Genome & Annotation

English oak reference genome and structural annotation

Reference genome dhQueRobu3.1 (GCF_932294415.1), annotated with the NCBI Gnomon pipeline. This site provides the sequence of 12 nuclear chromosomes together with gene, transcript and exon/CDS coordinates, which can be queried jointly with the expression data of 645 RNA-seq libraries or browsed visually in JBrowse.

784.36 Mb

Nuclear assembly length

Nuclear chromosomes

40,439

Nuclear genes

32,142

Protein-coding genes

67,635

Transcripts

440,561

Exons

JBrowse browser

Browse

Pan and zoom in the genome browser to inspect gene structure tracks for any region, from whole chromosomes down to individual exon boundaries.

12 chromosomesReference sequenceAnnotation track

Gene search

Genes

Search by gene ID or product keyword to view coordinates, transcript structure and exon composition.

40,573 genes67,635 transcripts

RNA-seq libraries

Libraries

Metadata for 645 public libraries: tissue, treatment, time point, sequencing layout and data volume.

645 libraries9 tissues

Downloads

Download

Open downloads of genome sequence, GFF3 annotation, CDS and protein sequences — all direct pipeline products.

FASTAGFF3FAA

Chromosome composition

12 nuclear chromosomes · 784.36 Mb combined

Chromosome	Length (bp)	Length (Mb)	Genes	Gene density (genes/Mb)
Chr1	55,127,264	55.13	2,594	47.1	Browse
Chr2	98,168,673	98.17	5,122	52.2	Browse
Chr3	69,042,348	69.04	3,162	45.8	Browse
Chr4	86,535,673	86.54	3,604	41.6	Browse
Chr5	89,215,487	89.22	6,609	74.1	Browse
Chr6	54,563,945	54.56	2,876	52.7	Browse
Chr7	50,779,627	50.78	2,555	50.3	Browse
Chr8	68,065,914	68.07	3,486	51.2	Browse
Chr9	56,648,912	56.65	2,738	48.3	Browse
Chr10	55,958,786	55.96	2,621	46.8	Browse
Chr11	56,641,698	56.64	2,673	47.2	Browse
Chr12	43,614,803	43.61	2,399	55.0	Browse
Chr13 Plastid	161,172	0.161	134	—	Browse

Chr13 is the plastid genome carried in the assembly (161,172 bp, 134 genes); it is listed separately and is not counted among the 12 nuclear chromosomes.

Gene biotype distribution

Biotype	Genes
protein_coding	32,231
lncRNA	4,183
rRNA	2,989
tRNA	595
snoRNA	437
snRNA	137
misc_RNA	1

Annotation contents

Assembly: dhQueRobu3.1 (GCF_932294415.1)
Species: Quercus robur (English oak)
Chromosomes: 12 nuclear + 1 organelle
Nuclear length: 784,363,130 bp (784.36 Mb)
Plastid (Chr13): 161,172 bp · 134 genes
Genes: 40,573 (40,439 nuclear + 134 plastid)
Transcripts: 67,635
Exons: 440,561
CDS: 297,685
Proteins with GO: 49,987
Expression libraries: 645

The gene coordinate table and the expression matrix share exactly the same gene set (40,573 genes), so cross-module joins are safe.