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Transcriptome Landscape of Rice: 50 kbp from chr01:1..50,000

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Landmark or Region: Examples: Os03t0146800-01.	Download Decorated FASTA File Download Sequence File Download Track Data Download generic
Data Source Transcriptome Landscape of Rice	Scroll/Zoom:     Show 1 Mbp Show 500 kbp Show 200 kbp Show 100 kbp Show 50 kbp Show 20 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

 

  RAP Rep. transcripts (mRNA)  

  RAP Rep. transcripts (ab initio+EST)  

  RAP Predicted transcripts  

  unannotated PARPNTE  

  unannotated Cufflinks w/ strand  

  Drought, Control, Shoot  

  Drought, 1h, Shoot  

  Drought, 3h, Shoot  

  Drought, 6h, Shoot  

  Drought, 12h, Shoot  

  Drought, 1d, Shoot  

  Drought, Control, Root  

  Drought, 1h, Root  

  Drought, 3h, Root  

  Drought, 6h, Root  

  Drought, 12h, Root  

  Drought, 1d, Root  

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 Tracks

 Tracks

 

 1. RAP-DB Annotation

 1. RAP-DB Annotation

 All on All off 

RAP Predicted transcripts [?]

RAP Rep. transcripts (ab initio+EST) [?]

RAP Rep. transcripts (mRNA) [?]

 2. RNA-Seq transcripts

 2. RNA-Seq transcripts

 All on All off 

All Cufflinks w/ strand [?]	All PARPNTE [?]	unannotated Cufflinks w/o strand [?]
All Cufflinks w/o strand [?]	unannotated Cufflinks w/ strand [?]	unannotated PARPNTE [?]

 3. Other Annotation

 3. Other Annotation

 All on All off 

MSU Osa1 Rice Gene Models [?]	RAP3 transcripts [?]	Swiss-Prot plant division [?]
PLACE cis-element [?]	Repeat units [?]	TrEMBL plant division [?]
RAP1 and RAP2 transcripts [?]	Swiss-Prot (identical) [?]

 4. RNA-Seq read depth of coverage 

 4. RNA-Seq read depth of coverage 

 Root 

 Root 

 ABA

 ABA

 All on All off 

ABA, 12h, Root [?]	ABA, 1h, Root [?]	ABA, 6h, Root [?]
ABA, 1d, Root [?]	ABA, 3h, Root [?]	ABA, Control, Root [?]

 Cold

 Cold

 All on All off 

Cold, 12h, Root [?]	Cold, 1h, Root [?]	Cold, 6h, Root [?]
Cold, 1d, Root [?]	Cold, 3h, Root [?]

 Developmental time control

 Developmental time control

 All on All off 

DevTime, 0h, Root [?]	DevTime, 1h, Root [?]	DevTime, 5d, Root [?]
DevTime, 10d, Root [?]	DevTime, 3d, Root [?]	DevTime, 6h, Root [?]
DevTime, 12h, Root [?]	DevTime, 3h, Root [?]
DevTime, 1d, Root [?]	DevTime, 4d, Root [?]

 Drought

 Drought

 All on All off 

Drought, 12h, Root [?]	Drought, 1h, Root [?]	Drought, 6h, Root [?]
Drought, 1d, Root [?]	Drought, 3h, Root [?]	Drought, Control, Root [?]

 Flood

 Flood

 All on All off 

Flood, 12h, Root [?]	Flood, 3d, Root [?]	Flood, Control, Root [?]
Flood, 1d, Root [?]	Flood, 3h, Root [?]
Flood, 1h, Root [?]	Flood, 6h, Root [?]

 High and low phosphate

 High and low phosphate

 All on All off 

High P, 10d + 1d recovery, Root [?]	High P, 5d, Root [?]	Low P, 1d, Root [?]
High P, 10d, Root [?]	Low P, 10d + 1d recovery, Root [?]	Low P, 5d, Root [?]
High P, 1d, Root [?]	Low P, 10d, Root [?]	P, Control, Root [?]

 High cadmium

 High cadmium

 All on All off 

High Cd, 12h, Root [?]	High Cd, 1h, Root [?]	High Cd, Control, Root [?]
High Cd, 1d, Root [?]	High Cd, 5d, Root [?]

 High salinity

 High salinity

 All on All off 

High salinity, 1h, Root [?]

High salinity, Control, Root [?]

 JA

 JA

 All on All off 

JA, 12h, Root [?]	JA, 1h, Root [?]	JA, 6h, Root [?]
JA, 1d, Root [?]	JA, 3h, Root [?]	JA, Control, Root [?]

 Low and very low cadmium

 Low and very low cadmium

 All on All off 

Low Cd, 10d, Root [?]	Low/Very low Cd, Control, Root [?]	Very low Cd, 4d, Root [?]
Low Cd, 1d, Root [?]	Very low Cd, 10d, Root [?]
Low Cd, 4d, Root [?]	Very low Cd, 1d, Root [?]

 Osmotic

 Osmotic

 All on All off 

Osmotic, 12h, Root [?]	Osmotic, 3h, Root [?]	Osmotic, Control, Root [?]
Osmotic, 1h, Root [?]	Osmotic, 6h, Root [?]

 Shoot 

 Shoot 

 ABA

 ABA

 All on All off 

ABA, 12h, Shoot [?]	ABA, 1h, Shoot [?]	ABA, 6h, Shoot [?]
ABA, 1d, Shoot [?]	ABA, 3h, Shoot [?]	ABA, Control, Shoot [?]

 Cold

 Cold

 All on All off 

Cold, 12h, Shoot [?]	Cold, 3h, Shoot [?]	Cold, Control, Shoot [?]
Cold, 1d, Shoot [?]	Cold, 6h, Shoot [?]
Cold, 1h, Shoot [?]	Cold, Control, Shoot [?]

 Developmental time control

 Developmental time control

 All on All off 

DevTime, 0h, Shoot [?]	DevTime, 1h, Shoot [?]	DevTime, 5d, Shoot [?]
DevTime, 10d, Shoot [?]	DevTime, 3d, Shoot [?]	DevTime, 6h, Shoot [?]
DevTime, 12h, Shoot [?]	DevTime, 3h, Shoot [?]
DevTime, 1d, Shoot [?]	DevTime, 4d, Shoot [?]

 Drought

 Drought

 All on All off 

Drought, 12h, Shoot [?]	Drought, 1h, Shoot [?]	Drought, 6h, Shoot [?]
Drought, 1d, Shoot [?]	Drought, 3h, Shoot [?]	Drought, Control, Shoot [?]

 Flood

 Flood

 All on All off 

Flood, 12h, Shoot [?]	Flood, 3d, Shoot [?]	Flood, Control, Shoot [?]
Flood, 1d, Shoot [?]	Flood, 3h, Shoot [?]
Flood, 1h, Shoot [?]	Flood, 6h, Shoot [?]

 High and low phosphate

 High and low phosphate

 All on All off 

High P, 10d, Shoot [?]	Low P, 10d, Shoot [?]	P, Control, Shoot [?]
High P, 1d, Shoot [?]	Low P, 1d, Shoot [?]
High P, 5d, Shoot [?]	Low P, 5d, Shoot [?]

 High cadmium

 High cadmium

 All on All off 

High Cd, 12h, Shoot [?]	High Cd, 1h, Shoot [?]	High Cd, Control, Shoot [?]
High Cd, 1d, Shoot [?]	High Cd, 5d, Shoot [?]

 High salinity

 High salinity

 All on All off 

High salinity, 1h, Shoot [?]

High salinity, Control, Shoot [?]

 JA

 JA

 All on All off 

JA, 12h, Shoot [?]	JA, 1h, Shoot [?]	JA, 6h, Shoot [?]
JA, 1d, Shoot [?]	JA, 3h, Shoot [?]	JA, Control, Shoot [?]

 Low and very low cadmium

 Low and very low cadmium

 All on All off 

Low Cd, 10d, Shoot [?]	Low/Very low Cd, Control, Shoot [?]	Very low Cd, 4d, Shoot [?]
Low Cd, 1d, Shoot [?]	Very low Cd, 10d, Shoot [?]
Low Cd, 4d, Shoot [?]	Very low Cd, 1d, Shoot [?]

 Osmotic

 Osmotic

 All on All off 

Osmotic, 12h, Shoot [?]	Osmotic, 3h, Shoot [?]	Osmotic, Control, Shoot [?]
Osmotic, 1h, Shoot [?]	Osmotic, 6h, Shoot [?]

 5. Basic features

 5. Basic features

 All on All off 

DNA

Snapshots

Snapshot Name

Snapshot Timestamp [GMT]

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