New Release: FB2016_04, released July 28th, 2016
FB2016_04, released July 28, 2016
 
 

A Database of Drosophila Genes & Genomes

GBrowse Gene Models/Evidence view help

 

The Gene Models/Evidence view contains all the evidence related to the structure of our gene models. This includes such tracks as gene predictions, aligned cDNAs, and orthology information.

Links to other views:

Reference Genome Annotations
Gene Span Shows the total extent of the transcribed region of an annotated gene (including non-coding genes), with direction of transcription indicated. No transcript substructure is shown; corresponds to the entire extent defined by all annotated transcripts. Hyperlinked to Gene Report; label shows FlyBase gene symbol.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Transcript SO:0000673 Shows the exon (wider bars) and intron (black line) structure of each annotated coding transcript, with direction of transcription indicated. Hyperlinked to Transcript Report; if label option is on, shows FlyBase symbol.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
CDS Shows extent of sequence encoding each specific polypeptide, with direction of transcription indicated; introns indicated as narrow lines. Hyperlinked to Polypeptide Report; if label option is on, shows FlyBase symbol.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Natural TE SO:0000101 Shows the extent of a natural transposable element in the sequenced strain (at the time it was sequenced). Hyperlinked to Natural Transposon Report; if label option is on, shows FlyBase symbol.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Repeat region Regions of genomic repeats and low complexity DNA sequences, as computed using RepeatMasker and RepeatRunner (FBrf0194515)
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
General
Estimated Cytological band Approximate extent of the classical cytological chromosome bands described by Bridges. See Computed cytological data for a detailed description of how this computed cytological location is calculated. See Sorsa polytene maps for a collection of EM micrographs of chromosome regions aligned to Bridges' maps.
Available in these data source views:
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
3-frame translation (forward) If zoomed out (greater than 400bp), shows ticks at sites of stop codons for the three frames on the forward strand. If zoomed in (400bp or less), shows predicted translations for each frame, using single-letter amino acid code.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
3-frame translation (reverse) If zoomed out (greater than 400bp), shows ticks at sites of stop codons for the three frames on the reverse strand. If zoomed in (400bp or less), shows predicted translations for each frame, using single-letter amino acid code.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
DNA/GC Content If zoomed out (greater than 100bp) shows a graphic of GC content calculated over 10bp intervals. If zoomed in (100bp or less), shows the double-stranded DNA sequence.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Aligned Evidence
cDNA D. melanogaster cDNA sequences submitted to the sequence databases; shows the exon (wider bars) and intron (black line) structure, and direction of transcription. Sequences submitted prior to 2003 aligned using sim4 (FBrf0105376) or sim4tandem (sim4 modified by S. Shu, BDGP) to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase. Sequences submitted since 2003 aligned to Releases 4 and 5 by NCBI and submitted to FlyBase. Some genomic DNA submissions, including TPA submissions, are included in this tier.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • Gene Disruptions, Stocks, and Reagents (under track grouping 'Clones')
EST ("expressed sequence tag") Partial sequence of a cDNA; shows the exon (wider bars) and intron (black line) structure, and direction of transcription. D. melanogaster EST sequences submitted to the sequence databases prior to 2003 aligned using sim4 (FBrf0105376) to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase. D. melanogaster EST sequences submitted since 2003 aligned to Releases 4 and 5 by NCBI and submitted to FlyBase.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
mRNA D. melanogaster mRNA sequences submitted to the sequence databases; shows the exon (wider bars) and intron (black line) structure, and direction of transcription. Sequences are aligned to Release 5 by NCBI and submitted to FlyBase. These mRNA sequences frequently reflect composite assemblies of a conceptual transcript and therefore may not be available as reagents.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
other aligned sequences D. melanogaster aligned nucleotides submitted to the sequence databases. These aligned sequences were generally submitted prior to 2003 and aligned using sim4 (FBrf0105376) or sim4tandem (sim4 modified by S. Shu, BDGP) to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase. Some genomic DNA submissions, including TPA submissions, are included in this tier.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
RNA-Seq based exon junctions (FBlc0000204) (FBlc0000203)
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
PeptideAtlas peptides Indicated in yellow. Alignment of peptide sequences determined by mass spectroscopy, derived from polypeptides isolated from the sequenced strain at various developmental stages. Contributed by the Center for Model Organism Proteomes, SystemsX and Research Priority Project of the University of Zurich, Switzerland.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
Previous Gene Models
Recently deleted transcripts FlyBase annotated transcript models that have been deleted from FlyBase since annotation release 5.8; shows the exon (wider bars) and intron (black line) structure. FlyBase policy is to delete a transcript and create a new model if alteration of the existing model alters the coding region of the transcript in any way. In addition, transcripts can be retired if it is judged that the model is erroneous or lacks sufficient supporting evidence.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
Mapped Mutations
Transgene insertion site SO:0000368 Indicated by blue triangles with an arrow or diamonds with no arrow. An insertion indicated by a downward-pointing triangle and an arrow pointing to the right is oriented with its conventional 5' terminus to the left (assuming view is in conventional orientation of the Drosophila chromosome); this is described as being in the "plus" orientation. An insertion indicated by an upward-pointing triangle and an arrow pointing to the left is oriented with its conventional 5' terminus to the right (assuming view is in conventional orientation of the Drosophila chromosome); this is described as being in the "minus" orientation. An insertion indicated with a blue diamond has an unknown orientation. For all insertions, if the estimated insertion site is larger than 10 nucleotides, there are short dashes on either side of the triangle or diamond. In those cases, see the Insertion Report for more information about localization. Insertions are hyperlinked to their respective Insertion Report. NOTE: If the "Flip" option is selected, the orientations of the insertion triangles do not change and thus will be incorrect. For a guide on how to work out the orientation of an insertion relative to a transcript of interest, see this short powerpoint presentation.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Point mutation SO:1000008 A single nucleotide has been changed into another nucleotide. Location of mutation is indicated with a grey bar and labeled with the FlyBase allele symbol.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Sequence variant SO:0000109 A region of sequence where variation has been observed. Often these refer to natural variants of a protein that lead to two different functions. The location of the mutation is indicated with a grey bar and labeled with the FlyBase allele symbol.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Uncharacterized change in nucleotide sequence SO:1000007 The nature of the nucleotide substitution is either uncharacterized or only partially characterized. The location of the mutation is indicated with grey bar and labeled with the FlyBase allele symbol.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Aberration junction SO:0000687 Location of aberration breakpoint reported in the literature. Labeled with FlyBase aberration symbol designation and the numerical designation of the breakpoint mapped (where known). Generally the exact breakpoint location is unknown and the feature indicates a range within which the breakpoint has been mapped. References and supporting information available in the "Mapped features and mutations" section of the Gene Report for a nearby gene; genetic data available in the Aberration Report.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Complex substitution SO:1000005 The mutation occurred from a mutation event that cannot be determined from the observed DNA change. Location of mutation is indicated with a grey bar and labeled with the FlyBase allele symbol.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Indels SO:1000032 The junction where an insertion or deletion of one or more nucleotides occurred. Location of mutation is indicated with a grey bar and labeled with the FlyBase allele symbol. In the case of deletions, the extent of the deletion is indicated by a grey bar. In the case of insertions, the location of the nucleotide(s) insertion is indicated by a vertical grey line.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Rescue fragment SO:0000411 Locations of transgenic rescue fragment reported in the literature. Labeled with FlyBase allele symbol designation. Reference and supporting information available in the "Mapped features and mutations" section of the Gene Report; genetic data available in the Allele Report.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Gene Predictions
Augustus Gene prediction (coding region of transcript) generated via a generalized hidden Markov model using transcript alignment constraints and protein hit information, has been trained on D. melanogaster (Stanke, et al., 2006, BMC Bioinformatics 7:62); submitted by M. Stanke.
Available in these data source views:
  • Gene Models/Evidence
Genscan Gene prediction (coding region of transcript) using a system developed for annotation of the human genomic sequence (Burge and Karlin, 1997, J Mol Biol 268:78-94); used (in addition to Genie) for Release 3 annotations of D. melanogaster.
Available in these data source views:
  • Gene Models/Evidence
Genie Gene prediction (coding region of transcript) using a hidden Markov model-based system trained on D. melanogaster (FBrf0127289); the original gene prediction program used for D. melanogaster annotations (Releases 1 and 2).
Available in these data source views:
  • Gene Models/Evidence
GeneID Gene prediction (coding region of transcript) that incorporates available transcript data (Parra, Blanco, and Guigo, 2000, Genome Research, 10:511-515); submitted by R. Guigo.
Available in these data source views:
  • Gene Models/Evidence
NCBI gnomon Gene prediction (coding region of transcript) generated via a hidden Markov model using transcript alignment constraints and protein hit information, if available; allows prediction of alternatively spliced isoforms (Souvorov, et al., 2006, NCBI); submitted by J. Ostell.
Available in these data source views:
  • Gene Models/Evidence
CONTRAST Gene prediction (coding region of transcript) using a semi-Markov conditional random field (Gross, Do, and Batzoglou, 2005, BCATS 2005 Symposium Proceedings, p. 82); submitted by S. Batzoglou.
Available in these data source views:
  • Gene Models/Evidence
SNAP Gene prediction (coding region of transcript) using a generalized hidden Markov model designed to be easily adapted to different genomes (Korf, 2004, BMC Bioinformatics 5:59); submitted by D. Gilbert.
Available in these data source views:
  • Gene Models/Evidence
CONGO (exon prediction) Region of sequence conservation across multiple Drosophila species, with a pattern of conservation indicative of a protein-coding extent and termini consistent with exon structure (start, splice or stop); submitted by M. Lin and M. Kellis.
Available in these data source views:
  • Gene Models/Evidence
MB8 (modENCODE Transcription Group) FBlc0000285
Available in these data source views:
  • Gene Models/Evidence
Similarity: Synteny features
Orthologs Indicated by yellow bar covering extent of the orthologous region. Mousing over this bar will cause a pop-up box to appear which will contain links for all of the orthologs of the gene. The ortholog box will contain the drosophilid orthologs on the left and other orthologs on the right.
Available in these data source views:
  • Gene Models/Evidence
Similarity: Proteins
Dmel proteins D. melanogaster protein sequences submitted to the sequence databases. Sequences submitted prior to 2003 aligned by BLASTX to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase. Sequences submitted since 2003 aligned by TBLASTN to Releases 4 and 5 by NCBI and submitted to FlyBase.
Available in these data source views:
  • Gene Models/Evidence
Other proteins Protein sequences submitted to the sequence databases since 2003, from species other than D. melanogaster; aligned by TBLASTN to Releases 4 and 5 by NCBI and submitted to FlyBase.
Available in these data source views:
  • Gene Models/Evidence
Blast Hit
BLAST HSP If entry into GBrowse was via a linked hit using the FlyBase BLAST tool, the extent of the aligned region is shown as a vertical grey bar that extends through all the GBrowse tiers.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents