the expression levels of EIF2D (p=0.0634) in patients suffering from the disease more than 10years compared with the SZ patients from the other subgroup .
    Title: Time dependent expression of the blood biomarkers EIF2D and TOX in patients with schizophrenia.
  4. this is the first report which confirms the presence of ligatin and fibulin-7 in human aqueous humor, quantified their differential expression, and indicated the possibility of their involvement in the maintenance of the trabecular meshwork structure in glaucoma progression.
    Title: Possible role of differentially expressing novel protein markers (ligatin and fibulin-7) in human aqueous humor and trabecular meshwork tissue in glaucoma progression.
  5. a novel uORF-based regulatory mechanism that is employed under conditions of hyperosmotic stress by at least two human mRNAs, coding for translation reinitiation/recycling factor eIF2D and E3 ubiquitin ligase MDM2. This novel mode of translational control selectively downregulates their expression and requires as few as one uORF.
    Title: A novel uORF-based regulatory mechanism controls translation of the human MDM2 and eIF2D mRNAs during stress.
  6. Data suggest that neither eIF2A nor eIF2D are involved in the translation of this Sindbis virus subgenomic mRNA (sgmRNA) bearing non-AUG codons
    Title: Translation of Sindbis Subgenomic mRNA is Independent of eIF2, eIF2A and eIF2D.
  7. Reinitiation complexes involving initiation factors eIF2D, MCT-1, and DENR controls the translation of a large fraction of mammalian cellular mRNAs.
    Title: Structural and Functional Insights into Human Re-initiation Complexes.
Submit: New GeneRIF Correction

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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables signaling receptor activity TAS
Traceable Author Statement
more info
  
enables translation initiation factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables translation initiation factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in IRES-dependent viral translational initiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in formation of translation preinitiation complex IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in formation of translation preinitiation complex IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in intracellular protein transport TAS
Traceable Author Statement
more info
  
involved_in ribosome disassembly IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nuclear body IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
eukaryotic translation initiation factor 2D
Names
hepatocellular carcinoma-associated antigen 56
ligatin

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.

mRNA and Protein(s)

  1. NM_001201478.2 → NP_001188407.1  eukaryotic translation initiation factor 2D isoform 2

    See identical proteins and their annotated locations for NP_001188407.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two in-frame exons in the coding region. The resulting protein (isoform 2) is shorter, compared to isoform 1.
    Source sequence(s)
    AF262403, BC001585, DC399556
    Consensus CDS
    CCDS55680.1
    UniProtKB/Swiss-Prot
    P41214
    Related
    ENSP00000356081.3, ENST00000367114.7
    Conserved Domains (4) summary
    cd11608
    Location:366 → 450
    eIF2D_C; C-terminal domain of eIF2D and related proteins
    cd11610
    Location:6 → 81
    eIF2D_N; N-terminal domain of eIF2D and related proteins
    COG2016
    Location:7 → 170
    Tma20; Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ribosomal structure and biogenesis]
    cl00607
    Location:68 → 174
    PUA; PUA domain

  2. NM_006893.3 → NP_008824.2  eukaryotic translation initiation factor 2D isoform 1

    See identical proteins and their annotated locations for NP_008824.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC058905, BI465059
    Consensus CDS
    CCDS1465.1
    UniProtKB/Swiss-Prot
    P41214, Q5SY40, Q8IXV3, Q96DG3, Q96TG7, Q9NR27, Q9NSN0, Q9NV18, Q9NZ21
    Related
    ENSP00000271764.2, ENST00000271764.7
    Conserved Domains (3) summary
    cd11608
    Location:490 → 574
    eIF2D_C; C-terminal domain of eIF2D and related proteins
    pfam17832
    Location:2 → 90
    Pre-PUA; Pre-PUA-like domain
    cd21156
    Location:92 → 173
    PUA_eIF2d-like; PUA RNA-binding domain of eukaryotic translation initiation factor 2D and similar proteins

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    206569146..206612465 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509257.3 → XP_011507559.1  eukaryotic translation initiation factor 2D isoform X1

    Conserved Domains (4) summary
    cd11608
    Location:490 → 562
    eIF2D_C; C-terminal domain of eIF2D and related proteins
    cd11610
    Location:6 → 81
    eIF2D_N; N-terminal domain of eIF2D and related proteins
    COG2016
    Location:7 → 178
    Tma20; Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ribosomal structure and biogenesis]
    cl00607
    Location:68 → 174
    PUA; PUA domain

  2. XM_017000531.3 → XP_016856020.1  eukaryotic translation initiation factor 2D isoform X4

  3. XM_005277509.4 → XP_005277566.1  eukaryotic translation initiation factor 2D isoform X2

    Conserved Domains (4) summary
    cd11608
    Location:440 → 524
    eIF2D_C; C-terminal domain of eIF2D and related proteins
    cd11610
    Location:6 → 81
    eIF2D_N; N-terminal domain of eIF2D and related proteins
    COG2016
    Location:7 → 178
    Tma20; Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ribosomal structure and biogenesis]
    cl00607
    Location:68 → 174
    PUA; PUA domain

  4. XM_006711196.4 → XP_006711259.1  eukaryotic translation initiation factor 2D isoform X3

    Conserved Domains (1) summary
    cd11608
    Location:340 → 424
    eIF2D_C; C-terminal domain of eIF2D and related proteins

RNA

  1. XR_001737023.3 RNA Sequence

  2. XR_007095680.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    205827369..205876640 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334832.1 → XP_054190807.1  eukaryotic translation initiation factor 2D isoform X1

  2. XM_054334835.1 → XP_054190810.1  eukaryotic translation initiation factor 2D isoform X4

  3. XM_054334833.1 → XP_054190808.1  eukaryotic translation initiation factor 2D isoform X2

  4. XM_054334834.1 → XP_054190809.1  eukaryotic translation initiation factor 2D isoform X3

  5. XM_054334836.1 → XP_054190811.1  eukaryotic translation initiation factor 2D isoform X5

RNA

  1. XR_008485951.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P41214.3 GenPept UniProtKB/Swiss-Prot:P41214

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