BNL3140, BNL3140 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL3140
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL3140_orig
Source Typegenomic
Repeat Motif(GA)11
PCR ConditionAnnealing temperature: 55
Primer 1BNL3140_F: CACCATTGTGGCAACTGAGT
Primer 2BNL3140_R: GGAAAAGGGAAAGCCATTGT
PolymorphismP_ BNL3140
CommentPrimer data obtained in 2000
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D09chromosomeD09:41177911..41178017 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A09chromosomeA09:68786264..68786384 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018210.1chromosomeCM018210.1:64324420..64324534 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D10_09chromosomeD10_09:10757021..10757129 +Gossypium turneri (D10) genome NSF_v1_a2n/a
Dt_chr6chromosomeDt_chr6:10639249..10639355 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
At_chr6chromosomeAt_chr6:52373478..52373598 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D09chromosomeD09:39057480..39057586 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A09chromosomeA09:63860118..63860238 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D09chromosomeGhir_D09:41018983..41019089 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D09chromosomeD09:40700859..40700965 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A09chromosomeA09:70322674..70322794 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D09chromosomeD09:40776507..40776613 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A09chromosomeA09:70301247..70301367 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D09chromosomeD09:38847490..38847596 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
At09chromosomeAt09:66326434..66326548 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold1340supercontigscaffold1340:319609..319723 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_A09chromosomeGbar_A09:64736887..64737001 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
CM017618.1chromosomeCM017618.1:66162377..66162505 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017657.1chromosomeCM017657.1:41298698..41298802 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017644.1chromosomeCM017644.1:69114101..69114207 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017696.1chromosomeCM017696.1:66179151..66179267 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D09chromosomeD09:42482196..42482302 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A09chromosomeA09:71675999..71676119 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr09chromosomeChr09:39036815..39037004 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
Chr06chromosomeChr06:40829001..40829107 -Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Germplasm
Stock NameType
Deltapine 90accession
Relationships

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

Feature NameUnique NameSpeciesType
BNL3140_origBNL3140_origGossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1(SM3 x SM12) x (X4133 x 8891), 4WC (2008)AD_ch23_Dt.09N/A65.6BNL3140View
27235 x TM-1, RIL (2007)AD_ch23_Dt.09N/A40.1BNL3140View
3Guazuncho-2 x VH8-4602, consensus (2009)AD_ch03_At.03N/A38.48BNL3140View
4Guazuncho-2 x VH8-4602, RIL (2009)AD_ch03_At.03N/A25.61BNL3140View
5Handan-208 x Pima-90, F2:3 (2007)AD_ch23_Dt.09N/A138.1BNL3140View
6AD-genome wide Reference Map (2009)AD_ch23_Dt.09N/A121BNL3140View
7Xinluzao-1 x Hai-7124, F2 (2008)AD_ch23_Dt.09N/A60.5BNL3140View
8Zhongmiansuo-12 x 8891, RIL (2007)AD_ch23_Dt.09N/A39.8BNL3140View
9Yumian-1 x T586, RIL (2006)AD_ch23_Dt.09N/A7.1BNL3140View
10(YM1 x CCRI35) x (YM1 x 7235), 4WC (2012)AD_ch23_Dt.09N/A87.4BNL3140View
117235 x TM-1, F2:3 (2005)AD_ch23_Dt.09N/A53.9BNL3140View
12HS427-10 x TM-1, F2:3 (2005)AD_ch23_Dt.09N/A29.1BNL3140View
13Yumian-1 x T586, RIL (2015)AD_ch23_Dt.09N/A55.2BNL3140View
14Yumian-1 x 7235, RIL (2015)AD_ch23_Dt.09N/A67BNL3140View
15TM-1 x (TX-0256 + TX-1046), CSIL (2016)AD_ch23_Dt.09N/A46.7BNL3140View
16CCRI 12-4 x (AD)5-7, F2 (2015)AD_ch09_At.09N/A99.5BNL3140View
17CCRI-35 x Yumian-1, RIL (2015)AD_ch23_Dt.09N/A64.2BNL3140View
18901-001 x sGK156, F2 (2019)AD_ch09_At.09N/A37.48BNL3140View
19LMY22 x LY343, RIL (2020)D09N/A57.79BNL3140View
20TM-1 x 3-79, RIL (2012)AD_ch23_Dt.09N/A69.09BNL3140aView
21TM-1 x 3-79, RIL (2014)AD_ch23_Dt.09N/A74.4BNL3140aView
22Monsanto SSR Bin Map, (2009)AD_ch09_At.09N/A61BNL3140aView
23Monsanto SSR Bin Map, (2009)AD_ch23_Dt.09N/A41BNL3140bView
24TM-1 x 3-79, RIL (2012)AD_ch09_At.09N/A73.21BNL3140cView
25TM-1 x 3-79, RIL (2014)AD_ch09_At.09N/A69BNL3140cView
26TM-1 x Hai-7124, BC1 (2007)AD_ch23_Dt.09N/A100.3BNL3140-175View
27TM-1 x Hai-7124, BC1 (2008)AD_ch23_Dt.09N/A99.88BNL3140-175View
28TM-1 x Hai-7124, BC1 (2012)AD_ch23_Dt.09N/A97.6BNL3140-175View
29Yumian-1 x T586, RIL (2009)AD_ch23_Dt.09N/A7.1BNL3140/100t(C23)View
30CCRI-35 x Yumian-1, RIL (2017)AD_ch23_Dt.09N/A133.42BNL3140View
31TM-1 x 3-79, RIL (2012.v3)AD_ch09_At.09N/A68.99BNL3140cView
32TM-1 x 3-79, RIL (2012.v3)AD_ch23_Dt.09N/A74.41BNL3140aView
Sequence
>BNL3140 ID=BNL3140; Name=BNL3140; organism=Gossypium hirsutum; type=genetic_marker; length=107bp
CACCATTGTGGCAACTGAGTTTTTTCTAATAAAAAAGCAAAGAGAAAGTG
CTAATATATATGGAGAGAGAGAGAGAGAGAGAGAGTCACAATGGCTTTCC
CTTTTCC