Candida dubliniensis CD36 Genome Snapshot/Overview

This page provides information on the status of the C. dubliniensis CD36 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; Candida Go Slim Annotations File) on the CGD 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 Nov 21, 2024)

5841 ORFs, 99.64%

21 ORFs, 0.36%

Genome Inventory (as of Nov 21, 2024)

This table reports the number and types of features annotated in CGD, 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 CGD are not listed in the table below.)

Feature Type	Total	Chromosome
Feature Type	Total	Chr1	Chr2	Chr3	Chr4	Chr5	Chr6	Chr7	ChrR	Nuclear genome
Total ORFs	5862	1299	973	727	629	495	417	388	934	5862
Verified ORFs	21	5	0	5	3	1	1	2	4	21
Uncharacterized ORFs	5841	1294	973	722	626	494	416	386	930	5841
tRNA	130	23	25	24	17	6	4	1	30	130
Pseudogenes	73	17	7	9	8	8	5	8	11	73
Repeat_region	10	1	2	1	2	1	1	2	0	10
ncRNA	2	0	0	0	0	0	0	0	2	2
Total	6077	1340	1007	761	656	510	427	399	977	6077
Chromosome length (bp)	14,618,422	3,214,061	2,289,089	1,863,824	1,641,709	1,245,899	1,073,895	1,022,435	2,267,510	14,618,422

Summary of Chromosome Sequence and Annotation updates

As new data become available, CGD 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 CGD Download Data page. Detailed information about the sequence data in CGD, 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 CGD curators. At this time, CGD does not record sequence variation between SC5314 and other strains of C. dubliniensis CD36.

Chromosome History	Sequence Updates		Annotation Updates
Chromosome History	Total Number	Last Update	Total Number	Last Update
Chr1	0	N/A	3	2013-05-14
Chr2	0	N/A	2	2013-05-14
Chr3	0	N/A	2	2013-05-14
Chr4	0	N/A	2	2013-05-14
Chr5	0	N/A	3	2013-05-14
Chr6	0	N/A	2	2013-05-14
Chr7	0	N/A	3	2013-05-14
ChrR	0	N/A	2	2013-05-14

Summary of Gene Ontology (GO) annotations (as of Nov 21, 2024)

This table displays the current total number of C. dubliniensis CD36 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. Note that these counts do not include GO annotations made for ORFs classified as "Dubious", or for features of type "Pseudogene" or "Not physically mapped"

Ontology	Details of Annotations
Ontology	Total Number of Annotations	Graphical View
Molecular Function	3989	Go to Molecular Function Graph
Cellular Component	3508	Go to Cellular Component Graph
Biological Process	4306	Go to Biological Process Graph
All Ontologies	11803

Distribution of Gene Products by Process, Function, and Component (as of Nov 21, 2024)

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 Candida biology. GO Slim terms representing broad categories from a single aspect are listed for each graph, along with the percentage of C. dubliniensis CD36 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 "C_dubliniensis_CD36_go_distribution.tab" in the GO Slim downloads directory. An alternative processing of the same data is available in the file "GOSlim_gene_association.cgd.gz", also in the GO Slim downloads directory.

CGD Copyright © 2004-2024 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 CGD, please use the following reference: Skrzypek MS, Binkley J, Binkley G, Miyasato SR, Simison M, Sherlock G (2017). The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data. Nucleic Acids Res 45 (D1); D592-D596; see How to cite CGD.