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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 |
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 |
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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) |
|