Candida albicans SC5314 Genome Snapshot/Overview

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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.

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 Jun 28, 2017)

4415 ORFs, 71.00% 1651 ORFs, 26.55% 152 ORFs, 2.44%

Genome Inventory (as of Jun 28, 2017)

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 TypeTotalHaploid TotalChromosome
chr1Achr1Bchr2Achr2Bchr3Achr3Bchr4Achr4Bchr5Achr5Bchr6Achr6Bchr7Achr7BchrRAchrRBNuclear genomeMitochondrial genome
Total ORFs12405619813831383101710177607606746745235224394394074079909901238520
Verified ORFs32921651381381268268207207176176147147115115989825425432920
Uncharacterized ORFs88104395976976731731533533480480360360311311296296708708879020
Dubious ORFs303152262618182020181816151313131328283030
tRNA2821262323242421211717664411303025230
Long_terminal_repeat257129252520201010141410101010111129282570
snoRNA150752222131333111155443314141500
Repeat_region8442555511665555101055840
Retrotransposon24122222111100112233240
Centromere1681111111111111111160
Pseudogenes1681111000011110044160
Blocked_reading_frame1681133001100111111160
snRNA1050011111100000022100
rRNA104000000000000004482
ncRNA1050011000000000044100
Total1328066201463146310881088798798726726551550466466436436108710861322852
Chromosome length (bp)28,605,41815,473,7503,188,3413,188,3962,231,8832,231,7501,799,2981,799,2711,603,2591,603,3111,190,8691,190,9911,033,2921,033,212949,580949,6112,286,2372,285,69728,564,99840,420


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 HistorySequence UpdatesAnnotation Updates

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 Jun 28, 2017)

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"

OntologyDetails of Annotations
Total Number of AnnotationsGraphical View
Molecular Function4151Go to Molecular Function Graph
Cellular Component4653Go to Cellular Component Graph
Biological Process4655Go to Biological Process Graph
All Ontologies13459 

Distribution of Gene Products by Process, Function, and Component (as of Jun 28, 2017)

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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