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Configure Tracks on UCSC Genome Browser: D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)
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Control track and group visibility more selectively below.
-   PhyloCSF    
PhyloCSF Novel v6.15 PhyloCSF Candidate Coding Regions (PCCRs) Not In flybase v6.15 Gene Set
Smoothed PhyloCSF Smoothed PhyloCSF
     PhyloCSF-3     Smoothed PhyloCSF Strand - Frame 3
     PhyloCSF-2     Smoothed PhyloCSF Strand - Frame 2
     PhyloCSF-1     Smoothed PhyloCSF Strand - Frame 1
     PhyloCSF+3     Smoothed PhyloCSF Strand + Frame 3
     PhyloCSF+2     Smoothed PhyloCSF Strand + Frame 2
     PhyloCSF+1     Smoothed PhyloCSF Strand + Frame 1
PhyloCSF Regions PhyloCSF approximate coding regions
     PhyloCSF-3Regns     PhyloCSF approximate coding regions, Strand -, Frame 3
     PhyloCSF-2Regns     PhyloCSF approximate coding regions, Strand -, Frame 2
     PhyloCSF-1Regns     PhyloCSF approximate coding regions, Strand -, Frame 1
     PhyloCSF+3Regns     PhyloCSF approximate coding regions, Strand +, Frame 3
     PhyloCSF+2Regns     PhyloCSF approximate coding regions, Strand +, Frame 2
     PhyloCSF+1Regns     PhyloCSF approximate coding regions, Strand +, Frame 1
Raw PhyloCSF Raw PhyloCSF
     PhyloCSFraw-3     Raw PhyloCSF Strand - Frame 3
     PhyloCSFraw-2     Raw PhyloCSF Strand - Frame 2
     PhyloCSFraw-1     Raw PhyloCSF Strand - Frame 1
     PhyloCSFraw+3     Raw PhyloCSF Strand + Frame 3
     PhyloCSFraw+2     Raw PhyloCSF Strand + Frame 2
     PhyloCSFraw+1     Raw PhyloCSF Strand + Frame 1
PhyloCSF Power Relative branch length of local alignment, a measure of PhyloCSF statistical power
Splice Predictions Splice Predictions
     SplicePred-     Splice Predictions For - Strand
     SplicePred+     Splice Predictions For + Strand
-   Mapping and Sequencing Tracks    
Base Position Chromosome position in bases. (Clicks here zoom in 3x)
Chromosome Band Chromosome Bands
Gap Gap Locations
GC Percent GC Percent in 5-Base Windows
Assembly Assembly from Fragments
INSDC Accession at INSDC - International Nucleotide Sequence Database Collaboration
RefSeq Acc RefSeq Accession
Restr Enzymes Restriction Enzymes from REBASE
Short Match Perfect Matches to Short Sequence ()
Melting Temp. Melting Temperature Estimated by dan
RNASlider MFE Minimum Free Energy Estimated by RNASlider
+   Transgenic Insertions    
-   Chromatin Domains    
Het. Domains (R5) Broad H3K9me3+ Heterochromatin Domains (R5)
BG3 9-state (R5) modENCODE 9-state Model for BG3 cells (R5)
S2 9-state (R5) modENCODE 9-state Model for S2 cells (R5)
BG3 30-state (R5) modENCODE 30-state Model for BG3 cells (R5)
S2 30-state (R5) modENCODE 30-state Model for S2 cells (R5)
Kc 5-state (R5) 5-state Model for Kc cells (R5)
hiHMM Models (R5) hiHMM Chromatin State Tracks (R5)
S2 Zhou 30-state (R5) 30-state Model for S2 Cells Created by Zhou and Troyanskaya (R5)
LAD (R5) Lamina Associated Domains (LADs) in Kc Cells (R5)
Hi-C Domains (Embryos) (R5) Topological Domains Defined by Hi-C in Late Embryos (R5)
Topological Boundaries (R5) Topological Domain Boundaries Inferred from Chromatin States (R5)
TAD Boundaries (Nuc. Cycle 14) TAD Boundaries in Nuclear Cycle 14 Embryos
HiCseg Domains (Kc167) (R5) Domains Predicted by HiCseg Based Hi-C Data for Kc167 Cells (R5)
MARs (Embryos) Matrix Attachment Regions (MARs) in 0-16 Hour Embryos
Polytene TADs (R5) Polytene TADs Identified by Hi-C (R5)
GCSDI Models (R5) General Chromatin Sensitivity to DNase I Configuration Models (R5)
-   Genes and Gene Prediction Tracks    
FlyBase Genes FlyBase Protein-Coding Genes
FlyBase Exons FlyBase Transcribed Exons
FlyBase CDS FlyBase Coding Exons
FlyBase Pseudogenes FlyBase Pseudogenes
FlyBase Non-coding FlyBase Non-protein Coding Genes
Drosophila RefSeq Transcripts BLAT Alignment of Drosophila RefSeq Transcripts
piRNA Clusters (R5) piRNA Clusters from Brennecke et al. 2007 (R5)
Pfam in RefSeq Pfam Domains in RefSeq Genes
UniProt UniProt SwissProt/TrEMBL Protein Annotations
FlyBase 6.06 Genes FlyBase 6.06 Protein-Coding Genes
FlyBase 6.06 Proteins FlyBase 6.06 Protein-Coding Regions
FlyBase 6.06 Exons FlyBase 6.06 Transcribed Exons
FlyBase 6.06 CDS FlyBase 6.06 Coding Exons
FlyBase 6.06 Pseudogenes FlyBase 6.06 Pseudogenes
FlyBase 6.06 Non-coding FlyBase 6.06 Non-protein Coding Genes
-   ChIP Seq Tracks    
Phantom Peaks (R5) ChIP-Seq Phantom Peaks (R5)
modENCODE Histones ChIP-Seq modENCODE Chromatin State Mapping Using ChIP-Seq
PePr Histone Modifications Peaks ChIP-Seq Peaks Identified by PePr
MUSIC Histone Modifications Peaks ChIP-Seq Peaks Identified by MUSIC
Genome Mappability Genome Mappability
modENCODE PolII ChIP-Seq modENCODE RNA Polymerase II ChIP-Seq
MUSIC PolII ChIP-Seq Peaks modENCODE RNA Polymerase ChIP-Seq Peaks Identified by MUSIC
PolII ChIP-Seq (Cell Lines) RNA Polymerase II ChIP-Seq for Cell Lines
RNA PolII X-ChIP-Seq RNA PolII X-ChIP-Seq for Drosophila S2 Cells
Inhibit Topoisomerases PolII ChIP-Seq PolII ChIP-Seq After Inhibition of Topoisomerases
Basal Transcription Factors ChIP-Seq Basal Transcription Factors ChIP-Seq
GAF KD Differential Regions GAF vs. GAF_KD Differential Regions
Basal Transcription Factors ChIP-exo ChIP-exo of Basal Transcription Factors in S2R+ Cells
ORGANIC Enrichment (S2 Cells) ORGANIC Enrichment Profiles for S2 Cells (R5)
Architectural Proteins ChIP-Seq (Kc167) ChIP-Seq of Architectural Proteins in Kc167 Cells
Architectural Proteins ChIP-Seq (S2) ChIP-Seq of Architectural Proteins in S2 Cells
Heat Shock Proteins ChIP-Seq (S2) ChIP-Seq of Heat Shock Proteins in S2 Cells
TF ChIP-nexus ChIP-nexus of Basal Transcription Factors in Kc Cells
ChIP-Seq MBT Embryos ChIP-Seq of Embryos Under Midblastula Transition
CLAMP ChIP-Seq ChIP-Seq for Chromatin-linked Adapter for MSL Proteins (CLAMP)
Henriques 2018 ChIP-Seq ChIP-Seq Data from Henriques 2018 for S2 cells
Zelda ChIP-Seq ChIP-Seq of Zelda Transcription Factor
Su(H) ChIP-Seq ChIP-Seq of Suppressor of Hairless Proteins
Histone Variants ChIP-Seq (S2) ChIP-Seq of Histone Variants in S2 Cells
R-Loop DRIP-Seq (S2) R-Loop DRIP-Seq in S2 Cells
modENCODE Histone Modifications (R5) modENCODE ChIP-chip Data for Histone Modifications (R5)
modENCODE Chromosomal Proteins (R5) modENCODE ChIP-chip Data for Chromosomal Proteins (R5)
modERN TF Peaks modERN Optimal Peaks for Transcription Factors
-   ChIP-chip Tracks    
Unique ChIP-chip Probes Uniquely-Placed ChIP-chip Probes
Pausing Factors ChIP-chip (S2 Cells) Pausing Factors ChIP-chip in S2 Cells
+   Wolbachia Tracks    
+   Expression and Regulation    
+   MNase Tracks    
+   RNA Seq Tracks    
+   Comparative Genomics    
-   Variations    
Variants in lacO Mutants (All) Genetic Variations in lacO Mutants (All)
Variants in lacO Mutants (Filtered) Genetic Variations in lacO Mutants (Filtered)
UniProt Variants UniProt/SwissProt Amino Acid Substitutions
dbSNP Short Genetic Variations in dbSNP (v149)
dbVar Structural Variations in dbVar
DGRP v2 (R5) Drosophila Genetics Reference Panel 2 (R5)
DGRP TE Insertions (ngs_te_mapper) (R5) Transposon Insertions in DGRP Lines Identified by ngs_te_mapper (R5)
DGRP TE Insertions (TEMP) Transposon Insertions in DGRP Lines Identified by TEMP
FlyVar EMS Screen Variants Identified in FlyVar EMS Mutagenesis Screen
-   Repeats    
Natural TE Transposable Elements Annotated by FlyBase
Interrupted Rpts Fragments of Interrupted Repeats Joined by RepeatMasker ID
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
Simple Repeats Simple Tandem Repeats by TRF
WM + SDust Genomic Intervals Masked by WindowMasker + SDust
RepeatMasker Repeating Elements by RepeatMasker
TE Density RepeatMasker Transposon Density (1kb window, 100bp step size)
Combined Library Repeats Identified by the Combined Repeat Library
TransposonPSI Transposons Fragments Identified by TransposonPSI
TANTAN Simple Repeats Identified by TANTAN
Tallymer Repetitive Regions Identified by Tallymer
RepeatDetector Repeats Identified by RepeatDetector
Inverted Repeats Inverted Repeats Identified by Inverted Repeats Finder
+   Updated Transcriptome Tracks