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CategoryTrack nameDescriptionSource
Assembly Genome Reference (TAIR10) TAIR10 reference genome sequence TAIR10 (released 11/2010)
Assembly Tiling Path (TAIR9) Shows the whole-genome annotation including BAC and other genomic clones. TAIR9 data (released 06/2009)
TAIR10 TAIR10 - Gene Locus The total transcribed region of an annotated gene including coding and non-coding genes. The arrow indicates the direction of transcription. TAIR10 (released 11/2010)
Splicing RNA-seq Based Spliced Junction (Ecker and Mockler, 2011) RNA-seq data from Ecker and Mockler labs were aligned to TAIR7 using Tophat and Supersplat. The numbers indicate the supporting read counts for each junction. Ecker and Mockler labs (04/2011)
Splicing Alternative Splicing Variants (Marquez et al, 2012) A normalized cDNA library was generated from pooled seedling and floral tissues and sequenced with paired-end Illumina.The reads were aligned to the TAIR9 reference genome using Bowtie.TopHat was used to detect the splice junctions. Transcriptome survey reveals increased complexity of the alternative splicing landscape. Marquez et al., 2012
UTR PEAT Clusters, Root (Morton et al. 2014) A large-scale transcription start site (TSS) data set was generated from 10-day-old wild-type root using paired-end analysis of transcription start site (PEAT) protocol, providing TSS locations based on TAIR10 gene annotation. Each PEAT tag cluster (or “peak”) requires a minimum of 10 reads. Morton et al., 2014
UTR PEAT Coverage, Root (Morton et al. 2014) This track shows the read coverage of raw BAM files and reveals the landscape of transcription initiation in Arabidopsis whole root samples. Morton et al. 2014
UTR Direct RNA Sequencing, Forward, Seedling (Duc et al., 2013) This experiment examined the relative 3'UTR positioning and expression in 14-day-old Col-0 seedling samples using Helicos BioSciences Direct RNA Sequencing. This track displays the forward-strand read-depth data from the summed wild-type replicates for this experiment. Each peak indicates the number of reads that end at a given position. Duc et al., 2013
UTR Direct RNA Sequencing, Reverse, Seedling (Duc et al., 2013) This experiment examined the relative 3'UTR positioning and expression in 14-day-old Col-0 seedling samples using Helicos BioSciences Direct RNA Sequencing. This track displays the forward-strand read-depth data from the summed wild-type replicates for this experiment. Each peak indicates the number of reads that end at a given position. Duc et al., 2013
EST and Protein Alignments EST/Full-Length cDNA (Campbell et al. 2014) Arabidopsis thaliana ESTs and FL-cDNAs downloaded from GenBank and mapped to the genome using MAKER optimized est2genome. Data provided courtesy of Yandell Lab. Yandell lab, Campbell et al. 2014
EST and Protein Alignments SwissProt Non-Arabidopsis Plant Protein (Campbell et al. 2014) Non-Arabidopsis Plant protein sequences from SwissProt plant (release 2011_12) were mapped to the genome using MAKER optimized protein2genome. Data provided courtesy of Yandell Lab. Yandell lab, Campbell et al. 2014, SwissProt 201112
EST and Protein Alignments SwissProt Non-Arabidopsis Plant Protein (2015 Mar) Protein sequences from 2123 non-Arabidopsis plant species were downloaded from UniprotKB (SwissProt, 20150304) and mapped to TAIR10 genome using MAKER-P protein2genome pipeline. SwissProt 201503 mapped at JCVI
TAIR10 TAIR10 - Protein Coding Genes Shows the exon (boxes) and intron (lines) structure of each protein-coding transcript with direction of transcription indicated. The gene model confidence rankings are embedded in this track. Documentation for the ranking system can be found at: TAIR10 (released 11/2010)
Repeat Natural Transposons (TAIR9) Incorporates TE annotation from TAIR and external sources including TIGR and Colot group. TAIR9 data (released 06/2009)
TAIR10 TAIR10 - Unconfirmed Exon Shows the exons in TAIR10 which are neither supported by experimental evidence nor bioinformatic analysis. The detailed scoring strategy is available at: TAIR10 (released 11/2010)
TAIR10 TAIR10 - Pseudogene Shows the pseudogene transcript. TAIR10 (released 11/2010)
TAIR10 TAIR10 - Non-Coding RNA Shows the non-coding RNA transcripts. TAIR10 (released 11/2010)
Repeat Tandem Repeat (TAIR10) Regions of tandem repeats including microsatellite, minisatellite, and satellite, as computed using Tandem Repeats Finder v4.04. TAIR10 (released 11/2010)
Assembly Assembly Gap (TAIR9) Shows the regions where greater than four Ns are included in the current golden path sequence. TAIR9 data (released 07/2010)
Assembly Assembly Updates (TAIR9) Changes to sequences following TIGR 5 genome release. TAIR9 data (released 07/2010)
Microarray Microarray ATH1-121501 probes (TAIR) This genome array is based on the initial release of Arabidopsis genome in 2000 and subsequent TIGR reannotation. TAIR9 data (released 06/2009)
Proteomics AtProteome (Baerenfaller et al. 2008) AtProteome assembles proteomic data of and provides information about identified proteotypic peptides, abundances and tissue and organelle-specific appearance. Baerenfaller et al. 2008
Proteomics AtPeptide (Castellana et al. 2008) Proteomics data. Discovery and revision of Arabidopsis genes by proteogenomics Natalie E. Castellana, Samuel H. Payne, Zhouxin Shen, Mario Stanke, Vineet Bafna, and Steven P. Briggs. The white/blue box colour indicates pValue (higher to lower). Castellana et al. 2008
Variation 1001 Genomes (Ensembl) Ensembl variants from 1001 Arabidopsis Genomes project. Variant metadata retrieved via Ensembl REST Web Services. Real-time from Ensembl for metadata, static VCF
Variation 1001 Genomes (1001genomes.org) 1001 Genomes Variants from the 1001genomes.org website. Genotype Accession name resolved against GMI/master_accession_list webservice VCF from 1001genomes.org
Variation TDNA-seq (O'Malley R et al. 2014) Annotations for 166,439 insertions identified in 100,013 existing segregating T-DNA insertion lines (from SALK, SAIL, WISC, and GABI-kat collections) using TDNA-seq technology O'Malley et al. (released to GenBank Dec 2014)
Variation TDNA Classical (TAIR9) Shows approximate positions of T-DNA and transposon insertion sites. TAIR9 data (released 06/2010)
Variation Polymorphism (TAIR9) Shows the positions of polymorphisms , including SNPs, TILLing mutations, small insertions and deletions. TAIR9 data (released 06/2009)
Variation Genetic Marker (TAIR9) Shows the positions of genetic markers. TAIR9 data (released 06/2009)
Binding Site RNA-binding Protein Protected Sites (Gosai et al., 2015) RNA-binding protein protected sites (PPS) were detected using protein interaction profile sequencing (PIP-seq) on total nuclei from 10-day-old seedlings. A total of 61,632 PPSs were detected from two-replicate nuclear PIP-seq experiments, 64.7% of which overlap. Consolidation of two replicates yields 40,131 distinct sites which are presented in this track. Gosai et al., 2015
VISTA Plots Vista Plot:Ahalleri v1 (Phytozome) VISTA alignment between Arabidopsis thaliana genome TAIR9 release and Arabidopsis halleri version v1.0 release Real-time from Phytozome
VISTA Plots Vista Plot: Alyrata v1 (Phytozome) VISTA alignment between Arabidopsis thaliana genome TAIR9 release and Arabidopsis lyrata genome October 2008 release Real-time from Phytozome
VISTA Plots Vista Plot: BrapaFPsc v1 (Phytozome) VISTA alignment between Arabidopsis thaliana genome TAIR9 release and Brassica rapa FPsc version v1.0 release Real-time from Phytozome
VISTA Plots Vista Plot: Bstricta v1 (Phytozome) VISTA alignment between Arabidopsis thaliana genome TAIR9 release and Boechera stricta version v1.0 release Real-time from Phytozome
VISTA Plots Vista Plot: Crubella v1 (Phytozome) VISTA alignment between Arabidopsis thaliana genome TAIR9 release and Capsella rubella genome version 1.0 release Real-time from Phytozome
Araport11 Annotation Araport11 Protein Coding Genes Protein coding gene models annotated as part of the Araport11 Pre-Release 3 (Dec 2015) Araport11 Pre-Release 3 (Dec 2015)
Araport11 Annotation Araport11 Locus Araport11 gene loci supplemented with TAIR10 pseudogenes, TE genes and ncRNA loci Araport11 Pre-Release 3 (Dec 2015)
Araport11 Splice Junctions
(11 tracks)
Aerial, Root, Carpel, Pollen, Stage 12 Flower, Dark Grown Seedling, Shoot Apical Meristem, Root Apical Meristem, Leaf, Receptacle, Light Grown Seedling TopHat-predicted splice junctions. Each glyph spans the intron junction and its label corresponds to the read counts supporting that junction Araport11
Araport11 Transcript Assembly
(11 tracks)
Aerial, Carpel, Dark Grown Seedling, Stage 12 Flower, Leaf, Light Grown Seedling, Pollen, Root Apical Meristem, Receptacle, Root, Shoot Apical Meristem Transcript assemblies generated by PASA, using a combination of de novo and genome guided Trinity assemblies. Minimum contig length of 183 bp and maximum intron length of 2000 bp were applied Araport11
Araport11 Mapping Coverage
(11 tracks)
Aerial, Shoot Apical Meristem, Dark Grown Seedling, Leaf, Light Grown Seedling, Pollen, Root Apical Meristem, Receptacle, Root, Stage 12 Flower, Carpel RNA-seq reads from SRA aligned to the TAIR10 genome using TopHat. Alignment BAM files were merged based on tissue/organ of origin and converted to BigWig format NCBI SRA
Araport11 Novel Transcribed Regions Araport11 Novel Transcribed Regions Novel transcripts assembled from the 113 RNA-seq data sets Araport11 Pre-Release 3 (Dec 2015)
Motifs Chromatin States
(9 tracks)
Functional topography of the Arabidopsis genome organized in linear motifs of Chromatin States Sequeira-Mendes et al. 2014
Epigenetics
(26 tracks)
EPIC-CoGe Epigenomic datasets generated by members of the Epigenomics of Plants International Consortium (EPIC), hosted within the iPlant powered CoGe system and made available for public consumption via CoGe REST API Real-time from EPIC-CoGe