Aspergillus oryzae RIB40 Genome Snapshot/Overview

This page provides information on the status of the A. oryzae RIB40 genome. Data on this page are updated once a day. All the data displayed on this page are available in one or more files (Chromosomal Feature File; GO Annotations File) on the AspGD Download Data page. The Advanced Search tool can also be used to retrieve chromosomal features that match specific criteria.

1. Graphical View of Protein Coding Genes

2. Genome Inventory

3. Summary of Chromosome Sequence and Annotation Updates

4. Summary of GO annotations

5. Distribution of Gene Products by Process, Function, and Component

Graphical View of Protein Coding Genes (as of Jun 19, 2013)

11746 ORFs, 98.69%

156 ORFs, 1.31%

Genome Inventory (as of Jun 19, 2013)

This table reports the number and types of features annotated in AspGD, per chromosome (excluding unmapped features). To get a list of all features of a certain type (e.g., Verified ORF, tRNA, etc.), select that feature type. To access more information on the individual chromosome (e.g., sequence, a listing of all features on that chromosome, etc.), select each chromosome name. (Feature types that are not yet annotated in AspGD are not listed in the table below.)

Feature Type	Total	Chromosome number
Feature Type	Total	Chr1_A_oryzae_RIB40	Chr2_A_oryzae_RIB40	Chr3_A_oryzae_RIB40	Chr4_A_oryzae_RIB40	Chr5_A_oryzae_RIB40	Chr6_A_oryzae_RIB40	Chr7_A_oryzae_RIB40	Chr8_A_oryzae_RIB40	contig_11.1_A_oryzae_RIB40	contig_28.1_A_oryzae_RIB40	contig_7.1_A_oryzae_RIB40	Nuclear genome	Mitochondrial genome
Total ORFs	11902	2014	1974	1638	1497	1466	1291	903	1091	6	5	1	11886	16
Verified ORFs	156	13	30	28	15	18	16	10	26	0	0	0	156	0
Uncharacterized ORFs	11746	2001	1944	1610	1482	1448	1275	893	1065	6	5	1	11730	16
tRNA	268	39	30	44	40	30	15	16	28	0	0	0	242	26
Pseudogenes	3	1	1	0	0	0	1	0	0	0	0	0	3	0
rRNA	3	0	0	0	0	0	0	3	0	0	0	0	3	0
Total	12176	2054	2005	1682	1537	1496	1307	922	1119	6	5	1	12134	42
Chromosome length (bp)	37,912,014	6,520,266	6,264,705	5,123,684	4,887,096	4,533,889	4,190,347	2,933,481	3,395,259	18,226	8,921	6,938	37,882,812	29,202

Summary of Chromosome Sequence and Annotation updates

As new data become available, AspGD curators update the systematic sequence and its annotation. This table summarizes the sequence and/or annotation updates made for each chromosome.

Select the chromosome number to retrieve the corresponding Chromosome History page, which provides details on all the updates for that chromosome. Current and past versions of the sequence and annotation are also available on the AspGD Download Data page. Detailed information about the sequence data in AspGD, including the sources from which sequence-based information are dervived, and a history of the reference strain genome assemblies, is found on the Sequence Documentation page.

If you are aware of additional sequence or annotation changes that should be made to the reference sequence, please send a message to AspGD curators. At this time, AspGD does not record sequence variation between the genome reference strain and other strains of A. oryzae RIB40.

Chromosome History	Sequence Updates		Annotation Updates
Chromosome History	Total Number	Last Update	Total Number	Last Update
Chr1_A_oryzae_RIB40	0	N/A	59	2012-10-22
Chr2_A_oryzae_RIB40	0	N/A	109	2012-10-24
Chr3_A_oryzae_RIB40	0	N/A	36	2012-10-24
Chr4_A_oryzae_RIB40	0	N/A	46	2012-10-24
Chr5_A_oryzae_RIB40	0	N/A	49	2012-08-30
Chr6_A_oryzae_RIB40	0	N/A	57	2012-10-22
Chr7_A_oryzae_RIB40	0	N/A	46	2012-08-30
Chr8_A_oryzae_RIB40	0	N/A	40	2012-08-30
contig_11.1_A_oryzae_RIB40	0	N/A	4	2012-08-30
contig_28.1_A_oryzae_RIB40	0	N/A	6	2012-08-30
contig_7.1_A_oryzae_RIB40	0	N/A	5	2012-08-30
mito_A_oryzae_RIB40	0	N/A	6	2012-08-30

Summary of Gene Ontology (GO) annotations (as of Jun 19, 2013)

This table displays the current total number of A. oryzae RIB40 gene products that have been annotated to one or more terms in each GO aspect (Process, Function, Component). These counts include GO annotations made for ORFs classified as either "Verified" or "Uncharacterized", transposable element genes, and all RNA gene products.

Ontology	Details of Annotations
Ontology	Total Number of Annotations	Graphical View
Molecular Function	6579	Go to Molecular Function Graph
Cellular Component	4396	Go to Cellular Component Graph
Biological Process	6537	Go to Biological Process Graph
All Ontologies	17512

Distribution of Gene Products by Process, Function, and Component (as of Jun 19, 2013)

These graphical views representing the GO annotation state of the entire genome are provided using a GO Slim (a high-level subset of Gene Ontology terms that allows grouping of genes into broad categories such as "DNA replication", "protein kinase activity", or "nucleus") tailored to Aspergillus biology. GO Slim terms representing broad categories from a single aspect are listed for each graph, along with the percentage of A. oryzae RIB40 gene products annotated to a specific term that maps up the ontology to the GO Slim term. Note that some gene products may be represented more than once, if they are annotated to one or more GO terms that map to more than one GO Slim term.

More information on GO and GO Slim can be found at SGD's GO help page or in the Gene Ontology documentation. To obtain the GO data summarized in these graphs, please contact AspGD curators or use the GO Slim Mapper. An alternative processing of the same data, with some redundancies removed, is available in the Aspergillus GO Slim Annotations File on the AspGD Download Data page.

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