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  Past Announcements
Links to Map Viewer      November 16, 2017

Map Viewer recently announced that it is being retired. In conjunction with this change, links in CCDS to Map Viewer are being removed. For similiar functionality, click the link from CCDS to NCBI Nucleotide, and then click the link for Graphics or FASTA as desired.


CCDS Release 21 - Update for Mouse      December 8, 2016

The NCBI, Ensembl, and Sanger (Havana) annotation of the GRCm38.p4 reference genome (assembly GCF_000001635.24, NCBI annotation release 106, Ensembl annotation release 86) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 938 new CCDS IDs, and adds 137 genes into the mouse CCDS set. CCDS Release 21 includes a total of 25,757 CCDS IDs that correspond to 20,354 GeneIDs. See the Releases & Statistics report for details.


CCDS Review Status      October 6, 2016

All current CCDS IDs are now identified on the full report page as being either Reviewed or Provisional, depending on whether they have been reviewed by the RefSeq, Havana or CCDS collaboration groups. A Reviewed status indicates that the CCDS ID has undergone a review by both individual annotation groups (RefSeq and Havana), or jointly by all members of the CCDS collaboration, or a combination of these options. A Provisional status indicates that the CCDS ID has not been reviewed to that extent.


CCDS Release 20 - Update for Human      September 8, 2016

The NCBI, Ensembl, and Sanger (Havana) annotation of the GRCh38 reference genome (assembly GCF_000001405.33, NCBI annotation release 108, Ensembl annotation release 85) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 1,158 new CCDS IDs, and adds 98 Genes into the human CCDS set. CCDS Release 20 includes a total of 32,524 CCDS IDs that correspond to 18,892 GeneIDs. See the Releases & Statistics report for details.


CCDS Release 19 - Update for Mouse      July 30, 2015

The NCBI, Ensembl, and Sanger (Havana) annotation of the GRCm38 reference genome (assembly GCF_000001635.23, NCBI annotation release 105, Ensembl annotation release 81) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 1,003 new CCDS IDs, and adds 148 Genes into the mouse CCDS set. CCDS Release 19 includes a total of 24,834 CCDS IDs that correspond to 20,215 GeneIDs. See the Releases & Statistics report for details.


CCDS Release 18 - Update for Human      May 12, 2015

The NCBI, Ensembl, and Sanger (Havana) annotation of the GRCh38 reference genome (assembly GCF_000001405.28, NCBI annotation release 107, Ensembl annotation release 79) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 808 new CCDS IDs, and adds 86 Genes into the human CCDS set. CCDS Release 18 includes a total of 31,371 CCDS IDs that correspond to 18,826 GeneIDs. See the Releases & Statistics report for details.


New Display of Combined Annotation      November 5, 2014

The current CCDS releases for human and mouse have been updated with a display of the combined NCBI and Ensembl annotation using the NCBI Sequence Viewer tool. This display can be accessed using the link which will be shown in search results and on the CCDS report pages. (See an example.)

The Sequence Viewer content is highly configurable. Please see https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/tools/sviewer for complete instructions on how to use Sequence Viewer.


CCDS Release 17 - Update for Human      August 7, 2014

The NCBI, Ensembl, and Sanger (Havana) annotation of the GRCh38 reference genome (assembly GCF_000001405.26, NCBI annotation release 106, Ensembl annotation release 76) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 1871 new CCDS IDs, and adds 195 Genes into the human CCDS set. CCDS Release 17 includes a total of 30,499 CCDS IDs that correspond to 18,800 GeneIDs. See the Releases & Statistics report for details.


CCDS Curation Guidelines Updated      May 22, 2014

The CCDS collaboration has updated the curation guidelines document found in the left-hand blue sidebar of this website. The updated document includes updates to our guidelines for considering alternate in-frame translation start sites. Additionally, guidelines for nonsense-mediated mRNA decay (NMD) representations, readthrough gene representations and inferred exon combination representations have been added. The definitions section has also been expanded.


Additional Collaborators - HGNC and MGI      May 7, 2014

The CCDS project welcomes our newest members, the HUGO Gene Nomenclature Committee (HGNC) and the Mouse Genome Informatics group (MGI), who will contribute curation review of human and mouse protein-coding gene annotations, respectively.


CCDS Release 16 - Update for Mouse      April 7, 2014

The NCBI, Ensembl, and Sanger (Havana) annotation of the mouse reference genome (assembly GCF_000001635.22, NCBI annotation release 104, Ensembl annotation release 75) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 803 new CCDS IDs, and adds 97 Genes into the mouse CCDS set. CCDS Release 16 includes a total of 23,880 CCDS IDs that correspond to 20,079 GeneIDs. See the Releases & Statistics report for details.


Reporting Matches to UniProtKB/SwissProt Proteins      January 9, 2014

CCDS Report pages now include a table of related UniProtKB/SwissProt proteins in the Sequence IDs section. The matches that are currently reported are determined by identifying proteins that are derived from the same splice pattern and have the same termini.

These matches are also reported in a new file named CCDS2UniProtKB on the CCDS FTP site.


CCDS Release 15 - Update for Human      November 29, 2013

The NCBI, Ensembl, and Sanger (Havana) annotation of the human reference genome (assembly GCF_000001405.25, NCBI annotation release 105, Ensembl annotation release 74) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 349 new CCDS IDs, and adds 12 Genes into the human CCDS set. CCDS Release 15 includes a total of 29,045 CCDS IDs that correspond to 18,683 GeneIDs. See the Releases & Statistics report for details.


CCDS Release 14 - Update for Human      October 24, 2013

The NCBI, Ensembl, and Sanger (Havana) annotation of the human reference genome (assembly GCF_000001405.25, NCBI annotation release 105, Ensembl annotation release 73) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 978 new CCDS IDs, and adds 74 Genes into the human CCDS set. CCDS Release 14 includes a total of 28,694 CCDS IDs that correspond to 18,673 GeneIDs. See the Releases & Statistics report for details.


New report of CCDS attributes      August 12, 2013

A new report of CCDS attributes has been added to the CCDS FTP site. As with other CCDS FTP files, there are separate reports for human and mouse, and the files are updated weekly. The latest version of the file is named CCDS_attributes.current.txt.

Presently there are six attribute categories being reported:

  • CDS uses downstream AUG
  • Contains selenocysteine
  • Inferred exon combination
  • Non-AUG initiation codon
  • Nonsense-mediated decay (NMD) candidate
  • Ribosomal slippage (translational frameshift)


CCDS Release 13 - Update for Mouse      August 5, 2013

The NCBI, Ensembl, and Sanger (Havana) annotation of the mouse reference genome (assembly GCF_000001635.21, NCBI annotation release 103, Ensembl annotation release 72) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 96 new CCDS IDs, and adds 61 Genes into the mouse CCDS set. CCDS Release 13 includes a total of 23,093 CCDS IDs that correspond to 19,988 GeneIDs. See the Releases & Statistics report for details.


CCDS Release 12 - Update for Human      April 30, 2013

The NCBI, Ensembl, and Sanger (Havana) annotation of the human reference genome (assembly GCF_000001405.22, NCBI annotation release 104, Ensembl annotation release 71) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 302 new CCDS IDs, and adds 79 Genes into the human CCDS set. CCDS Release 12 includes a total of 27,752 CCDS IDs that correspond to 18,606 GeneIDs. See the Releases & Statistics report for details.


Attributes section added to the CCDS Report page      February 13, 2013

We are now reporting some additional information about the annotated CDS or support evidence in the new Attributes section of the CCDS report page. The initial data release includes three attribute categories:

Attribute categoryExample
CDS uses downstream AUGCCDS 117
Inferred exon combinationCCDS 33337
Nonsense-mediated decay (NMD) candidateCCDS 53542

CCDS Release 11 Issued for Human      October 25, 2012

The NCBI, Ensembl, and Sanger (Havana) annotation of the human reference genome (assembly GCF_000001405.21, NCBI annotation release 103, Ensembl annotation release 68) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 1138 new CCDS IDs, reinstates 2 previously withdrawn CCDS IDs, and adds 93 Genes into the human CCDS set. CCDS Release 11 includes a total of 27,511 CCDS IDs that correspond to 18,535 GeneIDs. See the Releases & Statistics report for details.


Updates to the CCDS Website      October 18, 2012

Several changes have been made to the CCDS web site, including the search result and CCDS report pages.

Build Terminology

As announced this past July, the term build has been superceded by the term annotation release.

Reporting Annotation Releases

Displays have been updated to report annotation release numbers for both NCBI and Ensembl.

Reporting CCDS Releases

Each CCDS release is assigned a release number which is now being reported.

Reporting Assembly Information

CCDS report pages now include the reference genome assembly name and accession.version number in the "Chromosomal Locations" section. Also in this section, a Genome Browser link (the blue 'N' icon) has been added to support navigation to a graphical report in NCBI Nucleotide for the entire genomic range of the CDS.


CCDS Update Released for Mouse      August 14, 2012

The NCBI, Ensembl, and Sanger (Havana) annotation of the mouse reference genome (NCBI assembly ID GCF_000001635.20, NCBI annotation release 38.1, Ensembl annotation release 68) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 958 new CCDS IDs, reinstates 1 previously withdrawn CCDS ID, and adds 506 Genes into the mouse CCDS set. Mouse build 38.1 includes a total of 23,027 CCDS IDs that correspond to 19,945 GeneIDs. See the Releases & Statistics report for details.


Reporting of CCDS Releases      July 12, 2012

The BuildInfo file in the CCDS FTP site is being updated to add additional information about CCDS releases. This file contained the NCBI taxonomy ID and the NCBI build number and version. The new layout for this file adds five columns and reflects a new style for the NCBI build number:

tax_idNCBI taxonomy identifier
ncbi_release_numberNCBI build number and version (current; for example "37.3")
NCBI annotation release number (future; for example "103")
ensembl_release_numberEnsembl release number
assembly_nameThe short name of the assembly on which this CCDS release is based
assembly_idThe assembly accession and version
ccds_release_numberCCDS release number
date_made_publicDate when the CCDS release was made public, in YYYYMMDD format

The complete report of CCDS releases and their release numbers can be found by clicking the Releases & Statistics link on the left hand sidebar.


Search by NCBI GI      May 10, 2012

When searching for an NCBI sequence in CCDS by Nucleotide ID or Protein ID, you may now specify a GI or the more general accession identifier. As a new GI identifier is provided for any sequence change, addition of this query support facilitates rapid identification of a CCDS ID and version that is associated with a specific sequence.


CCDS Update Released for Human      September 7, 2011

The NCBI, Ensembl, and Sanger (Havana) annotation of the human reference genome (NCBI build 37.3) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 972 new CCDS IDs, reinstates 2 previously withdrawn CCDS IDs, and adds 91 Genes into the human CCDS set. Human build 37.3 includes a total of 26,473 CCDS IDs that correspond to 18,471 GeneIDs. See the statistics report for details.


CCDS Update Released for Human      April 22, 2011

The NCBI, Ensembl, and Sanger (Havana) annotation of the human reference genome (NCBI build 37.2) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update adds 2,126 new CCDS IDs, reinstates 13 previously withdrawn CCDS IDs, and adds 365 Genes into the human CCDS set. Human build 37.2 includes a total of 25,564 CCDS IDs that correspond to 18,409 GeneIDs. See the statistics report for details.


CCDS Update Released for Mouse      January 24, 2011

The NCBI, Ensembl, and Sanger (Havana) annotation of the mouse reference genome (NCBI build 37.2) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update includes the addition of 4,561 new CCDS IDs and adds 2,685 Genes into the mouse CCDS set. Mouse build 37.2 includes a total of 22,187 CCDS IDs that correspond to 19,509 GeneIDs. See the statistics report for details.


New FTP Reports of Exons      November 9, 2010

Two new reports of CDS exons are available from the CCDS FTP site.

The first report, named CCDS_exons.txt, is a tabular report of exons, which includes residue number and phase information, and can be used to identify which amino acids are encoded across a splice junction.

The second report, named CCDS_protein_exons.faa.gz, is a compressed file with a report of each exon sequence in FASTA format.

For a complete description of these files, please see the README file on the FTP site.


Change in FTP Filename      November 9, 2010

As documented in the README file on the FTP site, the protein FASTA FTP file named CCDS_protein.fna.gz has been renamed to CCDS_protein.faa.gz in order to accurately describe its contents.


Weekly FTP Updates      December 14, 2009

The FTP site, which can be accessed from the FTP link on the left hand sidebar, reports CCDS and sequence information when a CCDS build is made public. The site is now being updated on a weekly basis with current CCDS information, and will include both the original and current reports. The original reports from the time when the build was made public can be identified by the date stamp (in YYYYMMDD format) in the filenames, while the current reports will include the word current in their filenames. The current reports for CCDS summary information (CCDS.txt) and CCDS sequence information (CCDS2Sequence.txt) will change every week, but the other reports (BuildInfo.txt, CCDS_nucleotide.fna.gz and CCDS_protein.fna.gz) generally will not change from one week to the next.


Links to PubMed      October 22, 2009

When a CCDS has a public Note, that note often mentions one or more PubMed Identifiers (PMID). These identifiers now link directly to PubMed via hyperlink. Simply click on the PMID in the CCDS Note text, and it will take you to the record for the publication in PubMed.


Translation Exceptions      October 22, 2009

The CCDS Sequence Data section of the CCDS Report page has been updated to show translation exceptions in cases where the translation from the genomic sequence differs from the actual protein sequence. The report includes the translated symbol, the actual symbol, and the position in the sequence where the exception occurs. When you click on the replacement symbol in the text, the corresponding locations are highlighted in the nucleotide sequence and the translation below. For an example, see CCDS 192.


Update released: human       September 2, 2009

CCDS released an update for human following the full annotation of the human genome. This update adds 3852 CCDS IDs corresponding to 1300 GeneIDs. See the Statistics report for more information.


CCDS Curation Guidelines      April 15, 2009

The CCDS collaboration has developed curation guidelines for annotation of coding sequence regions (CDS). These guidelines include considerations of alternate in-frame translation start sites and alternate open reading frames found in the 5'UTR. CCDS Guidelines (PDF)


History Report Updates      September 2, 2008

The History Report has been updated to show the disposition of each CCDS identifier in each NCBI build. This information can be used to track identifiers and their status over time. The disposition categories are:

Made publicIndicates the NCBI build when the CCDS identifier was first publicly available
 
WithdrawnIndicates when an identifier was withdrawn from CCDS
 
RetainedIndicates that a CCDS identifier and version were carried over from the prior NCBI build to the next build without a version increment, indicating the annotation remained stable
 
UpdatedIndicates that a CCDS identifier was carried over from the prior NCBI build, and the CCDS version was incremented, indicating an annotation change
 
Partial matchIndicates that there was only a partial match between the NCBI and Ensembl annotation in this build
 
Withdrawn, inconsistent annotation: no matchIndicates that no match was found for this CDS between the NCBI and Ensembl annotation
 
 
Under review, withdrawal: no matchIndicates that no match was found for this CDS between the NCBI and Ensembl annotation. However, the CCDS was already under discussion to withdraw, indicating the loss reflects asynchronous annotation updates.
 
ReinstatedIndicates when a CCDS identifier that was previously a partial match or no match has been reinstated as a full match. The reinstatement may also include a CCDS version change.

Using CCDS 38 as an example, the history shows that CCDS 38.1 was made public in NCBI build 35.1, was retained in build 36.2, and was updated to CCDS 38.2 in build 36.3.

For CCDS 714, the history shows that CCDS 714.1 was made public in NCBI build 35.1, was a partial match in build 36.2, and was reinstated as a full match in build 36.3.


CCDS Public Notes Available:      July 9, 2008

CCDS Public Notes are now available for CCDS IDs that were recently updated or withdrawn, following consensus agreement from the NCBI, UCSC and WTSI/EBI groups. Public Notes will be added prospectively but will not be added comprehensively for previous changes. The purpose of these notes is to provide an explanation to users as to why a particular CCDS was either updated or withdrawn, and/or to explain representation choices for more complex cases. The Public Notes can be found in the Report, above the Sequence ID table, for a given CCDS ID that recently underwent a change in representation. For example, see CCDS ID 7726.2.


CCDS update released for human:       May 1, 2008

The NCBI, Ensembl, and Sanger (Havana) annotation of the human reference genome (NCBI build 36.3) was analyzed to identify additional coding sequences (CDS) that are consistently annotated. Existing CCDS IDs were tracked based on re-identification of matching annotation (both identical and partial matches of CCDS collaboration updates that were asynchronous). CCDS data is available in the CCDS web site and FTP site and will become available in the collaborators' genome and/or gene browser web sites according to each browser's update cycle.

This update includes the addition of 2,151 new CCDS IDs and adds 1,249 Genes into the human CCDS set. Human build 36.3 includes a total of 20,159 CCDS IDs that correspond to 17,052 GeneIDs. See the statistics report for details.


Search by build      February 26, 2007

A search in the CCDS database will include only current builds by default. To include data from prior builds in the search, change the search selection from Current Builds to All Builds.


Re-query by sequence ID      January 10, 2007

When viewing the sequence IDs for a CCDS, you can re-query the CCDS DB by Nucleotide ID or Protein ID by clicking the red "N" or "P" icon, respectively. These two new icons are in the Links column for each sequence ID shown in the table of sequence IDs for a CCDS.


Search capability enhanced      November 8, 2006

A new choice named All has been added to the Search box. This choice is now the default selection instead of Gene Symbol. The All search infers the type of search to be performed based on the search term that is entered, eliminating the need to select a type of search:

  • If the search term entered is a numeric identifier, or a numeric identifier preceded by "CCDS", then a search by CCDS ID is performed.
  • If the search term entered appears to be a nucleotide or protein identifier, then a search by Nucleotide ID or Protein ID is performed, respectively.
  • If none of the above is true, then a search by Gene Symbol is performed.

The existing search type selections are still available if you want to perform a specific type of search.