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

    Gene ID: 1939, updated on 28-Oct-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
    mouse all
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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. 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
    3. 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
    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 (42) 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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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