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

Gene ID: 498225, updated on 18-Sep-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
EnsemblRapid: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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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 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
  
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
    ENSRNOP00000104595.1, ENSRNOT00000151553.1
    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
    ENSRNOP00000006768.3, ENSRNOT00000006768.6
    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
    A0A8I6AJ85, A6IC14
    Related
    ENSRNOP00000079849.2, ENSRNOT00000111867.2

  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

    Related
    ENSRNOT00000117695.2
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5PPG7.1 GenPept UniProtKB/Swiss-Prot:Q5PPG7

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