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Configure Tracks on UCSC Genome Browser: D. melanogaster Apr. 2006 (BDGP R5/dm3)
  Tracks:    Groups:
Control track and group visibility more selectively below.
-   Custom Tracks    
5 types 5 state chromatin model in Kc167
black chromatin 5 types
BRN_LAM_HMM Brains Lam 2xHMM domains
cLADs constitutive LADs shared between neurons, glia, FB, embryos, Kc cells
Colors_S2 Chromatin states for S2 from Kharchenko et. al 2011
dsElys_rep1_RNA-seq dsElys_S2_rep1_RNA-seq_100bp bins
dsElys_rep2_RNA-seq dsElys_S2_rep2_RNA-seq_100bp bins
dsElys_rep3_RNA-seq dsElys_S2_rep3_RNA-seq_100bp bins
dsElys_RNA-seq dsElys_S2_RNA-seq_merged_100bp bins
dsLacZ_rep1_RNA-seq dsLacZ_S2_rep1_RNA-seq_100bp bins
dsLacZ_rep2_RNA-seq dsLacZ_S2_rep2_RNA-seq_100bp bins
dsLacZ_rep3_RNA-seq dsLacZ_S2_rep3_RNA-seq_100bp bins
dsLacZ_RNA-seq dsLacZ_S2_RNA-seq_merged_100bp bins
Elys 3xHMM gf ELYS_3xHMM domains for 16-18h embryos_reads merged for replicates_0.3kb bins_0.9kb gaps filled
ELYS Emb 3xHMM 0.3 ELYS_3xHMM domains for 16-18h embryos_reads merged for replicates_0.3kb bins
ELYS Emb HMM 0.3 ELYS_2xHMM domains for 16-18h embryos_reads merged for replicates_0.3kb bins
ELYS embryo 0.3kb Elys_16-18h embryos_replicates merged_0.3kb bins
Elys_cePC1 Annotated 20kb cePC1 chromatin A/B compartments for Elys
Elys_ChIP-seq_profile_S2_Capelson Elys_ChIP-seq_profile_S2_Capelson
Elys_ChIP_seq_S2/LADs_Kc Elys_ChIP_seq_S2/LADs_Kc
Elys_embr_overl_rep Elys_3xHMM domains overlaped between replicates in embryos
Elys_embr_rep1 Dam-Elys_rep1/Dam_rep1 embryos
Elys_embr_rep2 Dam-Elys_rep2/Dam_rep2 embryos
Elys_NPC overlap regions between Nup98_NPC domains that do not intersect with Nup98_nucleopl and Elys_embryo domains_0.9kb gaps filled
Elys_NPC/active Elys_NPC sites located within active (1-5) chromatin colors
Elys_NPC/j.active Elys_NPC sites located within joint active (1-5) chromatin
Elys_NPC/j.g.f.active Elys_NPC sites located within joint active (1-5) chromatin with <=900bp gaps filled
Elys_NPC/j.g.f.inactive Elys_NPC sites located within joint inactive (6-9) chromatin with <=900bp gaps filled
Elys_NPC/j.inactive Elys_NPC sites located within joint inactive (6-9) chromatin
Elys_NPC/Pc Elys_NPC sites located within Pc-related (#6) chromatin color
Elys_NPC/silent Elys_NPC sites located within silent (#9) chromatin color
Elys_nucl overlap regions between Nup98_nucleoplasmic domains that do not intersect with Nup98_NPC and Elys_embryo domains with <=900bp gaps filled
Elys_TADs Annotated Elys TADs for 5kb contact maps
Enhancers_S2 Strong STARR-seq enhancers in S2 (Arnold et al. 2013)
FB LAM HMM FB HMM domains for LAM
GAF_chip_mock_reps_treat_ GAF_chip_mock_reps_treat_ Shifted Merged Normalized MACS tag counts
GAF_S2_confident_peaks GAF_chip_mock_reps_treat_ Shifted Merged Normalized MACS tag counts - only high confidence peaks
GAF_S2_peaks GAF_chip_mock_reps_treat_ Shifted Merged Normalized MACS tag counts
Glia LAM HMM Glia HMM domains for LAM
H3K27ac_3xHMM H3K27ac in S2 Modencode_3xHMM_Ilyin
H3K27ac_S2 H3K27ac/Input CHIP-chip, modENCODE, merged 4 replicates
H3K27me3 H3K27me3/Input CHIP-chip, modENCODE, merged 4 replicates
H3K36me3 H3K36me3/Input CHIP-chip, modENCODE, merged 4 replicates
H3K4me3 H3K4me3/Input CHIP-chip, modENCODE, merged 6 replicates
H3K9me3 H3K9me3/Input CHIP-chip, modENCODE, merged 4 replicates
LacZ_cePC1 Annotated 20kb cePC1 chromatin A/B compartments for LacZ
LacZ_TADs Annotated LacZ TADs for 5kb contact maps
LADs_embryo gf Lam_3xHMM domains for 16-18h embryos_0.3kb bins_0.9kb gaps filled
LADs_Kc Lam Domains in Kc retrived from Filion et al 2010 and merged, gaps less 0.9 kb filled
LAM Emb 3xHMM 0.3 LAM_3xHMM domains for 16-18h embryos_reads merged for replicates_0.3kb bins
LAM Emb HMM 0.3 LAM_2xHMM domains for 16-18h embryos_reads merged for replicates_0.3kb bins
Lam embryo 0.3kb Lamin_16-18h embryos_replicates merged_0.3kb bins
LAM.NRN.mf_min.norm.qn.DATA bedgraph_profile
LAM_BR_sum_1kb_qn Lam_BR_merged reads from replicates_1kb bins_quantile normalized
LAM_FB_sum_1kb_qn Lam_FB_merged reads from replicates_1kb bins_quantile normalized
LAM_Glia_sum_1kb_qn Lam_Glia_merged reads from replicates_1kb bins_quantile normalized
LAM_NRN_sum_1kb_qn Lam_NRN_merged reads from replicates_1kb bins_quantile normalized
LamDam KC MA HMM LamDam microarray data in Kc HMM Domains
LamDam_profiling log2(LamDam/Dam)_averaged_Kc
neuronal enhancers neuronal enhancers
NRN LAM HMM NRN HMM domains for LAM
NRN.LAM.mf_min.norm.ave.DATA bedgraph_profile
Nup93_S2_peaks Nup93_S2_ChIP_mock_reps_treat_Shifted Merged Normalized MACS tag counts_Capelson
Nup98*_nucl/Elys_S2 intersected regions between Nup98_nucl* and Elys ChIP-seq in S2
Nup98_NPC 3xHMM Nup98_NPC-tethered domains by 3xHMM_Ilyin
Nup98_NPC* Nup98_NPC 3xHMM domains that do not intersect with Nup98_nucleoplasmic domains
Nup98_NPC* gf Nup98_NPC 3xHMM domains that do not intersect with Nup98_nucleoplasmic domains_0.9kb gaps filled
Nup98_NPC*/Elys_embr overlap regions between Nup98_NPC domains that do not intersect with Nup98_nucl and Elys_embryo domains
Nup98_NPC*/Elys_embryo/LADs_Kc Nup98_NPC*/Elys_embryo within LADs_Kc
Nup98_NPC*/Elys_S2 intersected regions between Nup98_NPC* and Elys ChIP-seq in S2
Nup98_NPC_DamID Nup98 NPC-tethered DamID microarray from Fornerod 2010
Nup98_NPC_domains Nup98 NPC-tethered HMM domains
Nup98_nucl* Nup98_nucleoplasmic 3xHMM domains that do not intersect with Nup98_NPC domains
Nup98_nucl* gf Nup98_nucl 3xHMM domains that do not intersect with Nup98_NPC domains_0.9kb gaps filled
Nup98_nucl*/Elys_embr overlap regions between Nup98_nucleoplasmic domains that do not intersect with Nup98_NPC and Elys_embryo domains
Nup98_nucl*/Elys_embr.g.f. overlap regions between Nup98_nucleoplasmic domains that do not intersect with Nup98_NPC and Elys_embryo domains_with <=0.6kb gaps filled
Nup98_nucl*/Elys_embryo gf overlap regions between Nup98_nucleoplasmic domains that do not intersect with Nup98_NPC and Elys_embryo domains_0.9kb gaps filled
Nup98_nucl_3xHMM Nup98_nucleoplasmic domains by 3xHMM_Ilyin
Nup98_nucleo_DamID Nup98 nucleoplasmic DamID microarray from Fornerod 2010
Nup98_nucleo_domains Nup98 nucleoplasmic HMM domains
Pc domain S2 3xHMM Pc domains in S2_Ilyin_ChIP on chip_modENCODE
Pc_S2 Pc ChIp on chip_ModEncode
Peaks_Elys Elys ChIPseq peaks
RNAseq_rep1 S2 RNAseq rep1, CPM normalized
RNAseq_rep2 S2 RNAseq rep2, CPM normalized
S2_active 9-state color in S2_active (1-5) sdomains merged
S2_BAP/PBAP S2_BAP/PBAP_ChIP-chip
S2_BAP111 S2_BAP111_ChIP-chip
S2_BRM S2_BRM_ChIP-chip
S2_inactive 9-state color S2_merged inactive 6-9 domains
starr_no_ecd.merged.bw starr_no_ecd.merged.bw
starr_with_ecd.merged.bw starr_with_ecd.merged.bw
blue chromatin 5 types
green chromatin 5 types
red chromatin 5 types
yellow chromatin 5 types
H3K27Ac_S2 500bp smoothed M values (S8_H3K27Ac.57 + S12_H3K27Ac.97)
+   Mapping and Sequencing    
-   Genes and Gene Predictions    
RefSeq Genes RefSeq Genes
FlyBase Genes FlyBase Protein-Coding Genes
FB Noncoding FlyBase Noncoding Genes
N-SCAN N-SCAN PASA-EST Gene Predictions
EvoFold EvoFold predictions of RNA secondary structure (id_strand_score)
AUGUSTUS AUGUSTUS ab initio gene predictions v3.1
CONTRAST CONTRAST Gene Predictions
Ensembl Genes Ensembl Genes
Human Proteins Human Proteins Mapped by Chained tBLASTn
Other RefSeq Non-D. melanogaster RefSeq Genes
-   Literature    
Publications Publications: Sequences in Scientific Articles
Web Sequences DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research
-   mRNA and EST    
Spliced ESTs D. melanogaster ESTs That Have Been Spliced
D. melanogaster ESTs D. melanogaster ESTs Including Unspliced
D. melanogaster mRNAs D. melanogaster mRNAs from GenBank
Other mRNAs Non-D. melanogaster mRNAs from GenBank
-   Expression and Regulation    
Affy Signal Affymetrix Drosophila Development Signal
Affy Transfrags Affymetrix Drosophila Development Transfrags
BDTNP DNase Accs Berkeley Drosophila Transcription Network Project Chromatin Accessibility (DNase)
BDTNP ChIP/chip Berkeley Drosophila Transcription Network Project Transcription Factor ChIP/chip
ORegAnno Regulatory elements from ORegAnno
-   Comparative Genomics    
Conservation (15) 12 Flies, Mosquito, Honeybee, Beetle Multiz Alignments & phastCons Scores
A. gambiae Chain A. gambiae (Feb. 2003 (IAGEC MOZ2/anoGam1)) Chained Alignments
A. gambiae Net A. gambiae (Feb. 2003 (IAGEC MOZ2/anoGam1)) Alignment Net
D. pseudo. Chain D. pseudoobscura (Nov. 2004 (FlyBase 1.03/dp3)) Chained Alignments
D. pseudo. Net D. pseudoobscura (Nov. 2004 (FlyBase 1.03/dp3)) Alignment Net
D. persimilis Chain D. persimilis (Oct. 2005 (Broad/droPer1)) Chained Alignments
D. persimilis Net D. persimilis (Oct. 2005 (Broad/droPer1)) Alignment Net
D. ananassae Chain D. ananassae (Aug. 2005 (Agencourt prelim/droAna2)) Chained Alignments
D. ananassae Net D. ananassae (Aug. 2005 (Agencourt prelim/droAna2)) Alignment Net
D. erecta Chain D. erecta (Aug. 2005 (Agencourt prelim/droEre1)) Chained Alignments
D. erecta Net D. erecta (Aug. 2005 (Agencourt prelim/droEre1)) Alignment Net
D. yakuba Chain D. yakuba (Nov. 2005 (WUGSC 7.1/droYak2)) Chained Alignments
D. yakuba Net D. yakuba (Nov. 2005 (WUGSC 7.1/droYak2)) Alignment Net
D. sechellia Chain D. sechellia (Oct. 2005 (Broad/droSec1)) Chained Alignments
D. sechellia Net D. sechellia (Oct. 2005 (Broad/droSec1)) Alignment Net
D. simulans Chain D. simulans (Apr. 2005 (WUGSC mosaic 1.0/droSim1)) Chained Alignments
D. simulans Net D. simulans (Apr. 2005 (WUGSC mosaic 1.0/droSim1)) Alignment Net
-   Variation and Repeats    
Microsatellite Microsatellites - Di-nucleotide and Tri-nucleotide Repeats
Simple Repeats Simple Tandem Repeats by TRF
RepeatMasker Repeating Elements by RepeatMasker