FB2014_04, released July 21st, 2014
 
 

A Database of Drosophila Genes & Genomes

Transcript report help

Last Updated: 28 March 2007

The Transcript Report provides information on individual annotated transcripts. Annotated transcripts are transcripts identified by FlyBase annotators based on a variety of evidence including cDNA/ESTs, protein alignment, and gene predictions. Transcripts described in the literature may or may not correspond exactly to annotated transcripts. Curated transcript data is found on the Gene Report, subsection Transcript Data, field Reported transcript sizes.

This is a field-by-field guide to the information provided in the Transcript Report.

hide General Information
Symbol

The valid symbol that is used in FlyBase for the transcript.

The first part of the symbol (before the '\') is the standard prefix for the species (from the Species Abbreviations list). For species other than D.melanogaster, the species prefix is displayed wherever the transcript symbol is used throughout FlyBase. For D.melanogaster transcripts, the species prefix is only displayed in the GENERAL INFORMATION section at the top of a Report.

Annotation symbol

The current symbol for the annotation that represents the transcript.

Associated gene

The gene that encodes the transcript.

Clicking on the gene symbol will take you to the relevant Gene Report.

Species

The organism that the transcript originates from, with the initial letter of the genus and the full species name listed.

FlyBase ID

The Primary FlyBase identifier number of the transcript, used to uniquely identify the transcript in the database.

A transcript may also have any number of Secondary FlyBase identifier numbers, which are listed in the SECONDARY FLYBASE IDs section of the Transcript Report.

Created/ Updated

The date that the transcript was entered into the database and the date that the transcript report was last updated. The dates are in the format: year-mm-dd.

Evidence Rank

A transcript is given a rank based on its Annotation Evidence Score. Transcripts with a score less than 5 are classified as 'Weakly Supported'. Those with a score between 5 and 8 are classified as 'Moderately Supported' and those with a score of 9 and above are classified 'Strongly Supported'.

These classifications should be considered as indicative but not definitive of support for a transcript annotation. Only the classes of evidence described in the 'Evidence Score' section are considered and there may be additional support for a transcript annotation that has not been assessed by these methods, for example, a transcript structure reported in literature for which no corresponding sequence record exists in the public databases.

Evidence Score

Each transcript gets a score that is based on the sum of the following categories:

  • 1 point if one or more aligned EST sequences are fully consistent with the annotated transcript.
  • 2 points if an annotated exon intersects a region of aligned protein similarity
    (note that similarity to self is excluded)
  • 4 points if there is any gene prediction that is fully consistent with the annotated transcript
  • 8 points if one or more aligned cDNAs are fully consistent with the annotated transcript.

The points assigned for each type of evidence allow one to easily and unambiguously determine what types of evidence exist that support a particular transcript annotation as each possible combination of supporting types receives a unique score.

Length (nt)

The length in nucleotides of the transcript.

Map

GBrowse shapshot showing gene region plus 2kb on either side of the gene. Snapshot includes transcripts of the gene of interest, plus transcripts of neighboring genes. The transcript of interest is hilighted in pink.

hide Supporting cDNA Clones (Num)
cDNA Clones, Fully Sequenced

Contains a list of cDNA clones which have been fully sequenced and which support the transcript

Exact Match

Clones are an exact match at the nucleotide level to the annotated transcript. This includes the 5 prime and 3 prime ends as well as all splice junctions.

Contained within the annotated transcript, internally consistent

Clones that support the transcript, but do not extend the full length of the transcript.

End(s) extend beyond the annotated transcript, internally consistent

Clones may be full length or partial, and support the internal structure of the transcript, but extend beyond the transcript at the 5 prime and/or the 3 prime end.

cDNA Clones, End Sequence Only (ESTs)

cDNA clones which have not yet been fully sequenced. The clones may or may not be full length.

Contained within the annotated transcript, internally consistent

Clones that support the annotated transcript but the sequence begins and ends within the transcript.

End(s) extend beyond the annotated transcript, internally consistent

Clones that are consistent with the annotated transcript, but extend beyond at either the 3' or 5' end.

hide Sequence

The nucleotide sequence of the transcript.

hide Other Products of this Gene
Other Transcripts

A table of other transcripts derived from the same gene, which lists each transcript symbol, its Primary FlyBase identifier number and its length in nucleotides.

Clicking on a transcript symbol will take you to the relevant Transcript Report.

Polypeptides

A table of polypeotides encoded by the same gene, which lists each polypeptide symbol, its Primary FlyBase identifier number and its length in amino acid residues.

The table is subdivided into the polypeptides derived from this transcript and polypeptides derived from other transcripts.

Clicking on a polypeptide symbol will take you to the relevant Polypeptide Report.

hide Comments

Comments regarding the annotation of the transcript, including whether the transcript contains any unconventional features.

This section is only displayed in an individual Transcript Report if it contains data.

hide External Crossreferences

A table of DDBJ/EMBL/Genbank sequence accession numbers corresponding to the transcript.

Clicking on the accession number will take you to the appropriate entry in the GenBank database.

hide Synonyms

A list of symbols that have been used in the literature, or by FlyBase, to describe the transcript.

hide References

A list of publications that discuss the transcript, subdivided into fields by type of publication. Publications which discuss the associated gene but not this particular transcript can be found on the Gene Report. Only those fields containing data are displayed in an individual Transcript Report.