Rätsch Lab GBrowse instance for Arabidopsis thaliana (19 MAGIC founder lines)

 

 

Browser Select Tracks Snapshots Custom Tracks Preferences

 Search

 Search

Landmark or Region: Examples: Chr1:844,200..847,799, AT2G29630, AT1G04295.1, AT3TE60465, rRNA.

Annotate Restriction Sites Download Decorated FASTA File Download Track Data filter Genes

Data Source Arabidopsis lyrata (JGI) Arabidopsis thaliana (19 MAGIC founder lines) Arabidopsis thaliana (NMD2013) Arabidopsis thaliana (PTB2012) Arabidopsis thaliana (TAIR9/10) Caenorhabditis briggsae (cb210) Caenorhabditis elegans (ce199) Caenorhabditis elegans (ce200) Caenorhabditis remanei (cr210) Drosophila melanogaster (r5.19) Homo sapiens (hg19) Mus musculus (RefSeq/ENSEMBL) Pristionchus pacificus (WS210) Saccharomyces cerevisiae (SGD)

Scroll/Zoom:     Show 1 Mbp Show 500 kbp Show 200 kbp Show 100 kbp Show 50 kbp Show 20 kbp Show 13 kbp Show 10 kbp Show 5 kbp Show 2 kbp Show 1 kbp Show 200 bp Show 100 bp     Flip

 Overview

 Overview

 

 Region

 Region

 

 Details

 Details

 

  Genes TAIR10  

  Pseudogene TAIR10  

  TE gene TAIR10  

  Transposable element TAIR10  

  MAGIC Duplicate RNA-Seq tracks [log2 converted]  

Clear highlighting

<< Back to Browser Show Active Tracks Only Show Favorites Only Clear All Favorites

 Tracks

 Tracks

 

 1. Gene models (TAIR 10) 

 1. Gene models (TAIR 10) 

 Gene models

 Gene models

 All on All off 

Coding segments TAIR10 [?]

Genes TAIR10 [?]

Pseudogene TAIR10 [?]

 Non-coding RNA

 Non-coding RNA

 All on All off 

tRNA TAIR10 [?]	small nucleolar RNA TAIR10 [?]	ribosomal RNA TAIR10 [?]
micro RNA TAIR10 [?]	small nuclear RNA TAIR10 [?]	ncRNA TAIR10 [?]

 Transposable elements

 Transposable elements

 All on All off 

TE gene TAIR10 [?]

Transposable element TAIR10 [?]

Transposon fragment TAIR10 [?]

 2. Gene models (TAIR 9) 

 2. Gene models (TAIR 9) 

 Gene models

 Gene models

 All on All off 

Coding segments TAIR9 [?]

Genes TAIR9 [?]

Pseudogene TAIR9 [?]

 Non-coding RNA

 Non-coding RNA

 All on All off 

tRNA TAIR9 [?]	miRNA TAIR9 [?]	snRNA TAIR9 [?]
rRNA TAIR9 [?]	snoRNA TAIR9 [?]	ncRNA TAIR9 [?]

 Transposable elements

 Transposable elements

 All on All off 

TE gene TAIR9 [?]

 3. Genome information 

 3. Genome information 

 Genome information

 Genome information

 All on All off 

Deletion in at least one strain

50nt Repeats

78nt Repeats

 Genomic region uncovered

 Genomic region uncovered

 All on All off 

BUR-0 uncovered [?]	LER-0 uncovered [?]	SF-2 uncovered [?]
CAN-0 uncovered [?]	MT-0 uncovered [?]	TSU-0 uncovered [?]
CT-1 uncovered [?]	NO-0 uncovered [?]	WIL-2 uncovered [?]
EDI-0 uncovered [?]	OY-0 uncovered [?]	WS-0 uncovered [?]
HI-0 uncovered [?]	PO-0 uncovered [?]	WU-0 uncovered [?]
KN-0 uncovered [?]	RSCH-4 uncovered [?]	ZU-0 uncovered [?]

 Magic variants

 Magic variants

 All on All off 

Magic variants

 Expression tracks 

 Expression tracks 

  Differential gene expression

  Differential gene expression

 All on All off 

Pairwise differential gene expression

 Alternative Splicing Events

 Alternative Splicing Events

 All on All off 

Exon Skipping [?]

Intron Retentions [?]

 Gene Prediction Experiments 

 Gene Prediction Experiments 

 1. De novo gene annotations by mGene.ngs

 1. De novo gene annotations by mGene.ngs

 All on All off 

COL-0 cor. genes [?]	LER-0 cor. genes [?]	TSU-0 cor. genes [?]
BUR-0 cor. genes [?]	MT-0 cor. genes [?]	WIL-2 cor. genes [?]
CAN-0 cor. genes [?]	NO-0 cor. genes [?]	WS-0 cor. genes [?]
CT-1 cor. genes [?]	OY-0 cor. genes [?]	WU-0 cor. genes [?]
EDI-0 cor. genes [?]	PO-0 cor. genes [?]	ZU-0 cor. genes [?]
HI-0 cor. genes [?]	RSCH-4 cor. genes [?]
KN-0 cor. genes [?]	SF-2 cor. genes [?]

 2. Consolidated gene annotations (TAIR10+mGene.ngs)

 2. Consolidated gene annotations (TAIR10+mGene.ngs)

 All on All off 

Consolidate genes BUR-0 (nss) [?]	Consolidate genes LER-0 (nss) [?]	Consolidate genes TSU-0 (nss) [?]
Consolidate genes CAN-0 (nss) [?]	Consolidate genes MT-0 (nss) [?]	Consolidate genes WIL-2 (nss) [?]
Consolidate genes COL-0 (nss) [?]	Consolidate genes NO-0 (nss) [?]	Consolidate genes WS-0 (nss) [?]
Consolidate genes CT-1 (nss) [?]	Consolidate genes OY-0 (nss) [?]	Consolidate genes WU-0 (nss) [?]
Consolidate genes EDI-0 (nss) [?]	Consolidate genes PO-0 (nss) [?]	Consolidate genes ZU-0 (nss) [?]
Consolidate genes HI-0 (nss) [?]	Consolidate genes RSCH-4 (nss) [?]
Consolidate genes KN-0 (nss) [?]	Consolidate genes SF-2 (nss) [?]

 3. Consolidated gene annotations (TAIR10+mGene.ngs, ss)

 3. Consolidated gene annotations (TAIR10+mGene.ngs, ss)

 All on All off 

Consolidate genes COL-0 (ss) [?]

Consolidate genes CAN-0 (ss) [?]

 4. Novel gene annotations (mGene.ngs+cufflinks)

 4. Novel gene annotations (mGene.ngs+cufflinks)

 All on All off 

mGene or Cufflinks genes [?]

 Short Read Coverage experiments 

 Short Read Coverage experiments 

  MAGIC Introns

  MAGIC Introns

 All on All off 

Founder strains and MAGIC lines [?]

Founder strains only [?]

  MAGIC founder strains read coverage plots (Duplicate)

  MAGIC founder strains read coverage plots (Duplicate)

 All on All off 

COL-0 (D)	LER-0 (D)	TSU-0 (D)
BUR-0 (D)	MT-0 (D)	WIL-2 (D)
CAN-0 (D)	NO-0 (D)	WS-0 (D)
CT-1 (D)	OY-0 (D)	WU-0 (D)
EDI-0 (D)	PO-0 (D)	ZU-0 (D)
HI-0 (D)	RSCH-4 (D)
KN-0 (D)	SF-2 (D)

  MAGIC founder strains read coverage plots (Duplicate) in 3D

  MAGIC founder strains read coverage plots (Duplicate) in 3D

 All on All off 

MAGIC Duplicate RNA-Seq tracks [log2 converted]

  MAGIC founder strains read coverage plots (No Duplicate)

  MAGIC founder strains read coverage plots (No Duplicate)

 All on All off 

COL-0 (NoD)	LER-0 (NoD)	TSU-0 (NoD)
BUR-0 (NoD)	MT-0 (NoD)	WIL-2 (NoD)
CAN-0 (NoD)	NO-0 (NoD)	WS-0 (NoD)
CT-1 (NoD)	OY-0 (NoD)	WU-0 (NoD)
EDI-0 (NoD)	PO-0 (NoD)	ZU-0 (NoD)
HI-0 (NoD)	RSCH-4 (NoD)
KN-0 (NoD)	SF-2 (NoD)

  MAGIC founder strains read coverage plots (No Duplicate) in 3D

  MAGIC founder strains read coverage plots (No Duplicate) in 3D

 All on All off 

MAGIC No Duplicate RNA-Seq tracks [log2 converted]

  MAGIC founder strains read display (Duplicate)

  MAGIC founder strains read display (Duplicate)

 All on All off 

COL-0 (D)	LER-0 (D)	TSU-0 (D)
BUR-0 (D)	MT-0 (D)	WIL-2 (D)
CAN-0 (D)	NO-0 (D)	WS-0 (D)
CT-1 (D)	OY-0 (D)	WU-0 (D)
EDI-0 (D)	PO-0 (D)	ZU-0 (D)
HI-0 (D)	RSCH-4 (D)
KN-0 (D)	SF-2 (D)

  MAGIC founder strains read display (No Duplicate)

  MAGIC founder strains read display (No Duplicate)

 All on All off 

COL-0 (NoD)	LER-0 (NoD)	TSU-0 (NoD)
BUR-0 (NoD)	MT-0 (NoD)	WIL-2 (NoD)
CAN-0 (NoD)	NO-0 (NoD)	WS-0 (NoD)
CT-1 (NoD)	OY-0 (NoD)	WU-0 (NoD)
EDI-0 (NoD)	PO-0 (NoD)	ZU-0 (NoD)
HI-0 (NoD)	RSCH-4 (NoD)
KN-0 (NoD)	SF-2 (NoD)

 Strain specific (19 genomes) polymorphisms

 Strain specific (19 genomes) polymorphisms

 All on All off 

BUR-0 (SNP/IN-DEL) [?]	LER-0 (SNP/IN-DEL) [?]	SF-2 (SNP/IN-DEL) [?]
CAN-0 (SNP/IN-DEL) [?]	MT-0 (SNP/IN-DEL) [?]	TSU-0 (SNP/IN-DEL) [?]
CT-1 (SNP/IN-DEL) [?]	NO-0 (SNP/IN-DEL) [?]	WIL-2 (SNP/IN-DEL) [?]
EDI-0 (SNP/IN-DEL) [?]	OY-0 (SNP/IN-DEL) [?]	WS-0 (SNP/IN-DEL) [?]
HI-0 (SNP/IN-DEL) [?]	PO-0 (SNP/IN-DEL) [?]	WU-0 (SNP/IN-DEL) [?]
KN-0 (SNP/IN-DEL) [?]	RSCH-4 (SNP/IN-DEL) [?]	ZU-0 (SNP/IN-DEL) [?]

 Analysis

 Analysis

 All on All off 

Restriction Sites

Snapshots

Snapshot Name

Snapshot Timestamp [GMT]

Custom Tracks

[Help with uploading custom tracks]

There are no tracks yet.

Add custom tracks : [From text] [From a URL] [From a file]

Show grid	Image Width 450 640 800 1024 1280 1440 1600	Highlight feature(s) (feature1 feature2...) Clear highlighting
Cache tracks		Highlight regions (region1:start..end region2:start..end) Clear highlighting
Show tooltips		Region Size (bp) 200000 20000 10000 5000 1000

The Generic Genome Browser v2.54. For questions about the data at this webpage, please contact me.