CIR0401, CIR0401 (genetic_marker) Gossypium hirsutum

Marker Overview


Name	CIR0401
Alias	CIR401
Genbank ID	AJ567325
Type	SSR
Species	Gossypium hirsutum
Germplasm	Guazuncho-2
Source Sequence	AJ567325
Source Type	genomic
Repeat Motif	(GT)8
PCR Condition	Annealing temperature: 55
Primer 1	CIR401_F: TGGCGACTCCCTTTT
Primer 2	CIR401_R: AAAAGATGTTACACACACACAC
Product Length	125
Polymorphism	P_ CIR0401
Publication	[view all]
Comment	Primer data obtained in 2005

Cross References

External references for this genetic_marker


Database	Accession
DB:genbank	AJ567325

Alignments

The following features are aligned


Aligned Feature	Feature Type	Alignment Location
A02	chromosome	A02:13059602..13059727 +
CM018203.1	chromosome	CM018203.1:12607183..12607306 +
Chr03_CRI-A2_v1.0.a1	chromosome	Chr03_CRI-A2_v1.0.a1:14206062..14206187 +
At_chr3	chromosome	At_chr3:38222791..38222916 +
A02	chromosome	A02:12747425..12747550 +
Ghir_A02	chromosome	Ghir_A02:12796812..12796937 +
A02	chromosome	A02:12267331..12267456 +
A02	chromosome	A02:12914388..12914513 +
A02	chromosome	A02:12964621..12964746 +
scaffold3276	supercontig	scaffold3276:292942..293065 -
Gbar_A02	chromosome	Gbar_A02:12669623..12669746 +
A02	chromosome	A02:12626001..12626124 +
CM017611.1	chromosome	CM017611.1:12745040..12745165 +
CM017637.1	chromosome	CM017637.1:13099120..13099245 +
CM017689.1	chromosome	CM017689.1:12845494..12845619 +
A02	chromosome	A02:13041624..13041749 +
Chr03	chromosome	Chr03:110440492..110440617 -
Chr03	chromosome	Chr03:117898634..117898759 -
Chr03	chromosome	Chr03:117915992..117916117 -
Chr03	chromosome	Chr03:116667386..116667511 -

Publications


Year	Publication
2004	Nguyen TB, Giband M, Brottier P, Risterucci AM, Lacape JM. Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers. Theoretical and applied genetics. 2004 Jun; 109(1):167-75

Germplasm


Stock Name	Type
Guazuncho-2	accession

Relationships

The following sequence_feature feature(s) derives from this genetic_marker:


Feature Name	Unique Name	Species	Type
AJ567325	AJ567325	Gossypium hirsutum	sequence_feature

Map Positions


#	Map Name	Linkage Group	Bin	Position	Locus	MapViewer
1	CCRI-36 x Hai-7124, F2 (2007)	AD_ch02_At.02	N/A	54.4	CIR401a	View
2	Emian-22 x 3-79, BC1 (2011)	AD_ch05_At.05	N/A	148.52	CIR401a	View
3	Emian-22 x 3-79, BC1 (2015)	AD_ch05_At.05	N/A	142.6	CIR401a	View
4	CCRI-36 x Hai-7124, F2 (2007)	AD_ch05_At.05	N/A	125.4	CIR401b	View
5	Emian-22 x 3-79, BC1 (2011)	AD_ch02_At.02	N/A	73.14	CIR401b	View
6	Guazuncho-2 x VH8-4602, BC1 (2005)	AD_ch02_At.02	N/A	65.9	CIR401	View
7	Guazuncho-2 x VH8-4602, consensus (2009)	AD_ch02_At.02	N/A	39.28	CIR401	View
8	Guazuncho-2 x VH8-4602, RIL (2009)	AD_ch02_At.02	N/A	32.04	CIR401	View
9	Handan-208 x Pima-90, F2:3 (2007)	AD_ch23_Dt.09	N/A	141.5	CIR401	View
10	AD-genome wide Reference Map (2009)	AD_ch05_At.05	N/A	158	cir0401	View
11	AD-genome wide Reference Map (2009)	AD_ch02_At.02	N/A	136	cir0401	View
12	PD 94042 x (AD)4-08, F2 (2016)	AD_ch10_At.10	N/A	94.5	CIR401	View

Sequence

>CIR0401 ID=CIR0401; Name=CIR0401; organism=Gossypium hirsutum; type=genetic_marker; length=125bp
TGGCGACTCCCTTTTTTAATAAAAATCGAAAGTCAGTTTTCAAATTTCCA
ATAAGTCACTCAATTAGCGAACAAGCAAAAATTTTTACGTCGCTACATGG
TGTGTGTGTGTGTGTAACATCTTTT

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CIR0401, CIR0401 (genetic_marker) Gossypium hirsutum