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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.
-   JASPAR TFBS    
JASPAR2020 TFBS dm6 TFBS predictions in Drosophila melanogaster (dm6) for all profiles in the JASPAR CORE insects collection (2020)
JASPAR2022 TFBS dm6 TFBS predictions in Drosophila melanogaster (dm6) for all profiles in the JASPAR CORE insects collection (2022)
-   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    
-   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    
+   ChIP-chip Tracks    
+   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    
FlyBase Exon Junctions FlyBase RNA-Seq Exon Junctions
Combined modENCODE RNA-Seq (Development) (R5) Combined modENCODE RNA-Seq for Multiple Developmental Stages (R5)
modENCODE RNA-Seq (Development) (R5) modENCODE RNA-Seq for Different Developmental Stages (R5)
modENCODE RNA-Seq (Cell Lines) modENCODE RNA-Seq for Different Cell Lines
Aggregated RNA-Seq Coverage NCBI SRA Aggregated RNA-Seq Coverage (Oliver Lab)
-   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    
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    
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)