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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 Feb 22, 2012)

4628 ORFs, 74.62% 1422 ORFs, 22.93% 152 ORFs, 2.45%

Genome Inventory (as of Feb 22, 2012)

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 TypeTotalChromosome number
Ca21chr1_C_albicans_SC5314Ca21chr2_C_albicans_SC5314Ca21chr3_C_albicans_SC5314Ca21chr4_C_albicans_SC5314Ca21chr5_C_albicans_SC5314Ca21chr6_C_albicans_SC5314Ca21chr7_C_albicans_SC5314Ca21chrR_C_albicans_SC5314Nuclear genomeMitochondrial genome
Total ORFs620213811016759673521436407989618220
Verified ORFs1422339230184152125958920814220
Uncharacterized ORFs46281016768555503380328305753460820
Dubious ORFs15226182018161313281520
tRNA156232421176413012630
Long_terminal_repeat12925201014101011291290
snoRNA75221331154314750
Repeat_region42551655105420
Retrotransposon1222110123120
Pseudogenes70100110470
Centromere81111111180
Blocked_reading_frame81301011180
snRNA50111000250
rRNA60000000442
ncRNA30000000330
Total6653146010867977255494634361085660152
Chromosome length (bp)14,324,3153,188,5482,232,0351,799,4061,603,4431,190,9281,033,530949,6162,286,38914,283,89540,420

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

Ca21chr1_C_albicans_SC5314

108

2008-11-25

64

2011-09-30

Ca21chr2_C_albicans_SC5314

262

2008-11-07

46

2011-09-30

Ca21chr3_C_albicans_SC5314

59

2011-09-16

24

2011-09-30

Ca21chr4_C_albicans_SC5314

82

2008-11-07

30

2011-09-30

Ca21chr5_C_albicans_SC5314

51

2010-05-04

37

2011-09-30

Ca21chr6_C_albicans_SC5314

77

2008-11-07

23

2011-09-30

Ca21chr7_C_albicans_SC5314

12

2008-11-07

19

2011-09-30

Ca21chrR_C_albicans_SC5314

85

2008-11-07

47

2011-09-30

Ca19-mtDNA

0

N/A

3

2011-07-26

Summary of Gene Ontology (GO) annotations (as of Feb 22, 2012)

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 Function3965Go to Molecular Function Graph
Cellular Component3935Go to Cellular Component Graph
Biological Process4275Go to Biological Process Graph
All Ontologies12175 

Distribution of Gene Products by Process, Function, and Component (as of Feb 22, 2012)

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, please contact CGD curators or use the GO Slim Mapper. An alternative processing of the same data, with some redundancies removed, is available in the Candida GO Slim Annotations File on the CGD 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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