Aspergillus niger CBS 513.88 Genome Snapshot/Overview

This page provides information on the status of the A. niger CBS 513.88 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 Apr 01, 2020)

13811 ORFs, 98.24%

247 ORFs, 1.76%

Genome Inventory (as of Apr 01, 2020)

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
Feature Type	Total	An01	An02	An03	An04	An05	An06	An07	An08	An09	An10	An11	An12	An13	An14	An15	An16	An17	An18	An19	Nuclear genome
Total ORFs	14058	1451	1488	664	1031	254	262	1024	1200	676	103	1084	1053	396	734	776	916	240	665	41	14058
Verified ORFs	247	31	36	15	16	3	3	18	14	13	2	24	16	2	18	12	13	2	8	1	247
Uncharacterized ORFs	13811	1420	1452	649	1015	251	259	1006	1186	663	101	1060	1037	394	716	764	903	238	657	40	13811
tRNA	265	50	22	14	7	3	7	15	16	8	2	31	29	7	7	18	8	1	20	0	265
Repeat_region	101	4	11	0	12	2	6	6	9	10	3	16	4	5	2	1	4	1	5	0	101
rRNA	65	4	0	17	0	4	0	1	2	1	0	7	17	1	3	1	5	0	1	1	65
Pseudogenes	14	2	4	1	3	0	0	0	1	0	0	0	1	1	0	1	0	0	0	0	14
uORF	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
Total	14504	1512	1525	696	1053	263	275	1046	1228	695	108	1138	1104	410	746	797	933	242	691	42	14504
Chromosome length (bp)	33,975,768	3,625,813	3,626,085	1,609,811	2,525,243	603,204	683,630	2,341,370	2,925,080	1,595,066	263,333	2,721,467	2,566,738	908,643	1,734,209	1,879,820	2,132,688	594,599	1,542,301	96,668	33,975,768

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. niger CBS 513.88.

Chromosome History	Sequence Updates		Annotation Updates
Chromosome History	Total Number	Last Update	Total Number	Last Update
An01	0	N/A	29	2013-08-12
An02	0	N/A	18	2013-07-30
An03	0	N/A	17	2013-07-30
An04	0	N/A	11	2013-03-14
An05	0	N/A	16	2013-07-30
An06	0	N/A	10	2013-03-14
An07	0	N/A	17	2013-07-30
An08	0	N/A	21	2013-07-30
An09	0	N/A	18	2013-07-30
An10	0	N/A	8	2013-03-14
An11	0	N/A	16	2015-08-20
An12	0	N/A	11	2013-03-14
An13	0	N/A	11	2013-03-14
An14	0	N/A	11	2013-03-14
An15	0	N/A	11	2013-03-14
An16	0	N/A	13	2013-07-30
An17	0	N/A	13	2015-08-20
An18	0	N/A	15	2013-03-14
An19	0	N/A	9	2013-03-14

Summary of Gene Ontology (GO) annotations (as of Apr 01, 2020)

This table displays the current total number of A. niger CBS 513.88 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	6557	Go to Molecular Function Graph
Cellular Component	4344	Go to Cellular Component Graph
Biological Process	6662	Go to Biological Process Graph
All Ontologies	17563

Distribution of Gene Products by Process, Function, and Component (as of Apr 01, 2020)

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. niger CBS 513.88 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, you may use the GO Slim Mapper, or view and download the file "A_niger_CBS_513_88_go_distribution.tab" in the GO Slim downloads directory. An alternative processing of the same data is available in the file "GOSlim_gene_association.aspgd.gz", also in the GO Slim downloads directory.

AspGD Copyright © 2008-2020 The Board of Trustees, Leland Stanford Junior University.
Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
To cite AspGD, please use the following reference: Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR (2014). The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res 42 (1); D705-10; see How to cite AspGD.