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IRGSP-1.0: 2.267 kbp from chr12:20,670,329..20,672,595

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Landmark or Region: Examples: ABC transporter, chr1, chr02:1..105000, Os03g0100300, AK060852, LOC_Os01g54390.
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Overview

Overview

Region

Region

Details

Details

Organelle

Representative transcripts

Predicted genes

Repeat regions

MSU Osa1 Rice Gene Models

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Tracks

Tracks

FSTs

FSTs

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CGT (Ds) [?]	GSNU (Ds) [?]	TRIM (T-DNA) [?]
CSIRO (T-DNA) [?]	NIAS (Tos17) [?]	UCD (Ds) [?]
Genoplante (T-DNA) [?]	POSTECH (T-DNA) [?]

Gene predictions

Gene predictions

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JIGSAW [?]

General

General

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DNA/GC Content

IsoSeq

IsoSeq

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IsoSeq, Leaf, GC [?]

Markers

Markers

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SSR [?]

Masked regions

Masked regions

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Organelle [?]

Repeat regions [?]

Repeat units [?]

Misc

Misc

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Centromere [?]

Minimum Tiling Path [?]

OMAP

OMAP

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Oryza alta [?]	Oryza glaberrima [?]	Oryza officinalis [?]
Oryza australiensis [?]	Oryza granulata [?]	Oryza punctata [?]
Oryza brachyantha [?]	Oryza minuta [?]	Oryza ridleyi [?]
Oryza coarctata [?]	Oryza nivara [?]	Oryza rufipogon [?]

Other rice annotations

Other rice annotations

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MSU Osa1 Rice Gene Models [?]

RAP1, RAP2, and RAP3 transcripts [?]

RefSeq Annotation Release 102 [?]

Protein alignments

Protein alignments

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Swiss-Prot (identical) [?]

Swiss-Prot plant division [?]

TrEMBL plant division [?]

RAP annotation

RAP annotation

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Gene locus [?]	Predicted locus [?]
Predicted genes [?]	Representative transcripts [?]

RNA-seq

RNA-seq

Phosphate (Oono et al.)

Phosphate (Oono et al.)

Root

Root

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HighP, 10d, Root [?]	HighP, 5d, Root [?]	LowP, 1d, Root [?]
HighP, 10d-Rec, Root [?]	LowP, 10d, Root [?]	LowP, 5d, Root [?]
HighP, 1d, Root [?]	LowP, 10d-Rec, Root [?]	P, Cont, Root [?]

Shoot

Shoot

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HighP, 10d, Shoot [?]	LowP, 10d, Shoot [?]	P, Cont, Shoot [?]
HighP, 1d, Shoot [?]	LowP, 1d, Shoot [?]
HighP, 5d, Shoot [?]	LowP, 5d, Shoot [?]

Phosphate (Secco et al.)

Phosphate (Secco et al.)

Root

Root

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+P, 1h, Root [?]	+P, 6h, Root [?]	-P, 24h, Root [?]
+P, 21d, Root [?]	+P, 7d, Root [?]	-P, 3d, Root [?]
+P, 21d_1h, Root [?]	-P, 1h, Root [?]	-P, 6h, Root [?]
+P, 21d_24h, Root [?]	-P, 21d, Root [?]	-P, 7d, Root [?]
+P, 21d_6h, Root [?]	-P, 21d_1h, Root [?]	P_resupply, 21d_1h, Root [?]
+P, 24h, Root [?]	-P, 21d_24h, Root [?]	P_resupply, 21d_24h, Root [?]
+P, 3d, Root [?]	-P, 21d_6h, Root [?]	P_resupply, 21d_6h, Root [?]

Shoot

Shoot

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+P, 1h, Shoot [?]	+P, 6h, Shoot [?]	-P, 24h, Shoot [?]
+P, 21d, Shoot [?]	+P, 7d, Shoot [?]	-P, 3d, Shoot [?]
+P, 21d_1h, Shoot [?]	-P, 1h, Shoot [?]	-P, 6h, Shoot [?]
+P, 21d_24h, Shoot [?]	-P, 21d, Shoot [?]	-P, 7d, Shoot [?]
+P, 21d_6h, Shoot [?]	-P, 21d_1h, Shoot [?]	P_resupply, 21d_1h, Shoot [?]
+P, 24h, Shoot [?]	-P, 21d_24h, Shoot [?]	P_resupply, 21d_24h, Shoot [?]
+P, 3d, Shoot [?]	-P, 21d_6h, Shoot [?]	P_resupply, 21d_6h, Shoot [?]

Salinity (Mizuno et al.)

Salinity (Mizuno et al.)

Root

Root

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Salt, 1h, Root [?]

Salt, Cont, Root [?]

Shoot

Shoot

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Salt, 1h, Shoot [?]

Salt, Cont, Shoot [?]

Tissues (Sakai et al.)

Tissues (Sakai et al.)

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Callus [?]	Panicle (before flowering) [?]	Shoot [?]
Leaf [?]	Root [?]
Panicle (after flowering) [?]	Seed [?]

RNAs

RNAs

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miRBase [?]	rRNA regions [?]	sRNAs [?]
miRBase (primary transcript) [?]	rRNAs [?]	tRNAs [?]

Short-Read Assembly Browser

Short-Read Assembly Browser

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Guangluai4 [?]

Koshihikari [?]

Transcript mapping

Transcript mapping

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ESTs (Oryza) [?]	mRNAs (Oryza) [?]	O. sativa indica & O. rufipogon FL-cDNAs [?]
ESTs (Other Poaceae) [?]	mRNAs (Other cereals) [?]	O. sativa japonica FL-cDNAs [?]

Organelle

Organelle

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organelle_predicted_gene [?]	organelle_rRNA
organelle_RNA_editing	organelle_tRNA

Analysis

Analysis

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Restriction Sites

Snapshots

Snapshot Name

Snapshot Timestamp [GMT]

Custom Tracks

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