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    Eed embryonic ectoderm development [ Rattus norvegicus (Norway rat) ]

    Gene ID: 293104, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Eedprovided by RGD
    Official Full Name
    embryonic ectoderm developmentprovided by RGD
    Primary source
    RGD:1309782
    See related
    EnsemblRapid:ENSRNOG00000017509 AllianceGenome:RGD:1309782
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables chromatin binding activity. Involved in negative regulation of transcription by RNA polymerase II and spinal cord development. Predicted to be located in cytosol; nucleus; and sex chromatin. Predicted to be part of ESC/E(Z) complex and chromatin silencing complex. Used to study transient cerebral ischemia. Orthologous to human EED (embryonic ectoderm development). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 141.0), Spleen (RPKM 131.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Eed in Genome Data Viewer
    Location:
    1q32
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (153280419..153307537, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (143867875..143895008, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (154189252..154216340, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene ferritin light chain 1-like Neighboring gene heat shock protein nuclear import factor hikeshi Neighboring gene large ribosomal subunit protein uL22-like Neighboring gene rho family GTPase 2, pseudogene 1

    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. The murine polycomb group protein Eed is required for global histone H3 lysine-27 methylation. Montgomery ND, et al. Curr Biol, 2005 May 24. PMID 15916951
    2. Epigenetic control of female puberty. Lomniczi A, et al. Nat Neurosci, 2013 Mar. PMID 23354331, Free PMC Article
    3. Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression. Wright H, et al. Sci Rep, 2021 Jan 21. PMID 33479437, Free PMC Article
    4. Molecular and functional mapping of EED motifs required for PRC2-dependent histone methylation. Montgomery ND, et al. J Mol Biol, 2007 Dec 14. PMID 17997413, Free PMC Article
    5. Early activation of nSMase2/ceramide pathway in astrocytes is involved in ischemia-associated neuronal damage via inflammation in rat hippocampi. Gu L, et al. J Neuroinflammation, 2013 Sep 3. PMID 24007266, Free PMC Article

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression.
      Title: Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables enzyme activator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables methylated histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    contributes_to nucleosome binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription corepressor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cellular response to leukemia inhibitory factor ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in facultative heterochromatin formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within genomic imprinting ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in heterochromatin formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within oligodendrocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of adaxial/abaxial pattern formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spinal cord development IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of ESC/E(Z) complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of ESC/E(Z) complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of chromatin silencing complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in pronucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in sex chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    polycomb protein EED

    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_001106278.2 → NP_001099748.1  polycomb protein EED

      See identical proteins and their annotated locations for NP_001099748.1

      Status: VALIDATED

      Source sequence(s)
      BC168872
      UniProtKB/TrEMBL
      A0A8I6A2I3, B5DF02, F1LMC5
      Related
      ENSRNOP00000024082.6, ENSRNOT00000024082.8
      Conserved Domains (2) summary
      sd00039
      Location:96 → 140
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:150 → 438
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    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_086019.1 Reference GRCr8

      Range
      153280419..153307537 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039105864.2 → XP_038961792.1  polycomb protein EED isoform X2

      UniProtKB/TrEMBL
      A0A8I6A2I3
      Conserved Domains (2) summary
      sd00039
      Location:96 → 140
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:150 → 385
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    2. XM_039105860.2 → XP_038961788.1  polycomb protein EED isoform X1

      UniProtKB/TrEMBL
      A0A8I6AJ96
      Related
      ENSRNOP00000093078.2, ENSRNOT00000114221.2
      Conserved Domains (2) summary
      sd00039
      Location:61 → 105
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:115 → 403
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    3. XM_006229664.4 → XP_006229726.1  polycomb protein EED isoform X3

      See identical proteins and their annotated locations for XP_006229726.1

      UniProtKB/TrEMBL
      A0A8I6AQZ9
      Conserved Domains (2) summary
      sd00039
      Location:96 → 140
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:81 → 264
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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