GBrowse evidence tiers help

Last Updated: 30 January 2007

A general description of GBrowse functionality may be found on the GBrowse page.

The sections below describe the evidence and data tiers specific to the FlyBase presentation of the D. melanogaster sequenced genome.

Gene Span Indicated in light blue. 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.

mRNA Indicated in peach/tan. Shows the exon (wider bars) and intron (narrow bars) structure of each annotated coding transcript, with direction of transcription indicated; introns indicated as narrow lines. Hyperlinked to Transcript Report; if label option is on, shows FlyBase symbol.

CDS Indicated in light grey. 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.

Blast hit Indicated in grey (vertical bar). 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.

NOTE: To clear the vertical grey bar, click on "Clear highlighting" at the bottom left of the GBrowse graphic.

3-frame translation (forward) Indicated in shades of blue. 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.

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.

3-frame translation (reverse) Indicated in shades of red. 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.

Affymetrix v1 Indicated in orange. Oligonucleotides (25-mers) designed by Affymetrix to correspond to annotated transcripts in D. melanogaster. Used for the Affymetrix GeneChip Drosophila Genome Array DrosGenome1 microarray, release date February 19, 2002.

Affymetrix v2 Indicated in orange. Oligonucleotides (25-mers) designed by Affymetrix to correspond to annotated transcripts in D. melanogaster. Used for the Affymetrix GeneChip Drosophila Genome 2.0 Array, release date July 1, 2004.

cDNA and other aligned sequences Indicated in dark green. D. melanogaster cDNA sequences submitted to the sequence databases; shows the exon (wider bars) and intron (narrow bars) structure, and direction of transcription. Sequences submitted prior to 2003 aligned using sim4 (Florea, et al., 1998, Genome Res. 8:967-74) 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.

DGRC-1 amplicons Indicated in orange. DNA fragments amplified from D. melanogaster genomic DNA (OregonR) by the Drosophila Genomics Resource Center (DGRC), using gene-specific primers made by Incyte and designed to target transcribed regions with minimal sequence similarity to other genes. Used for the DGRC-D.melanogaster-DGRC1-15552-v5 amplicon microarray, release date June 2, 2006 (original release of v1, May 2004).

DGRC-2 oligos Indicated in orange. "Long oligos" (65-69mers) designed to correspond to annotated transcripts in D. melanogaster (r4.3); synthesized by FlyChip and the Drosophila Genomics Resource Center (DGRC). Used for the DGRC-D.melanogaster-DGRC2-17328-v1 oligonucleotide microarray, release date June 20,2006.

DRSC RNAi amplicons Indicated in orange. A library of double-stranded RNAs (dsRNAs) directed against all predicted reading frames, generated by the Drosophila RNAi Screening Center (DRSC).

EST ("expressed sequence tag") Indicated in light green. Partial sequence of a cDNA; shows the exon (wider bars) and intron (narrow bars) structure, and direction of transcription. D. melanogaster EST sequences submitted to the sequence databases prior to 2003 aligned using sim4 (Florea, et al., 1998, Genome Res. 8:967-74) 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.

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.

Tiling BAC Indicated by narrow gray bar. BAC genomic clones used by the Berkeley Drosophila Genome Project as part of the minimal tiling path used for determination of the D. melanogaster genomic sequence (FBrf0155823).

Cytological band Approximate extent of the classical cytological chromosome bands described by Bridges. See Computed cytological data in FlyBase 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.

Non coding RNA Indicated in peach/tan. Extent of transcribed region corresponding to an annotated non-coding RNA (intron structure not shown). Hyperlinked to Transcript Report; if label option is on, shows FlyBase symbol.

tRNA Indicated in white. Extent of transcribed region corresponding to an annotated tRNA (intron structure not shown). Hyperlinked to Transcript Report; if label option is on, shows FlyBase symbol.

Natural transposon Indicated in pink. Extent of a natural transposable element in the sequenced strain (at the time it was sequenced). Hyperlinked to an a specially formatted version of the Gene Report describing the natural transposon; if label option is on, shows FlyBase symbol.

Transgene insertion site Indicated by blue triangles (which indicate orientation of the insertion) or diamonds (if orientation is not known). An insertion indicated by a downward-pointing triangle 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 a upward-pointing triangle 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. Hyperlinked to an Insertion Report; if label option is on, shows FlyBase symbol.

NOTE:

If the "Flip" option is selected, the orientations of the insertion triangles do not change and thus will be incorrect.

One of the "Data Source" options (one of the upper left menu windows) is "Insertions in Stock Collections."

Timecourse (Arbeitman et al.)

Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002)

Aberration_junction Indicated by grey bar. 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.

Enhancer Indicated by grey bar. Location of transcriptional enhancer reported in the literature. Reference and supporting information available in the "Mapped features and mutations" section of the Gene Report.

Point_mutation Indicated by grey bar. Site of point mutation 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.

Protein_binding_site Indicated by grey bar. Locations of protein binding site reported in the literature, as compiled by FlyBase and/or FlyReg). Reference and supporting information available in the "Mapped features and mutations" section of the Gene Report.

Regulatory_region Indicated by grey bar. Location of regulatory feature reported in the literature. Reference and supporting information available in the "Mapped features and mutations" section of the Gene Report.

Rescue_fragment Indicated by grey bar. 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.

Sequence_variant Indicated by grey bar. Site of mutation reported in the literature; labeled with FlyBase allele symbol designation. Mutation features that have an actual range greater than one base and features that have been mapped approximately (usually to a restriction fragment) appear in this tier. Reference and supporting information available in the "Mapped features and mutations" section of the Gene Report; genetic data available in the Allele Report.

Augustus prediction Indicated in light brown. 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.

CONGO exons Indicated in yellow. 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.

CONTRAST prediction Indicated in yellow. 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.

GeneID prediction Indicated in yellow. 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.

Genie prediction Indicated in yellow. 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).

Genscan prediction Indicated in light brown. 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.

HDP prediction Indicated in light brown. Gene prediction (coding region of transcript) based on ab initio gene predictions of lower stringency using Fgenesh software (Salamov and Solovyev, 2000, Genome Res 10:516-522) and supported by microarray evidence of expression during the fly life cycle, using the Heidelberg FlyArray (FBrf0167699). Submitted by M. Hild; only novel predictions submitted.

NCBI gnomon prediction Indicated in yellow. 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.

Promoter prediction Indicated by narrow purple line, bounded by vertical lines (a sideways "H"). Predicted location of a transcription start site (FBrf0155830); contributed by U. Ohler.

Repeat region Indicated in purple. Regions of genomic repeats and low complexity DNA sequences, as computed using RepeatMasker and RepeatRunner.

RNAiHDP prediction Indicated in light brown. Gene prediction (coding region of transcript) based on ab initio gene predictions of lower stringency using Fgenesh software (Salamov and Solovyev, 2000, Genome Res 10:516-522) that are supported by RNAi phenotypes as assessed in cell culture (FBrf0167699). Submitted by M. Hild; only novel predictions submitted.

SNAP prediction Indicated in yellow. 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.

tRNAscan prediction Indicated in yellow. Predicted location of a tRNA gene, using tRNAscan-SE (Lowe and Eddy, 1997, Nucleic Acids Res 25:955-964); used for Release 3 annotations of D. melanogaster.

Dmel ARGs Indicated in grey. D. melanogaster transcript annotation based on data reported in the literature; curated by FlyBase prior to annotation of the full genome (FBrf0155827).

Dmel ARGs CDS Indicated in grey. D. melanogaster predicted protein corresponding to transcript annotation based on data reported in the literature; curated by FlyBase prior to annotation of the full genome (FBrf0155827).

Dmel r2 transcript Indicated in grey. D. melanogaster transcript annotation from prior annotation/sequence release (Release 2, Oct. 2000; FBrf0127298).

Dmel r31 transcript Indicated in grey. D. melanogaster transcript annotation from prior annotation/sequence release (Release 3.1, Feb. 2003; FBrf0155827).

Dmel r32 transcript Indicated in grey. D. melanogaster transcript annotation from prior annotation/sequence release (Release 3.2, March 2004).

Dros smallRNA Indicated in grey. D. melanogaster small non-coding RNA sequences submitted to the sequence databases prior to 2003; aligned using sim4 (Florea, et al., 1998, Genome Res. 8:967-74) to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase.

D melanogaster protein Indicated in grey. 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.

Other Insect proteins Indicated in grey. Insect (other than D.melanogaster) protein sequences submitted to the sequence databases prior to 2003; aligned by BLASTX to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase.

Other invert. protein Indicated in grey. Invertebrate (other than those listed above) protein sequences submitted to the sequence databases prior to 2003; aligned by BLASTX to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase.

Other proteins Indicated in grey. 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.

Plant protein Indicated in grey. Plant protein sequences submitted to the sequence databases prior to 2003; aligned by BLASTX to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase.

Primate protein Indicated in grey. Primate protein sequences submitted to the sequence databases prior to 2003; aligned by BLASTX to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase.

Vertebrate protein Indicated in grey. Vertebrate (other than primate) protein sequences submitted to the sequence databases prior to 2003; aligned by BLASTX to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase.

Worm protein Indicated in grey. C. elegans protein sequences submitted to the sequence databases prior to 2003; aligned by BLASTX to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase.

Yeast protein Indicated in grey. Yeast protein sequences submitted to the sequence databases prior to 2003; aligned by BLASTX to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase.

Ortholog (FlyBase) Indicated in green. Region of homology between D. melanogaster and D. pseudoobscura likely to be orthologous, as determined by Richards, et al. (FBrf0184012). Hyperlinked to GBrowse view of the orthologous region in the other species.

Ortholog (GLEANR) Indicated in green. Region of homology between Drosophila species likely to be orthologous, as determined by Eisen et al. (AAA). Hyperlinked to GBrowse view of the orthologous region in the other species.

Syntenic region (FlyBase) Indicated in rose pink. Extent of a region syntenic between D. melanogaster and D. pseudoobscura (i.e., an orthologous chromosomal region encompassing two or more genes), as determined by Richards, et al. (FBrf0184012).

D pseudoobscura contigs Indicated in grey. D. pseudoobscura DNA sequence aligned by TBLASTX to Release 3 (FBrf0184012)and promoted to Releases 4 and 5 by FlyBase.

Insect dbEST Indicated in grey. Predicted protein sequences derived from insect cDNA and EST sequences submitted to the sequence databases prior to 2003; aligned by TBLASTX to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase.

Mosquito NA Indicated in grey. Predicted protein sequences derived from Anopheles cDNA and EST sequences submitted to the sequence databases prior to 2003; aligned by TBLASTX to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase.