Difference between revisions of "FlyBase:GBrowse Tracks"

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'''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.
 
'''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.
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== Blast Hit ==
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'''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.

Revision as of 15:41, 30 July 2014

Reference Genome Annotations (Iso-1)

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.

Transcript SO:0000673::/cgi-bin/cvreport.html?id=SO:0000673 Shows the exon (wider bars) and intron (black line) structure of each annotated coding transcript, with direction of transcription indicated. Hyperlinked Transcript Report; if label option is on, shows FlyBase symbol.

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.

Natural TE SO:0000101::/cgi-bin/cvreport.html?id=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::/static_pages/newhelp/natural_transposon_help.html; if label option is on, shows FlyBase symbol.

Repeat region Regions of genomic repeats and low complexity DNA sequences, as computed using RepeatMasker and RepeatRunner (Smith, et al., 2007).

General

Estimated 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.

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.

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.

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.

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 (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.

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.

mRNA D. melanogaster mRNA sequences submitted to the sequence databases;  shows the exon (wider bars) and intron (narrow bars) 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.

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 (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.  Some genomic DNA submissions, including TPA submissions, are included in this tier.

RNA-Seq based exon junctions FBlc0000204, FBlc0000203

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.

Mapped Mutations

Transgene insertion site SO:0000368 Indicated by blue triangles (which indicate orientation of the transgene insertion site) 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. For a guide on how to work out the orientation of an insertion relative to a transcript of interest, see this short powerpoint presentation.

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.

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.

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.

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.

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.

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.

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.

Gene Predictions

NCBI gnomon, 2014 Gene model prediction, transcript prediction.

NCBI gnomon, 2006 (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.

CONTRAST (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.

PhyloCSF (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.

Similarity: Synteny features

Proteins (aligned by BLAST)

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.

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.

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.

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.