Control track and group visibility more selectively below.
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| 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 |
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| 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 |
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| 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 |
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| 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) |
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| 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 |
| InterProScan |
| InterPro Signatures Identified by InterProScan |
| 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 |
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| 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 |
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| Unique ChIP-chip Probes |
| Uniquely-Placed ChIP-chip Probes |
| Pausing Factors ChIP-chip (S2 Cells) |
| Pausing Factors ChIP-chip in S2 Cells |
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| wAna Alignments |
| Regions with Sequence Similarity to wAna Genome Assembly |
| wRi Alignments |
| Regions with Sequence Similarity to wRi Genome Assembly |
| wMel Alignments |
| Regions with Sequence Similarity to wMel Genome Assembly |
| Wolbachia Proteins |
| TBLASTN Alignment of Proteins from Wolbachia |
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| 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 |
| Pupal Wings ATAC-Seq |
| ATAC-Seq of Pupal Wings |
| Ovaries ATAC-Seq |
| ATAC-Seq of Female Ovaries |
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| MNase Accessibility (R5) |
| MNase Accessibility of S2 Cells (R5) |
| GAF RNAi MNase |
| GAF RNAi MNase-Seq for Drosophila S2 Cells |
| GAF vs. LacZ RNAi MNase |
| GAF vs. LacZ RNAi MNase-Seq for Drosophila S2 Cells |
| NELF RNAi MNase |
| NELF RNAi MNase-Seq for Drosophila S2 Cells |
| NELF RNAi vs. Mock MNase |
| NELF RNAi vs. Mock MNase-Seq for Drosophila S2 Cells |
| MBT Embryos MNase |
| MNase-Seq of Drosophila Embryos Under Midblastula Transition |
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| 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) |
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| 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 |
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| 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 |
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| 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 |
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| 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) |
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