JESPR0179, JESPR0179 (genetic_marker) Gossypium hirsutum

Marker Overview


Name	JESPR0179
Alias	JESPR179
Genbank ID	AF351417
Type	SSR
Species	Gossypium hirsutum
Germplasm	Tamcot Sphinx
Source Sequence	AF351417.1
Source Type	genomic
Repeat Motif	(CTT)12
Primer 1	JESPR0179_F: CTGACACTGTATGCTTGCAG
Primer 2	JESPR0179_R: CATATTTGGCATATCACATAGAG
Publication	[view all]
Comment	Primer data obtained in 2002

Cross References

External references for this genetic_marker


Database	Accession
DB:genbank	AF351417

Alignments

The following features are aligned


Feature Name	Type	Location	Analysis	Reference
A02	chromosome	A02:8675160..8675333 -	Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1	n/a
CM018203.1	chromosome	CM018203.1:7808935..7809087 -	Gossypium barbadense (AD2) '3-79' genome HGS_v1.1	n/a
Chr03_CRI-A2_v1.0.a1	chromosome	Chr03_CRI-A2_v1.0.a1:8843544..8843765 -	Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1	n/a
scaffold2214.1	supercontig	scaffold2214.1:36149..36322 +	Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1	n/a
A02	chromosome	A02:8007436..8007609 -	Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1	n/a
Ghir_A02	chromosome	Ghir_A02:7963615..7963788 -	Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1	n/a
A02	chromosome	A02:7674197..7674370 -	Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1	n/a
A02	chromosome	A02:8226215..8226388 -	Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1	n/a
A02	chromosome	A02:8204847..8205020 -	Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1	n/a
scaffold6235	supercontig	scaffold6235:111390..111542 +	Gossypium barbadense (AD2) '3-79' genome HAU_v1	n/a
Gbar_A02	chromosome	Gbar_A02:7915261..7915413 -	Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1	n/a
A02	chromosome	A02:7858088..7858240 -	Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1	n/a
CM017611.1	chromosome	CM017611.1:7868364..7868531 -	Gossypium tomentosum (AD3) genome HGS_v1.1	n/a
CM017637.1	chromosome	CM017637.1:8226385..8226597 -	Gossypium mustelinum (AD4) genome JGI_v1.1	n/a
CM017689.1	chromosome	CM017689.1:7976109..7976261 -	Gossypium darwinii (AD5) genome HGS_v1.1	n/a
A02	chromosome	A02:8292286..8292459 -	Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1	n/a
Chr03	chromosome	Chr03:123199013..123199255 +	Gossypium herbaceum (A1) 'Mutema' genome WHU_v1	n/a
Chr03	chromosome	Chr03:121941335..121941556 +	Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1	n/a
chr05	chromosome	chr05:5904963..5906033 -	Gossypium armourianum (D2-1) genome ISU_v1	n/a

Publications


Year	Publication
2001	Reddy O, Pepper A, Abdurakhmonov I, Saha S, Jenkins J, Brooks T, Bolek Y, El-Zik K. New dinucleotide and trinucleotide microsatellite marker resources for cotton genome research. Journal of cotton science. 2001; 5(2):103-113

Germplasm


Stock Name	Type
Tamcot Sphinx	accession

Relationships

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


Feature Name	Unique Name	Species	Type
AF351417.1	AF351417.1	Gossypium hirsutum	sequence_feature

Map Positions


#	Map Name	Linkage Group	Bin	Position	Locus	MapViewer
1	Acala-44 x Pima S-7, F2 (2004)	AD_chU	N/A	48	JESPR-179	View
2	Guazuncho-2 x VH8-4602, BC1 (2005)	AD_ch02_At.02	N/A	51.1	JESPR179a	View
3	Guazuncho-2 x VH8-4602, BC1 (2005)	AD_ch14_Dt.02	N/A	37.8	JESPR179b	View
4	Guazuncho-2 x VH8-4602, consensus (2009)	AD_ch14_Dt.02	N/A	38.72	JESPR179	View
5	Guazuncho-2 x VH8-4602, consensus (2009)	AD_ch02_At.02	N/A	35.62	JESPR179	View
6	Guazuncho-2 x VH8-4602, RIL (2009)	AD_ch02_At.02	N/A	24.57	JESPR179	View
7	TM-1 x 3-79, RIL (2012)	AD_ch02_At.02	N/A	76.19	JESPR179	View
8	Xinluzao-1 x Hai-7124, F2 (2008)	AD_ch02_At.02	N/A	65.2	JESPR179	View
9	(YM1 x CCRI35) x (YM1 x 7235), 4WC (2012)	AD_ch02_At.02	N/A	0	JESPR179	View
10	Yumian-1 x 7235, RIL (2015)	AD_ch02_At.02	N/A	41.1	JESPR179	View
11	TM-1 x 3-79, RIL (2014)	AD_ch02_At.02	N/A	78.2	JESPR179	View
12	CCRI 12-4 x (AD)5-7, F2 (2015)	AD_ch02_At.02	N/A	73.9	JESPR179	View
13	Monsanto SSR Bin Map, (2009)	AD_ch02_At.02	N/A	61	JESPR179	View
14	AD-genome wide Reference Map (2009)	AD_ch14_Dt.02	N/A	56	jespr0179	View
15	AD-genome wide Reference Map (2009)	AD_ch02_At.02	N/A	148	jespr0179	View
16	TM-1 x Hai-7124, BC1 (2008)	AD_ch02_At.02	N/A	61.37	JESPR179-175	View
17	TM-1 x Hai-7124, BC1 (2012)	AD_ch02_At.02	N/A	58.2	JESPR179-175	View
18	TM-1 x 3-79, RIL (2012.v3)	AD_ch02_At.02	N/A	78.15	JESPR179	View

Sequence

>JESPR0179 ID=JESPR0179; Name=JESPR0179; organism=Gossypium hirsutum; type=genetic_marker; length=174bp
CTGACACTGTATGCTTGCAGTAAAATTGGGATTTCAAATTTGTTATATAA
ATTCGTTGTTTTAATGCGCACGCGCGCAACTGGTCAATTGGCTTCTTTTT
CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTATGTCTCTTAAATA
TCTCTATGTGATATGCCAAATATG

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JESPR0179, JESPR0179 (genetic_marker) Gossypium hirsutum