BNL2443, BNL2443 (genetic_marker) Gossypium hirsutum

Marker Overview


Name	BNL2443
Genbank ID	N/A
Type	SSR
Species	Gossypium hirsutum
Germplasm	Deltapine 90
Source Sequence	BNL2443_orig
Source Type	genomic
Repeat Motif	(AG)7+N+(AG)20, (CT)20
PCR Condition	Annealing temperature: 55
Primer 1	BNL2443_F: TTTATTGGTCGGTCTTTGCC
Primer 2	BNL2443_R: TTAGGGTGTTCTTTGGGCAC
Polymorphism	P_ BNL2443
Comment	Primer data obtained in 2000

Alignments

The following features are aligned


Feature Name	Type	Location	Analysis	Reference
A03	chromosome	A03:11285257..11285412 +	Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1	n/a
D03	chromosome	D03:42405449..42405600 -	Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1	n/a
CM018217.1	chromosome	CM018217.1:42787972..42788144 -	Gossypium barbadense (AD2) '3-79' genome HGS_v1.1	n/a
D5_02	chromosome	D5_02:36708888..36709025 -	Gossypium raimondii (D5) 'D5-4' genome NSF_v1	n/a
At_chr5	chromosome	At_chr5:27536868..27537023 +	Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1	n/a
A03	chromosome	A03:9848778..9848933 +	Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1	n/a
D03	chromosome	D03:36299481..36299786 -	Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1	n/a
A03	chromosome	A03:11670931..11671086 +	Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1	n/a
A03	chromosome	A03:12107520..12107673 +	Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1	n/a
D03	chromosome	D03:42459685..42459838 -	Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1	n/a
Gbar_D03	chromosome	Gbar_D03:41203409..41203575 -	Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1	n/a
D03	chromosome	D03:43718254..43718424 -	Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1	n/a
CM017625.1	chromosome	CM017625.1:42198992..42199128 -	Gossypium tomentosum (AD3) genome HGS_v1.1	n/a
CM017651.1	chromosome	CM017651.1:46228909..46229081 -	Gossypium mustelinum (AD4) genome JGI_v1.1	n/a
CM017703.1	chromosome	CM017703.1:43725464..43725636 -	Gossypium darwinii (AD5) genome HGS_v1.1	n/a
A03	chromosome	A03:12342618..12342773 +	Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1	n/a
D03	chromosome	D03:44395716..44395869 -	Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1	n/a
Chr02	chromosome	Chr02:38800777..38800915 -	Gossypium raimondii (D5) 'Grai D502' genome HAU_v1	n/a
Chr03	chromosome	Chr03:40120292..40120432 -	Gossypium thurberi (D1-5) genome CRI_v1	n/a
F02	chromosome	F02:66053799..66053932 -	Gossypium longicalyx (F1) genome NSF_v1	n/a
Chr03	chromosome	BNL2443:1..562 . Chr03:36198720..36199267 -		n/a
Chr1	chromosome	BNL2443:1..562 . Chr1:25767773..25768318 +		n/a

Germplasm


Stock Name	Type
Deltapine 90	accession

Relationships

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


Feature Name	Unique Name	Species	Type
BNL2443_orig	BNL2443_orig	Gossypium hirsutum	sequence_feature

Map Positions


#	Map Name	Linkage Group	Bin	Position	Locus	MapViewer
1	CCRI-36 x Hai-7124, F2 (2007)	AD_ch14_Dt.02	N/A	61.4	BNL2443	View
2	Emian-22 x 3-79, BC1 (2011)	AD_ch17_Dt.03	N/A	73.25	BNL2443	View
3	Guazuncho-2 x VH8-4602, BC2 (2005)	AD_ch17_Dt.03	N/A	35.9	BNL2443	View
4	Guazuncho-2 x VH8-4602, consensus (2009)	AD_ch17_Dt.03	N/A	18.01	BNL2443	View
5	Guazuncho-2 x VH8-4602, consensus (2009)	AD_ch03_At.03	N/A	24.81	BNL2443	View
6	Guazuncho-2 x VH8-4602, RIL (2009)	AD_ch17_Dt.03	N/A	20.66	BNL2443	View
7	Guazuncho-2 x VH8-4602, RIL (2009)	AD_ch03_At.03	N/A	14.55	BNL2443	View
8	AD-genome wide Reference Map (2009)	AD_ch14_Dt.02	N/A	27	BNL2443	View
9	AD-genome wide Reference Map (2009)	AD_ch17_Dt.03	N/A	67	BNL2443	View
10	TM-1 x 3-79, RIL (2006)	AD_ch03_At.03	N/A	38.3	BNL2443	View
11	TM-1 x 3-79, RIL (2012)	AD_ch17_Dt.03	N/A	22.01	BNL2443	View
12	Xinluzao-1 x Hai-7124, F2 (2008)	AD_chU	N/A	25.8	BNL2443	View
13	AD-genome wide Reference Map (2009)	AD_ch03_At.03	N/A	43	BNL2443	View
14	T582 x Hai-7124, F2 (2010)	AD_ch03_At.03	N/A	75	BNL2443	View
15	TM-1 x 3-79, RIL (2014)	AD_ch17_Dt.03	N/A	0	BNL2443	View
16	TM-1 x 3-79, RIL (2012.v3)	AD_ch17_Dt.03	N/A	0	BNL2443	View
17	Monsanto SSR Bin Map, (2009)	AD_ch17_Dt.03	N/A	61	BNL2443	View
18	Guazuncho-2 x VH8-4602, BC1 (2005)	AD_ch03_At.03	N/A	25.4	BNL2443b	View
19	Monsanto SSR Bin Map, (2009)	AD_ch17_Dt.03	N/A	81	BNL2443b	View
20	Guazuncho-2 x VH8-4602, BC1 (2005)	AD_ch17_Dt.03	N/A	23	BNL2443a	View
21	Handan-208 x Pima-90, F2:3 (2007)	AD_ch17_Dt.03	N/A	113.9	BNL2443a	View
22	Monsanto SSR Bin Map, (2009)	AD_ch03_At.03	N/A	61	BNL2443a	View
23	TM-1 x Hai-7124, BC1 (2007)	AD_ch03_At.03	N/A	75	BNL2443-140	View
24	TM-1 x Hai-7124, BC1 (2008)	AD_ch03_At.03	N/A	71.89	BNL2443-140	View
25	TM-1 x Hai-7124, BC1 (2012)	AD_ch03_At.03	N/A	70.1	BNL2443-140	View
26	TM-1 x Hai-7124, BC1 (2007)	AD_ch17_Dt.03	N/A	75.4	BNL2443-160	View
27	TM-1 x Hai-7124, BC1 (2008)	AD_ch17_Dt.03	N/A	35.24	BNL2443-160	View
28	Vsg x (TM-1 x Hai-7124), DH (2005)	AD_ch17_Dt.03	N/A	24.6	BNL2443-160	View
29	TM-1 x Hai-7124, BC1 (2012)	AD_ch17_Dt.03	N/A	74.3	BNL2443-160	View
30	Guazuncho-2 x VH8-4602, consensus (2009)	AD_ch03_At.03	N/A	26.44	BNL2443	View
31	Guazuncho-2 x VH8-4602, RIL (2009)	AD_ch03_At.03	N/A	16.49	BNL2443	View

Sequence

>BNL2443 ID=BNL2443; Name=BNL2443; organism=Gossypium hirsutum; type=genetic_marker; length=155bp
TTTATTGGTCGGTCTTTGCCCCCCCCCCCCTCTCTCTCTCTCTCTCTCTC
TCTCTCTCTCTCTCTCTCTTTCTTTTTTTATGTAATATTGATCAATATTA
TAATGTACTTTTTCATTCTCTCTCTCTCTCTTGCCGTGCCCAAAGAACAC
CCTAA

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BNL2443, BNL2443 (genetic_marker) Gossypium hirsutum