SELECTION [X]
Zoom in
Recenter on this region
Dump this selection as FASTA

Glycine max genome assembly version Glyma.Wm82.a1 (Gmax1.01): 55.92 Mbp from Gm01:1..55,915,595

Browser Select Tracks Snapshots Custom Tracks Preferences

Search

Landmark or Region: Examples: Gm02, Gm20:43000001..44000000, Satt320, drought.
Data Source	Scroll/Zoom: Flip

Overview

centromere (approx)

pericentromere (approx)

Region

Details

Glyma1.1 gene models (zoom <= 2 Mbp)

recent duplication blocks (soy-soy 13 Mya)

soybean markers (map version 4.0)

Clear highlighting

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

Clear All Favorites

Tracks

General soybean features

All on All off

assembly supercontigs

centromere (approx) [?]

pericentromere (approx) [?]

Genes

All on All off

Glyma1.0 gene models [?]	Glyma1.1 exon density [?]	NCBI Glycine max annotation [?]
Glyma1.0 gene models (transposon-like) [?]	Glyma1.1 gene models [?]	published genes [?]

Noncoding RNAs

All on All off

miRNA (miRBase) [?]

Genome structure

All on All off

Assembly 1.0-2.0 comparison (relaxed) [?]	old duplication blocks (soy-soy 58 Mya) [?]	synteny blocks (with Cajanus) [?]
Assembly 1.0-2.0 comparison (stringent) [?]	recent duplication blocks (soy-soy 13 Mya) [?]	synteny blocks (with Medicago) [?]

Mutants

All on All off

fast neutron [?] [showing 2/2 subtracks]

Tgm9 [?]

transposable element insertions [?] [showing 2/2 subtracks]

Naturally occurring sequence variants

All on All off

BARCSoy6K [?]

NJAU355K [?]

SoySNP50K [?] [showing 3/3 subtracks]

BAC clones

All on All off

Wm82 FPC contigs [?]	Phaseolus vulgaris (common bean) [?]	Wm82 BACs (minimum tiling path) [?]
Wm82 sequenced BACs [?]	Wm82 BACs [?]

Gene expression

(, )

GeneChip hybridization

All on All off

Affy SoyChip1 [?]	Effect of day length on Bragg SAM [?] [showing 5/5 subtracks]	Effect of transgenes on global soybean gene expression [?] [showing 5/5 subtracks]
Bragg pollen development [?] [showing 2/2 subtracks]	Effect of GmMPK4 RNAi on Wiiiiams 82 [?] [showing 2/2 subtracks]	Expression in cultivars inoculated with P. sojae [?] [showing 31/31 subtracks]
Characterization of Rpp4 on P. pachyrhizi resistance [?] [showing 24/24 subtracks]	Effect of heat Williams 82 leaflet photosynthesis [?] [showing 4/4 subtracks]	Expression in cultivars inoculated with P. sojae set 2 [?] [showing 39/39 subtracks]
Clark and IsoClark roots in iron deficiency [?] [showing 8/8 subtracks]	Effect of iron deficiency on Clark and IsoClark [?] [showing 4/4 subtracks]	Expression in seed compartments at cotyledon stage [?] [showing 9/9 subtracks]
Comparison of Bragg RAM and leaflet [?] [showing 2/2 subtracks]	Effect of LCO on Bayfield leaflets [?] [showing 4/4 subtracks]	Expression in seed compartments at early maturation stage [?] [showing 17/17 subtracks]
Comparison of low and high protein-oil isolines [?] [showing 7/7 subtracks]	Effect of Mg on Al stress [?] [showing 8/8 subtracks]	Expression in seed compartments at globular stage [?] [showing 10/10 subtracks]
Comparison of mycorrhization and GmNARK in Bragg [?] [showing 10/10 subtracks]	Effect of MSH1 RNAi on Thune [?] [showing 3/3 subtracks]	Expression in seed compartments at heart stage [?] [showing 10/10 subtracks]
Development of Bragg RAM [?] [showing 2/2 subtracks]	Effect of nitrogen sink on Wye leaflet [?] [showing 2/2 subtracks]	Nanahomare seed development [?] [showing 2/2 subtracks]
Development of Bragg SAM [?] [showing 3/3 subtracks]	Effect of Nod Factor on OAC Bayfield leaflet expression [?] [showing 2/2 subtracks]	RNAi:oleosin [?] [showing 2/2 subtracks]
Effect of Al stress on PI 416937 root [?] [showing 8/8 subtracks]	Effect of P. pachyrhizi on 5601T expression [?] [showing 2/2 subtracks]	RNAi:storage protein [?] [showing 2/2 subtracks]
Effect of Al stress on sens. and tolerant cultivar roots [?] [showing 16/16 subtracks]	Effect of P. pachyrhizi on PI 200492 expression [?] [showing 9/9 subtracks]	Tamahoamare seed development [?] [showing 2/2 subtracks]
Effect of alkaline stress on G07256 root [?] [showing 7/7 subtracks]	Effect of R.tropici on Minsoy [?] [showing 3/3 subtracks]	Tamahoamare seed pod development [?] [showing 2/2 subtracks]
Effect of Aphid predation on sens. and resist. Cultivars [?] [showing 8/8 subtracks]	Effect of Rpp2 on Asian soybean rust (ASR) [?] [showing 40/40 subtracks]	Tamahomare and Nanahomare seeds [?] [showing 4/4 subtracks]
Effect of B. japonicum on Williams 82 root hair cells [?] [showing 12/12 subtracks]	Effect of Rpp3 on virulent and avirulent P. pachyrhizi (ASR) [?] [showing 18/18 subtracks]	Wye bud removal effect on leaf gene expression [?] [showing 7/7 subtracks]
Effect of bud removal on Wye leaflet [?] [showing 7/7 subtracks]	Effect of Rpp4 RNAi on ASR infection [?] [showing 2/2 subtracks]	Wye paraveinal mesophyll and palisade parenchyma cells [?] [showing 2/2 subtracks]
Effect of Clark seed coat color on expression [?] [showing 2/2 subtracks]	Effect of salt stress on Williams 82 seedlings [?] [showing 2/2 subtracks]
Effect of constant light on Williams 82 seeds [?] [showing 13/13 subtracks]	Effect of temperature on photosynthesis [?] [showing 4/4 subtracks]

RNA Sequencing

All on All off

Expression profies of seed tissues at the cotyledon stage [?] [showing 10/10 subtracks]	Expression profiling of Hutcheson, PI471938 and PI471938 lines under low and high vapor pressure deficits. [?] [showing 12/12 subtracks]	Expression profiling Wyandot susceptible and resistant NILs to aphid exposure [?] [showing 20/20 subtracks]
Expression profile of BR16 expression during water stress over 24 hrs [?] [showing 36/36 subtracks]	Expression profiling of normal and low phytate lines [?] [showing 30/30 subtracks]	Expression time course of leaflet and cotyledon [?] [showing 8/8 subtracks]
Expression profile of seed tissues at early-maturation stage [?] [showing 17/17 subtracks]	Expression profiling of seed development in Williams [?] [showing 16/16 subtracks]	Normal and glaborus Clark isolines [?] [showing 2/2 subtracks]
Expression profile of seed tissues at globular stage [?] [showing 8/8 subtracks]	Expression profiling of Williams 82 under abiotic stresses [?] [showing 21/21 subtracks]	Prima 2000 root nodule expression [?] [showing 3/3 subtracks]
Expression profile of seed tissues at heart stage [?] [showing 8/8 subtracks]	Expression profiling Williams 82 unifoliate leaf subjected to cold stress [?] [showing 9/9 subtracks]	Profiling of Defective Seed Coat Mutants of Clark and Harsoy [?] [showing 12/12 subtracks]
Expression profile of weed stress in Asgrow AG1631 [?] [showing 12/12 subtracks]	Expression profiling Williams cotyledon development [?] [showing 14/14 subtracks]

Markers

All on All off

Phaseolus vulgaris (common bean) [?]	soybean (map version 3.0) [?]	Williams 82 x PI479752 [Hyten 2010] [?]
Conserved Orthologous Sequence [Doug Cook] [?]	soybean (map version 4.0) [?]	Wm82_potential_SSR [?]
Pigeonpea SSR markers [?]	soybean markers [?] [showing 5/5 subtracks]

Repetitive sequence

All on All off

TE1 LTR V2 (all) [?]	TE1 LTR V2 (LTR) [?]	telomeric repeats [?]
TE1 LTR V2 (Helitron_ukn) [?]	TE1 LTR V2 (TIR) [?]
TE1 LTR V2 (LINE_ukn) [?]	TE1 LTR V2 density (all) [?]

SoyMap2 Diversity Browser

Alignments

BAC End Sequence

All on All off

G. canescens [?]	G. falcata [?]	G. syndetika [?]
G. cyrtoloba [?]	G. soja [?]	G. tomentella D3 [?]
G. dolichocarpa [?]	G. stenophita [?]

BAC End Sequence (abnormally long insert size)

All on All off

G. canescens [?]	G. falcata [?]	G. syndetika [?]
G. cyrtoloba [?]	G. soja [?]	G. tomentella D3 [?]
G. dolichocarpa [?]	G. stenophita [?]

BAC End Sequence (relaxed filtering)

All on All off

G. canescens [?]	G. falcata [?]	G. tomentella D3 [?]
G. cyrtoloba [?]	G. stenophita [?]
G. dolichocarpa [?]	G. syndetika [?]

Transcripts

Dana Farber Cancer Institute

All on All off

Glycine max [?]

Lotus japonicus [?]

Medicago truncatula [?]

JCVI

All on All off

Arachis hypogaea [?]	Lotus japonicus [?]	Vigna unguiculata [?]
Arachis stenosperma [?]	Phaseolus coccineus [?]	Lupinus albus transcripts [JCVI] [?]
Glycine max [?]	Phaseolus vulgaris [?]
Glycine soja [?]	Pisum sativum [?]

Various sources

All on All off

Cajanus cajan v.1 [Varshney et al.] [?]	Cajanus cajan v.2 [Varshney et al.] [?]	Chamaecrista fasciculata - clean [Singer et al. 2010] [?]
Cajanus cajan v.1 primers [Varshney et al.] [?]	Cajanus cajan v.2 primers [Varshney et al.] [?]	Phaseolus vulgaris [Phil McClean] [?]

Overview

All on All off

centromere (approx) [?]

pericentromere (approx) [?]

Cotyledon Stage Whole Seed Methylation Sites [?] [showing 3/3 subtracks]	Late Maturity Stage Whole Seed Methylation Sites [?] [showing 9/9 subtracks]	Pre-Dormancy Stage 2 Seed Methylation Sites [?] [showing 3/3 subtracks]
Cotyledon Stage Whole Seed Read Depth [?] [showing 1/1 subtracks]	Late Maturity Stage Whole Seed Read Depth [?] [showing 3/3 subtracks]	Pre-Dormancy Stage 2 Seed Read Depth [?] [showing 1/1 subtracks]
Early Maturation Stage Whole Seed Methylation Sites [?] [showing 3/3 subtracks]	Mid-Maturity Stage Whole Seed Methylation Sites [?] [showing 6/6 subtracks]	Whole Dry Seed Methylation Sites [?] [showing 6/6 subtracks]
Early Maturation Stage Whole Seed Read Depth [?] [showing 1/1 subtracks]	Mid-Maturity Stage Whole Seed Read Depth [?] [showing 2/2 subtracks]	Whole Dry Seed Read Depth [?] [showing 2/2 subtracks]
Globular Stage Whole Seed Methylation Sites [?] [showing 3/3 subtracks]	Pre-Dormancy Stage 1 Seed Methylation Sites [?] [showing 3/3 subtracks]
Globular Stage Whole Seed Read Depth [?] [showing 1/1 subtracks]	Pre-Dormancy Stage 1 Seed Read Depth [?] [showing 1/1 subtracks]

Seedling 6 Days After Imbibition Methylation Sites [?] [showing 9/9 subtracks]	Seedling Cotyledon 6 Days After Imbibition Methylation Sites [?] [showing 9/9 subtracks]
Seedling 6 Days After Imbibition Read Depth [?] [showing 3/3 subtracks]	Seedling Cotyledon 6 Days After Imbibition Read Depth [?] [showing 3/3 subtracks]

Early Maturation Axis Vascular Bundle Methylation Sites [?] [showing 3/3 subtracks]	Early Maturation Seed Coat Palisade Methylation Sites [?] [showing 3/3 subtracks]	Early Maturation Seed Cotyledon Adaxial Parenchyma Methylation Sites [?] [showing 3/3 subtracks]
Early Maturation Axis Vascular Bundle Read Depth [?] [showing 1/1 subtracks]	Early Maturation Seed Coat Palisade Read Depth [?] [showing 1/1 subtracks]	Early Maturation Seed Cotyledon Adaxial Parenchyma Read Depth [?] [showing 1/1 subtracks]
Early Maturation Embryonic Axis Parenchyma Methylation Sites [?] [showing 3/3 subtracks]	Early Maturation Seed Coat Parenchyma Methylation Sites [?] [showing 3/3 subtracks]	Early Maturation Seed Cotyledon Methylation Sites [?] [showing 3/3 subtracks]
Early Maturation Embryonic Axis Parenchyma Read Depth [?] [showing 1/1 subtracks]	Early Maturation Seed Coat Parenchyma Read Depth [?] [showing 1/1 subtracks]	Early Maturation Seed Cotyledon Read Depth [?] [showing 1/1 subtracks]
Early Maturation Embryonic Axis Plumule Methylation Sites [?] [showing 3/3 subtracks]	Early Maturation Seed Coat Read Depth [?] [showing 1/1 subtracks]	Early Maturation Seed Embryonic Axis Root Tip Methylation Sites [?] [showing 3/3 subtracks]
Early Maturation Embryonic Axis Plumule Read Depth [?] [showing 1/1 subtracks]	Early Maturation Seed Cotyledon Abaxial Parenchyma Methylation Sites [?] [showing 3/3 subtracks]	Early Maturation Seed Embryonic Axis Root Tip Read Depth [?] [showing 1/1 subtracks]
Early Maturation Seed Coat Methylation Sites [?] [showing 3/3 subtracks]	Early Maturation Seed Cotyledon Abaxial Parenchyma Read Depth [?] [showing 1/1 subtracks]

Early Maturation Stage Embryonic Axis Methylation Sites [?] [showing 3/3 subtracks]	Early Maturation Stage Embryonic Cotyledon Methylation Sites [?] [showing 3/3 subtracks]
Early Maturation Stage Embryonic Axis Read Depth [?] [showing 1/1 subtracks]	Early Maturation Stage Embryonic Cotyledon Read Depth [?] [showing 1/1 subtracks]

Mid-maturation Stage Seed Coat Methylation Sites [?] [showing 3/3 subtracks]	Mid-maturation Stage Seed Cotyledon Methylation Sites [?] [showing 3/3 subtracks]	Mid-maturation Stage Seed Embryonic Axis Methylation Sites [?] [showing 3/3 subtracks]
Mid-maturation Stage Seed Coat Read Depth [?] [showing 1/1 subtracks]	Mid-maturation Stage Seed Cotyledon Read Depth [?] [showing 1/1 subtracks]	Mid-maturation Stage Seed Embryonic Axis Read Depth [?] [showing 1/1 subtracks]

Glycine max genome assembly version Glyma.Wm82.a1 (Gmax1.01): 55.92 Mbp from Gm01:1..55,915,595

Snapshots

Snapshot Name

Snapshot Timestamp [GMT]

Custom Tracks

Cotyledon Stage Seed Axis Methylation Sites [?] [showing 3/3 subtracks]	Cotyledon Stage Seed Coat Methylation Sites [?] [showing 3/3 subtracks]	Cotyledon Stage Seed Cotyledon Methylation Sites [?] [showing 3/3 subtracks]
Cotyledon Stage Seed Axis Read Depth [?] [showing 1/1 subtracks]	Cotyledon Stage Seed Coat Read Depth [?] [showing 1/1 subtracks]	Cotyledon Stage Seed Cotyledon Read Depth [?] [showing 1/1 subtracks]

Root Hair Methylation [?] [showing 6/6 subtracks]	Stripped Root Methylation [?] [showing 6/6 subtracks]
Root Hair Read Depth [?] [showing 2/2 subtracks]	Stripped Root Read Depth [?] [showing 2/2 subtracks]

Show grid	Image Width 450 640 800 1024 2560 2880	Highlight feature(s) (feature1 feature2...) Clear highlighting
Cache tracks		Highlight regions (region1:start..end region2:start..end) Clear highlighting
Show tooltips		Region Size (bp)