Candida glabrata CBS138 Genome Snapshot/Overview

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This page provides information on the status of the C. glabrata CBS138 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 25, 2017)

5064 ORFs, 95.67% 229 ORFs, 4.33%

Genome Inventory (as of Feb 25, 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 TypeTotalChromosome
ChrAChrBChrCChrDChrEChrFChrGChrHChrIChrJChrKChrLChrMNuclear genomeMitochondrial genome
Total ORFs5293205220235288282387440466470523564582620528211
Verified ORFs22951016121920182221172419252281
Uncharacterized ORFs5064200210219276263367422444449506540563595505410
tRNA230997189151814261722251820723
ncRNA68222213644414716671
Pseudogenes182312111111013180
Centromere111111111001111110
rRNA6000000000004042
Long_terminal_repeat4000100300000040
Repeat_region2000100100000020
Total5632219235246313294407470485501546601620658559537
Chromosome length (bp)12,338,305491,328502,101558,804651,701687,738927,101992,2111,050,3611,100,3491,195,1291,302,8311,455,6891,402,89912,318,24220,063


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. glabrata CBS138.

Chromosome HistorySequence UpdatesAnnotation Updates

Total Number

Last Update

Total Number

Last Update

ChrA

0

N/A

15

2015-09-14

ChrB

0

N/A

17

2015-09-14

ChrC

0

N/A

10

2015-09-14

ChrD

0

N/A

13

2015-09-14

ChrE

0

N/A

11

2015-09-14

ChrF

0

N/A

13

2015-09-14

ChrG

0

N/A

15

2015-09-14

ChrH

0

N/A

15

2015-09-14

ChrI

0

N/A

13

2015-09-14

ChrJ

3

2011-09-15

18

2015-09-14

ChrK

0

N/A

15

2015-04-13

ChrL

0

N/A

13

2015-04-13

ChrM

0

N/A

10

2015-04-13

Mitochondrial Genome

0

N/A

2

2010-11-17

Summary of Gene Ontology (GO) annotations (as of Feb 25, 2017)

This table displays the current total number of C. glabrata CBS138 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 Function3912Go to Molecular Function Graph
Cellular Component4628Go to Cellular Component Graph
Biological Process4541Go to Biological Process Graph
All Ontologies13081 

Distribution of Gene Products by Process, Function, and Component (as of Feb 25, 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. glabrata CBS138 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_glabrata_CBS138_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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