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Configure Tracks on UCSC Genome Browser: D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)
  Tracks:    Groups:
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-   Polytract Repeats    
Fruitfly Polytracts Fruitfly MNR/DNR/TNR repeats plus hinges (breakpoints)
-   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    
1M-8M Screens (R5) 1M-8M Screens (R5)
9M Screen (R5) 9M Screen (R5)
GAA Screen GAA Mobilization Insertion Sites
Chr4 Constructs Chr4 Constructs
Landing Pad Lines (R5) phiC31 Landing Pad Insertion Lines (R5)
MiMIC Lines MiMIC Lines from the Gene Disruption Project
-   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    
Detected DHS Positions (Cell Lines) (R5) Detected High-Magnitude DHS Positions (Cell Lines) (R5)
DHS Read Density (Cell Lines) (R5) Smoothed DNaseI Read Density (Cell Lines) (R5)
Detected DHS Positions (Embryos) DHS Peaks Identified by MACS (Embryos)
DHS Read Density (Embryos) DNaseI Read Density (Embryos)
MACS2 DHS DNaseI Hypersensitive Sites Identified by MACS2
TSS (Embryonic) (R5) Transcription Start Sites (Embryonic) (R5)
TSS (Celniker) (R5) Transcription Start Sites (Celniker Group) (R5)
Combined modENCODE CAGE TSS Combined Transcription Start Sites Identified by modENCODE CAGE
modENCODE CAGE Tag Clusters modENCODE CAGE Tag Clusters for Different Developmental Stages
modENCODE CAGE Read Density modENCODE CAGE Read Density for Different Developmental Stages
Combined RAMPAGE TSS (R5) Combined RAMPAGE Transcription Start Sites (R5)
RAMPAGE TSS Read Density (R5) RAMPAGE Read Density for Different Developmental Stages (R5)
Combined RAMPAGE TSS (Replicate 2) (R5) Combined RAMPAGE Transcription Start Sites (Replicate 2) (R5)
RAMPAGE TSS Read Density (Replicate 2) (R5) RAMPAGE Read Density for Different Developmental Stages (Replicate 2) (R5)
Combined MachiBase TSS Combined MachiBase Transcription Start Sites
MachiBase TSS Read Density MachiBase Read Density for Different Developmental Stages
Combined Exo-seq TSS Combined Transcription Start Sites Identified by Exo-seq
Exo-seq Read Density Exo-seq Read Density at Different Zeitgeber Times and Temperatures
Exo-seq Tag Clusters Exo-seq Tag Clusters at Different Zeitgeber Times and Temperatures
MACE TSS TSS Identified by 5' Massive Amplification of cDNA Ends (5' MACE)
Exosome RNAi CAGE Exosome RNAi Knockdown CAGE TSS
Exosome RNAi CAGE Tag Clusters Exosome RNAi Knockdown CAGE Tag Clusters
PEAT (S2 Cells) Paired-End Analysis of Transcription Start Sites for S2 Cells
TES (Celniker) (R5) Transcription End Sites (Celniker Group) (R5)
TFBS HOT Spots (R5) Transcription Factor Binding Sites HOT Spots (R5)
MACS STARR-seq Peaks STARR-Seq Peaks Identified by MACS
MACS STARR-seq Enrichment Log Likelihood Ratio of STARR-seq Enrichment Versus Input
MUSIC STARR-seq Peaks STARR-seq Peaks Identified by MUSIC
MUSIC STARR-seq Enrichment MUSIC STARR-seq Smoothed Signal Profiles
PePr STARR-seq Peaks Sharp STARR-seq Peaks Identified by PePr
hkCP dCP STARR-Seq Housekeeping and Developmental Enhancers Identified by STARR-Seq
Enhancers (R5) Enhancers Identified by CBP ChIP-chip and ChIP-Seq (R5)
Silencers (R5) Putative Polycomb Response Elements (Silencers) (R5)
Insulators (R5) Class I and Class II Insulator Elements (R5)
Origins of Replication (R5) Early Activating Origins of Replication (R5)
SNS Origins of Replication (R5) Origins of Replication Detected by SNS (R5)
EPDnew Promoters D. melanogaster Curated Promoter Database (EPDnew)
Schor 2017 CAGE Peaks (R5) CAGE Peaks and TSS Clusters Identified by Schor et al. 2017 (R5)
REDfly Regulatory Elements Regulatory Elements Annotated by REDfly
CORE Promoters Promoters Annotated by the CORE Database
GRO-Seq (R5) GRO-Seq for Untreated S2 Cells (R5)
Core LJ 2012 GRO-Seq (R5) GRO-Seq for Drosophila S2 Cells (Core LJ, 2012) (R5)
PRO-seq (R5) PRO-seq for Drosophila S2 Cells (R5)
Schaaf CA 2013 BG3 PRO-seq PRO-seq for Drosophila BG3 Cells (Schaaf CA, 2013)
Duarte FM 2016 PRO-seq PRO-seq for Drosophila S2 Cells (Duarte FM, 2016)
FStitch Nascent Transcripts Nascent RNA Transcripts Predicted by FStitch
3'NT (S2 Cells) Three Prime Position of Nascent Transcript (3'NT)
CapSeq Tag Clusters CapSeq Tag Clusters for w1118 (wildtype) Ovaries
CapSeq Read Density CapSeq Read Density for w1118 (wildtype) Ovaries
Start-Seq TSS (Larvae) (R5) Transcription Start Sites Identified by Start-Seq (Larvae) (R5)
scRNAs (S2 Cells) Short Capped RNAs (scRNAs) in S2 Cells
Permanganate ChIP-Seq (R5) Permanganate ChIP-Seq on Drosophila Cell Lines (R5)
Embryos FAIRE-Seq FAIRE-Seq of Drosophila Embryos
Schulz FAIRE-Seq FAIRE-Seq of Drosophila Embryos (Schulz et al. 2015)
Embryos ATAC-Seq ATAC-Seq of Drosophila Embryos
3rd Instar Larvae ATAC-Seq ATAC-Seq of Whole 3rd Instar Larvae
Eye Discs ATAC-Seq ATAC-Seq of D. melanogaster Eye Discs
+   MNase Tracks    
+   RNA Seq Tracks    
-   Comparative Genomics    
Drosophila Conservation (36 Species) ROAST Alignment and Conservation (36 RefSeq Drosophila Genomes)
RefSeq Drosophila Chain/Net RefSeq Drosophila Genomes, Chain and Net Alignments
Drosophila Conservation (28 Species) ROAST Alignments & Conservation (28 Drosophila Species)
Drosophila Conservation (26 Species) ROAST Alignments & Conservation (26 Drosophila Species)
PhyloP (14 Species) PhyloP Basewise Conservation Scores (14 Drosophila Species)
PhastCons (14 Species) PhastCons Conserved Elements (14 Drosophila Species)
Conservation (14 Species) Drosophila Multiz Alignments & phastCons Scores for 14 Drosophila Species
Drosophila Chain/Net Drosophila Genomes, Chain and Net Alignments
(dm3) D. mel. Chain D. melanogaster (Apr. 2006 (BDGP R5/dm3)) Chained Alignments
(dm3) D. mel. Net D. melanogaster (Apr. 2006 (BDGP R5/dm3)) Alignment Net
+   Variations    
-   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    
Combined modENCODE RNA-Seq (Development) Combined modENCODE RNA-Seq for Multiple Developmental Stages
Combined Splice Junctions (Development) Combined Splice Junctions for Multiple Developmental Stages
modENCODE RNA-Seq (Development) modENCODE RNA-Seq for Different Developmental Stages
Combined modENCODE RNA-Seq (Tissues) Combined modENCODE RNA-Seq for Multiple Tissues
Combined Splice Junctions (Tissues) Combined Splice Junctions for Multiple Tissues
modENCODE RNA-Seq (Tissues) modENCODE RNA-Seq for Different Tissues
Combined modENCODE RNA-Seq (Cell Lines) Combined modENCODE RNA-Seq for Multiple Cell Lines
Combined Splice Junctions (Cell Lines) Combined Splice Junctions for Multiple Cell Lines
modENCODE RNA-Seq (Cell Lines) modENCODE RNA-Seq for Different Cell Lines
Combined RAMPAGE Embryos TSS Combined RAMPAGE Embryos Transcription Start Sites
TSRchitect RAMPAGE Embryos TSS TSRchitect RAMPAGE Embryos Transcription Start Sites
TSRchitect Combined RAMPAGE TSS (Replicate 1) TSRchitect Combined RAMPAGE Transcription Start Sites (Replicate 1)
TSRchitect RAMPAGE TSS Read Density (Replicate 1) TSRchitect RAMPAGE Read Density for Different Developmental Stages (Replicate 1)
TSRchitect Combined RAMPAGE TSS (Replicate 2) TSRchitect Combined RAMPAGE Transcription Start Sites (Replicate 2)
TSRchitect RAMPAGE TSS Read Density (Replicate 2) TSRchitect RAMPAGE Read Density for Different Developmental Stages (Replicate 2)