GBrowse Expression/Regulation view help

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 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.

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 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.

Repeat region Regions of genomic repeats and low complexity DNA sequences, as computed using RepeatMasker and RepeatRunner (FBrf0194515)

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Insulators class I FBlc0000058

Insulators class II FBlc0000059

Enhancers FBlc0000415

Silencers FBlc0000414

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.

TFBS - HOT spot analysis FBlc0000258

TFBS – zinc finger domain FBlc0000293 FBlc0000299 FBlc0000058 FBlc0000300 FBlc0000303 FBlc0000304 FBlc0000308 FBlc0000309 FBlc0000314 FBlc0000315 FBlc0000316 FBlc0000318 FBlc0000320 FBlc0000326

TFBS - homeodomain FBlc0000287 FBlc0000288 FBlc0000295 FBlc0000296 FBlc0000297 FBlc0000298 FBlc0000305 FBlc0000312 FBlc0000324 FBlc0000325

TFBS - helix-loop-helix domain FBlc0000292 FBlc0000302 FBlc0000307 FBlc0000323

TFBS - BTB/POZ domain FBlc0000286 FBlc0000289 FBlc0000321 FBlc0000322

TFBS - other FBlc0000290 FBlc0000291 FBlc0000294 FBlc0000301 FBlc0000306 FBlc0000310 FBlc0000311 FBlc0000313 FBlc0000317 FBlc0000319

Chromatin domains (5-state model, Kc cells) FBlc0000187

Chromatin domains (9-state model, S2 cells) FBlc0000199

Chromatin domains (9-state model, BG3 cells) FBlc0000200

Origins of replication FBlc0000188

Putative brain enhancers (Pfeiffer et al) FBlc0000201

RNA editing sites FBlc0000259

Affymetric v1 FBlc0000327 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.

Affymetric v2 FBlc0000029 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.

Timecourse, cDNA (Arbeitman et al.) Developmental timecourse, Costello et al., 2008 (Original data from FBrf0152339)

Timecourse, amplicons (Gauhar et al.). D. melanogaster life-cycle gene expression dataset. Gauhar and Ghanim et al. (FBrf0205914) original data from Stolc and Gauhar et al. (FBrf0180683)

Tissue Expression, Affy2 (FlyAtlas) FBlc0000157 FBlc0000175

Developmental stage subsets (Baylor) FBlc0000060

Developmental stage subsets, unique reads (modENCODE) FBlc0000085

Tissue culture cells (modENCODE Transcription Group) FBlc0000116

Tissue culture cells, by strand (modENCODE Transcription Group) FBlc0000260

Treatments/Conditions FBlc0000236

Digestive system Comprised of four RNA-Seq data sets: mE_mRNA_L3_Wand_dig_sys (FBlc0000227 mE_mRNA_A_1d_dig_sys FBlc0000219 mE_mRNA_A_4d_dig_sys FBlc0000223 mE_mRNA_A_20d_dig_sys FBlc0000221

Fat body and salivary glands mE_mRNA_L3_Wand_fat FBlc0000228 mE_mRNA_WPP_fat FBlc0000233 mE_mRNA_P8_fat FBlc0000235 mE_mRNA_L3_Wand_saliv FBlc0000230 mE_mRNA_WPP_saliv FBlc0000234

Imaginal disc and other carcass mE_mRNA_L3_Wand_imag_disc FBlc0000229 mE_mRNA_L3_Wand_carcass FBlc0000226 mE_mRNA_A_1d_carcass FBlc0000218 mE_mRNA_A_4d_carcass FBlc0000222 mE_mRNA_A_20d_carcass FBlc0000220

CNS and adult head mE_mRNA_L3_CNS FBlc0000225 mE_mRNA_P8_CNS FBlc0000224 mE_mRNA_A_MateM_1d_head FBlc0000209 mE_mRNA_A_MateM_4d_head FBlc0000216 mE_mRNA_A_MateM_20d_head FBlc0000214 mE_mRNA_A_VirF_1d_head FBlc0000210 mE_mRNA_A_VirF_4d_head FBlc0000211 mE_mRNA_A_VirF_20d_head FBlc0000231 mE_mRNA_A_MateF_1d_head FBlc0000207 mE_mRNA_A_MateF_4d_head FBlc0000213 mE_mRNA_A_MateF_20d_head FBlc0000212

Gonads and male accessory glands mE_mRNA_A_MateM_4d_testis FBlc0000217 mE_mRNA_A_MateM_4d_acc_gland FBlc0000215 mE_mRNA_A_VirF_4d_ovary FBlc0000232 mE_mRNA_A_MateF_4d_ovary FBlc0000208

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.