Candida parapsilosis CDC317 Genome Snapshot/Overview

This page provides information on the status of the C. parapsilosis CDC317 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 May 27, 2023)

5730 ORFs, 98.17%

107 ORFs, 1.83%

Genome Inventory (as of May 27, 2023)

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	Contig005504	Contig005569	Contig005806	Contig005807	Contig005809	Contig006110	Contig006139	Contig006372	Nuclear genome	Mitochondrial genome
Total ORFs	5837	375	1045	433	906	1412	427	423	796	5817	20
Verified ORFs	107	7	19	3	15	22	11	12	17	106	1
Uncharacterized ORFs	5730	368	1026	430	891	1390	416	411	779	5711	19
tRNA	115	2	18	2	13	28	2	8	18	91	24
Pseudogenes	26	0	6	4	3	7	1	2	3	26	0
rRNA	6	0	0	0	0	0	4	0	0	4	2
Total	5984	377	1069	439	922	1447	434	433	817	5938	46
Chromosome length (bp)	13,030,174	898,305	2,235,583	1,039,767	2,091,826	3,023,470	957,321	962,442	1,789,679	12,998,393	31,781

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. parapsilosis CDC317.

Chromosome History	Sequence Updates		Annotation Updates
Chromosome History	Total Number	Last Update	Total Number	Last Update
Contig005504	0	N/A	1	2012-03-12
Contig005569	0	N/A	1	2012-03-12
Contig005806	0	N/A	1	2012-03-12
Contig005807	0	N/A	1	2012-03-12
Contig005809	0	N/A	1	2012-03-12
Contig006110	0	N/A	1	2012-03-12
Contig006139	0	N/A	1	2012-03-12
Contig006372	0	N/A	1	2012-03-12
Mitochondrial Genome	0	N/A	7	2012-03-14

Summary of Gene Ontology (GO) annotations (as of May 27, 2023)

This table displays the current total number of C. parapsilosis CDC317 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	4090	Go to Molecular Function Graph
Cellular Component	3669	Go to Cellular Component Graph
Biological Process	4360	Go to Biological Process Graph
All Ontologies	12119

Distribution of Gene Products by Process, Function, and Component (as of May 27, 2023)

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. parapsilosis CDC317 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_parapsilosis_CDC317_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 © 2004-2023 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.