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    Eif2d eukaryotic translation initiation factor 2D [ Rattus norvegicus (Norway rat) ]

    Gene ID: 498225, updated on 3-Apr-2024

    Summary

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    Official Symbol
    Eif2dprovided by RGD
    Official Full Name
    eukaryotic translation initiation factor 2Dprovided by RGD
    Primary source
    RGD:1561765
    See related
    Ensembl:ENSRNOG00000004910 AllianceGenome:RGD:1561765
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Lgtn
    Summary
    Predicted to enable translation initiation factor activity. Predicted to be involved in IRES-dependent viral translational initiation; formation of translation preinitiation complex; and ribosome disassembly. Predicted to be located in cytosol and nuclear body. Predicted to be part of cytosolic small ribosomal subunit. Orthologous to human EIF2D (eukaryotic translation initiation factor 2D). [provided by Alliance of Genome Resources, Apr 2022]
    Annotation information
    Note: The name of this locus was changed from ligatin to eukaryotic translation initiation factor 2D based on the gene characterization of the human ortholog reported in PMID:20566627. [18 Aug 2011]
    Expression
    Biased expression in Thymus (RPKM 172.6), Spleen (RPKM 147.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Eif2d in Genome Data Viewer
    Location:
    13q13
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (45168161..45189362)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (42615901..42637107)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (47935138..47958459)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene MAPK activated protein kinase 2 Neighboring gene uncharacterized LOC134481555 Neighboring gene uncharacterized LOC134481556 Neighboring gene dual specificity tyrosine phosphorylation regulated kinase 3 Neighboring gene Ras association domain family member 5 Neighboring gene uncharacterized LOC134481557 Neighboring gene inhibitor of nuclear factor kappa B kinase subunit epsilon

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. GTP-independent tRNA delivery to the ribosomal P-site by a novel eukaryotic translation factor. Dmitriev SE, et al. J Biol Chem, 2010 Aug 27. PMID 20566627, Free PMC Article
    2. Activities of Ligatin and MCT-1/DENR in eukaryotic translation initiation and ribosomal recycling. Skabkin MA, et al. Genes Dev, 2010 Aug 15. PMID 20713520, Free PMC Article
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables translation initiation factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables translation initiation factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables translation initiation factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables translation initiation factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in IRES-dependent viral translational initiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in formation of translation preinitiation complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in formation of translation preinitiation complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in formation of translation preinitiation complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ribosome disassembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of cytosolic small ribosomal subunit ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    eukaryotic translation initiation factor 2D
    Names
    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_001017489.1 → NP_001017489.1  eukaryotic translation initiation factor 2D

      See identical proteins and their annotated locations for NP_001017489.1

      Status: PROVISIONAL

      Source sequence(s)
      BC087701
      UniProtKB/Swiss-Prot
      Q5PPG7
      UniProtKB/TrEMBL
      A0A8I6AJ85, A6IC14
      Related
      ENSRNOP00000006768.2, ENSRNOT00000006768.5
      Conserved Domains (4) summary
      cd11608
      Location:477 → 561
      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

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086031.1 Reference GRCr8

      Range
      45168161..45189362
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006249790.5 → XP_006249852.1  eukaryotic translation initiation factor 2D isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZPF1, A0A8I6AJ85
      Related
      ENSRNOP00000079849.1
      Conserved Domains (4) summary
      cd11608
      Location:477 → 542
      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_063272531.1 → XP_063128601.1  eukaryotic translation initiation factor 2D isoform X1

      UniProtKB/Swiss-Prot
      Q5PPG7
      UniProtKB/TrEMBL
      A6IC14

    3. XM_039090962.1 → XP_038946890.1  eukaryotic translation initiation factor 2D isoform X3

      Conserved Domains (1) summary
      cd11608
      Location:227 → 311
      eIF2D_C; C-terminal domain of eIF2D and related proteins

    RNA

    1. XR_010056927.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5PPG7.1 GenPept UniProtKB/Swiss-Prot:Q5PPG7

    Gene LinkOut

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

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