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

Summary

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, Dec 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

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_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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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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)

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

NC_086019.1 Reference GRCr8

Range

153280419..153307537 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
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 ...
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 ...