Aspergillus oryzae RIB40 Genome Snapshot/Overview

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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.

Contents

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 Jul 25, 2014)

11703 ORFs, 98.33% 199 ORFs, 1.67%

Genome Inventory (as of Jul 25, 2014)

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 TypeTotalChromosome number
Chr1_A_oryzae_RIB40Chr2_A_oryzae_RIB40Chr3_A_oryzae_RIB40Chr4_A_oryzae_RIB40Chr5_A_oryzae_RIB40Chr6_A_oryzae_RIB40Chr7_A_oryzae_RIB40Chr8_A_oryzae_RIB40contig_11.1_A_oryzae_RIB40contig_28.1_A_oryzae_RIB40contig_7.1_A_oryzae_RIB40Nuclear genomeMitochondrial genome
Total ORFs1190220141974163814971466129190310916511188616
Verified ORFs19918393718252312270001990
Uncharacterized ORFs1170319961935160114791441126889110646511168716
tRNA268393044403015162800024226
Pseudogenes31100010000030
rRNA30000003000030
Total1217620542005168215371496130792211196511213442
Chromosome length (bp)37,912,0146,520,2666,264,7055,123,6844,887,0964,533,8894,190,3472,933,4813,395,25918,2268,9216,93837,882,81229,202


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 HistorySequence UpdatesAnnotation Updates

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 Jul 25, 2014)

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.

OntologyDetails of Annotations
Total Number of AnnotationsGraphical View
Molecular Function6415Go to Molecular Function Graph
Cellular Component4926Go to Cellular Component Graph
Biological Process6439Go to Biological Process Graph
All Ontologies17780 

Distribution of Gene Products by Process, Function, and Component (as of Jul 25, 2014)

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.

Distribution of Gene Products among Molecular Function Categories

Distribution of Gene Products among Cellular Component Categories

Distribution of Gene Products among Biological Process Categories



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