BNL1672, BNL1672 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL1672
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL1672_orig=BNL3031_orig
Source Typegenomic
Repeat Motif(AG)14
PCR ConditionAnnealing temperature: 55
Primer 1BNL1672_F: TGGATTTGTCCCTCTGTGTG
Primer 2BNL1672_R: AACCAACTTTTCCAACACCG
PolymorphismP_ BNL1672
CommentPrimer data obtained in 2000
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D09chromosomeD09:34602778..34602911 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018223.1chromosomeCM018223.1:32829360..32829501 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
KI_09chromosomeKI_09:25626105..25626255 +Gossypioides kirkii genome ISU_v3n/a
D10_09chromosomeD10_09:16725354..16725489 -Gossypium turneri (D10) genome NSF_v1_a2n/a
Dt_chr6chromosomeDt_chr6:16496225..16496360 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
Ghir_D09chromosomeGhir_D09:34937966..34938099 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A09chromosomeGhir_A09:59974262..59974367 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D09chromosomeD09:34707422..34707557 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D09chromosomeD09:34535787..34535918 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D09chromosomeD09:32768153..32768290 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Dt09chromosomeDt09:35265643..35265790 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold5012supercontigscaffold5012:116184..116331 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold10661supercontigscaffold10661:61126..61225 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D09chromosomeGbar_D09:33437435..33437576 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A09chromosomeGbar_A09:56696869..56696968 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D09chromosomeD09:36107947..36108283 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017631.1chromosomeCM017631.1:33674356..33674497 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017618.1chromosomeCM017618.1:57575200..57575315 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017709.1chromosomeCM017709.1:34285963..34286086 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D09chromosomeD09:36092478..36092611 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr06chromosomeChr06:33326886..33327013 +Gossypium thurberi (D1-5) genome CRI_v1n/a
Chr_06chromosomeChr_06:22822829..22823019 +Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr06chromosomeChr06:34728558..34728677 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr06chromosomeChr06:24912677..24912874 +Gossypium aridum (D4) genome ISU_v1n/a
Chr06chromosomeChr06:22832743..22832961 +Gossypium lobatum (D7) genome ISU_v1n/a
F09chromosomeF09:51091502..51091628 +Gossypium longicalyx (F1) genome NSF_v1n/a
Chr09chromosomeChr09:102241513..102241626 +Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Chr06chromosomeBNL1672:1..454 .
Chr06:34185764..34186189 +		n/a
scaffold121supercontigBNL1672:1..454 .
scaffold121:932709..933134 +		n/a
Germplasm
Stock NameType
Deltapine 90accession
Relationships

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

Feature NameUnique NameSpeciesType
BNL1672_orig=BNL3031_origBNL1672_orig=BNL3031_origGossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1(SM3 x SM12) x (X4133 x 8891), 4WC (2008)AD_ch23_Dt.09N/A25.5BNL1672View
27235 x TM-1, RIL (2007)AD_ch09_At.09N/A0BNL1672View
3Guazuncho-2 x VH8-4602, consensus (2009)AD_ch09_At.09N/A50.56BNL1672View
4AD-genome wide Reference Map (2009)AD_ch23_Dt.09N/A99BNL1672View
5AD-genome wide Reference Map (2009)AD_ch09_At.09N/A130BNL1672View
6Zhongmiansuo-12 x 8891, RIL (2007)AD_ch23_Dt.09N/A0BNL1672View
7Guazuncho-2 x VH8-4602, consensus (2009)AD_ch23_Dt.09N/A57.46BNL1672View
87235 x TM-1, F2:3 (2005)AD_ch09_At.09N/A6.8BNL1672View
9CCRI 12-4 x (AD)5-7, F2 (2015)AD_ch23_Dt.09N/A69.8BNL1672View
10CCRI-36 x Hai-7124, F2 (2007)AD_ch09_At.09N/A124.8BNL1672bView
11Emian-22 x 3-79, BC1 (2011)AD_ch09_At.09N/A71.84BNL1672bView
12Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch09_At.09N/A118BNL1672bView
13Handan-208 x Pima-90, F2:3 (2007)AD_ch23_Dt.09N/A65.5BNL1672bView
14TM-1 x 3-79, RIL (2012)AD_ch23_Dt.09N/A91.64BNL1672bView
15TM-1 x 3-79, RIL (2014)AD_ch23_Dt.09N/A52BNL1672bView
16Monsanto SSR Bin Map, (2009)AD_ch23_Dt.09N/A81BNL1672bView
17CCRI-36 x Hai-7124, F2 (2007)AD_ch23_Dt.09N/A115.8BNL1672aView
18Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch23_Dt.09N/A117.7BNL1672aView
19Handan-208 x Pima-90, F2:3 (2007)AD_ch09_At.09N/A51BNL1672aView
20TM-1 x 3-79, RIL (2012)AD_ch09_At.09N/A91.51BNL1672aView
21Emian-22 x 3-79, BC1 (2011)AD_ch23_Dt.09N/A65.69BNL1672aView
22TM-1 x 3-79, RIL (2014)AD_ch09_At.09N/A49.4BNL1672aView
23Monsanto SSR Bin Map, (2009)AD_ch09_At.09N/A81BNL1672aView
24HS-46 x MARCABUCAG8US-1-88, RIL (2009)AD_ch09_At.09N/A144BNL1672-136View
25TM-1 x Hai-7124, BC1 (2007)AD_ch09_At.09N/A59.7BNL1672-110View
26TM-1 x Hai-7124, BC1 (2008)AD_ch09_At.09N/A60.02BNL1672-110View
27Vsg x (TM-1 x Hai-7124), DH (2005)AD_ch09_At.09N/A19.4BNL1672-110View
28TM-1 x Hai-7124, BC1 (2012)AD_ch09_At.09N/A60.3BNL1672-110View
29TM-1 x Hai-7124, BC1 (2007)AD_ch23_Dt.09N/A71.2BNL1672-140View
30TM-1 x Hai-7124, BC1 (2008)AD_ch23_Dt.09N/A70.92BNL1672-140View
31TM-1 x Hai-7124, BC1 (2012)AD_ch23_Dt.09N/A68.1BNL1672-140View
32Xinluzao-1 x Hai-7124, F2 (2008)AD_ch23_Dt.09N/A92.6BNL1672-1View
33Xinluzao-1 x Hai-7124, F2 (2008)AD_ch09_At.09N/A133.7BNL1672-2View
34TM-1 x Hai-7124, BC1S1 (2007)AD_ch23_Dt.09N/A62.9BNL1672_140View
35TM-1 x 3-79, RIL (2012.v3)AD_ch09_At.09N/A49.42BNL1672aView
36TM-1 x 3-79, RIL (2012.v3)AD_ch23_Dt.09N/A51.99BNL1672bView
37PD 94042 x (AD)4-08, F2 (2016)AD_ch09_At.09N/A71.1BNL1672bView
38PD 94042 x (AD)4-08, F2 (2016)AD_ch23_Dt.09N/A84.3BNL1672aView
Sequence
>BNL1672 ID=BNL1672; Name=BNL1672; organism=Gossypium hirsutum; type=genetic_marker; length=136bp
TGGATTTGTCCCTCTGTGTGTATAAAGAGAGAGAGAGAGAGAGAGAGAGA
GAGAGAGAGAGAGAGAGAGAGAGAGAGAGACTTTATTAGTAAAATTGTAA
TGATCCAATTTTCTGTCGGTGTTGGAAAAGTTGGTT