Candida albicans SC5314 Genome Snapshot/Overview

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Candida albicans SC5314 Genome Snapshot/Overview

This page provides information on the status of the C. albicans SC5314 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 15, 2018)

4379 ORFs, 70.42%

1687 ORFs, 27.13%

152 ORFs, 2.44%

Genome Inventory (as of Nov 15, 2018)

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	Haploid Total	Chromosome
Feature Type	Total	Haploid Total	chr1A	chr1B	chr2A	chr2B	chr3A	chr3B	chr4A	chr4B	chr5A	chr5B	chr6A	chr6B	chr7A	chr7B	chrRA	chrRB	Nuclear genome	Mitochondrial genome
Total ORFs	12405	6198	1383	1383	1017	1017	760	760	674	674	523	522	439	439	407	407	990	990	12385	20
Verified ORFs	3364	1687	391	391	275	275	211	211	181	181	151	151	115	115	100	100	258	258	3364	0
Uncharacterized ORFs	8738	4359	966	966	724	724	529	529	475	475	356	356	311	311	294	294	704	704	8718	20
Dubious ORFs	303	152	26	26	18	18	20	20	18	18	16	15	13	13	13	13	28	28	303	0
tRNA	282	126	23	23	24	24	21	21	17	17	6	6	4	4	1	1	30	30	252	30
Long_terminal_repeat	257	129	25	25	20	20	10	10	14	14	10	10	10	10	11	11	29	28	257	0
snoRNA	150	75	22	22	13	13	3	3	11	11	5	5	4	4	3	3	14	14	150	0
Repeat_region	84	42	5	5	5	5	1	1	6	6	5	5	5	5	10	10	5	5	84	0
Retrotransposon	24	12	2	2	2	2	1	1	1	1	0	0	1	1	2	2	3	3	24	0
Centromere	16	8	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	16	0
Pseudogenes	16	8	1	1	1	1	0	0	0	0	1	1	1	1	0	0	4	4	16	0
Blocked_reading_frame	16	8	1	1	3	3	0	0	1	1	0	0	1	1	1	1	1	1	16	0
snRNA	10	5	0	0	1	1	1	1	1	1	0	0	0	0	0	0	2	2	10	0
rRNA	10	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	8	2
ncRNA	10	5	0	0	1	1	0	0	0	0	0	0	0	0	0	0	4	4	10	0
Total	13280	6620	1463	1463	1088	1088	798	798	726	726	551	550	466	466	436	436	1087	1086	13228	52
Chromosome length (bp)	28,605,418	15,473,750	3,188,341	3,188,396	2,231,883	2,231,750	1,799,298	1,799,271	1,603,259	1,603,311	1,190,869	1,190,991	1,033,292	1,033,212	949,580	949,611	2,286,237	2,285,697	28,564,998	40,420

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. albicans SC5314.

Chromosome History	Sequence Updates		Annotation Updates
Chromosome History	Total Number	Last Update	Total Number	Last Update
chr1A	402	2016-01-21	67	2015-05-21
chr1B	424	2016-01-21	1	2014-06-24
chr2A	386	2016-01-21	49	2015-05-21
chr2B	405	2016-01-21	2	2015-01-26
chr3A	144	2016-06-22	32	2016-06-22
chr3B	138	2016-06-22	2	2016-06-22
chr4A	365	2016-01-21	33	2015-05-21
chr4B	275	2016-01-21	1	2014-06-24
chr5A	68	2016-01-21	42	2015-05-21
chr5B	71	2016-01-21	1	2014-06-24
chr6A	423	2016-01-21	27	2015-05-21
chr6B	386	2016-01-21	1	2014-06-24
chr7A	356	2016-01-21	18	2014-06-24
chr7B	363	2016-01-21	1	2014-06-24
chrRA	428	2016-01-21	55	2015-05-21
chrRB	483	2016-01-21	3	2014-06-25
Mitochondrial Genome	3	2016-01-21	7	2016-01-21

Summary of Gene Ontology (GO) annotations (as of Nov 15, 2018)

This table displays the current total number of C. albicans SC5314 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	4159	Go to Molecular Function Graph
Cellular Component	4041	Go to Cellular Component Graph
Biological Process	4675	Go to Biological Process Graph
All Ontologies	12875

Distribution of Gene Products by Process, Function, and Component (as of Nov 15, 2018)

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. albicans SC5314 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_albicans_SC5314_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.

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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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.

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