BNL1030, BNL1030 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL1030
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL1030_orig
Source Typegenomic
Repeat Motif(GT)16, (CA)13
PCR ConditionAnnealing temperature: 55
Primer 1BNL1030_F: TTTGGAGCCATTTACATGCA
Primer 2BNL1030_R: AAACCACTTCTGCATCTGGA
PolymorphismP_ BNL1030
CommentPrimer data obtained in 2000
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D09chromosomeD09:46146983..46147219 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A09chromosomeA09:74635715..74635945 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018223.1chromosomeCM018223.1:43903612..43903850 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018210.1chromosomeCM018210.1:69956954..69957178 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_09chromosomeD5_09:37421374..37421606 +Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
Chr09_CRI-A2_v1.0.a1chromosomeChr09_CRI-A2_v1.0.a1:76596745..76596973 +Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_09chromosomeD10_09:6286763..6286991 -Gossypium turneri (D10) genome NSF_v1_a2n/a
scaffold5426.1supercontigscaffold5426.1:22062..22292 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
Dt_chr6chromosomeDt_chr6:6505499..6505735 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D09chromosomeD09:43992085..43992321 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A09chromosomeA09:69004226..69004456 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D09chromosomeGhir_D09:45943086..45943322 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A09chromosomeGhir_A09:74301772..74302002 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D09chromosomeD09:45398774..45399010 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A09chromosomeA09:75860553..75860783 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D09chromosomeD09:45688961..45689195 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D09chromosomeD09:43782563..43782799 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A09chromosomeA09:72706698..72706928 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
At09chromosomeAt09:71776176..71776400 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold1874supercontigscaffold1874:450027..450251 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold19617supercontigscaffold19617:72435..72659 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D09chromosomeGbar_D09:44543674..44543912 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A09chromosomeGbar_A09:70486615..70486839 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D09chromosomeD09:47012662..47012900 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A09chromosomeA09:71901048..71901272 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017631.1chromosomeCM017631.1:44792473..44792711 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017618.1chromosomeCM017618.1:71838243..71838473 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017657.1chromosomeCM017657.1:46167199..46167429 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017644.1chromosomeCM017644.1:74757941..74758169 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017709.1chromosomeCM017709.1:45436857..45437099 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017696.1chromosomeCM017696.1:71988727..71988961 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D09chromosomeD09:47408965..47409201 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A09chromosomeA09:77560184..77560414 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr09chromosomeChr09:76633534..76633764 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr09chromosomeChr09:79490659..79490887 +Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr09chromosomeChr09:43638659..43638893 +Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_09chromosomeB_09:63242610..63242840 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr06chromosomeChr06:44168586..44168822 +Gossypium thurberi (D1-5) genome CRI_v1n/a
Chr_06chromosomeChr_06:30591296..30591643 +Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr06chromosomeChr06:45370345..45370591 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr06chromosomeChr06:33728103..33728401 +Gossypium aridum (D4) genome ISU_v1n/a
Chr06chromosomeChr06:25466322..25466558 +Gossypium gossypioides (D6) genome ISU_v1n/a
Chr06chromosomeChr06:31266386..31266618 +Gossypium lobatum (D7) genome ISU_v1n/a
E09chromosomeE09:8664516..8664754 -Gossypium stocksii (E1) genome NSF_v1n/a
Chr09chromosomeChr09:123446726..123446946 +Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Germplasm
Stock NameType
Deltapine 90accession
Relationships

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

Feature NameUnique NameSpeciesType
BNL1030_origBNL1030_origGossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
17235 x TM-1, RIL (2007)AD_ch23_Dt.09N/A18.9BNL1030View
2CCRI-36 x Hai-7124, F2 (2007)AD_ch09_At.09N/A55.7BNL1030View
3Emian-22 x 3-79, BC1 (2011)AD_ch09_At.09N/A123.36BNL1030View
4Guazuncho-2 x VH8-4602, consensus (2009)AD_ch09_At.09N/A87.42BNL1030View
5Hai-7124 x Junmian-1, BC1 (2008) partAD_ch09_At.09N/A19.5BNL1030View
6AD-genome wide Reference Map (2009)AD_ch23_Dt.09N/A147BNL1030View
7AD-genome wide Reference Map (2009)AD_ch09_At.09N/A155BNL1030View
8Xinluzao-1 x Hai-7124, F2 (2008)AD_ch09_At.09N/A60.9BNL1030View
9Yumian-1 x T586, F2:3 (2005)AD_ch05_At.05N/A50.5BNL1030View
10Guazuncho-2 x VH8-4602, consensus (2009)AD_ch23_Dt.09N/A99.54BNL1030View
11Palmeri x K-101, F2 (2007)AD_ch09_At.09N/A101.5BNL1030View
12Yumian-1 x T586, RIL (2006)AD_ch09_At.09N/A12.4BNL1030View
13Yumian-1 x T586, F2:3 (2005.v0)AD_ch05_At.05N/A50.5BNL1030View
147235 x TM-1, F2:3 (2005)AD_ch23_Dt.09N/A27.4BNL1030View
15Yumian-1 x T586, RIL (2015)AD_ch09_At.09N/A70.1BNL1030View
16CCRI 12-4 x (AD)5-7, F2 (2015)AD_ch09_At.09N/A125BNL1030View
17CCRI-35 x Yumian-1, RIL (2015)AD_ch09_At.09N/A79.7BNL1030View
18Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch09_At.09N/A215.5BNL1030bView
19TM-1 x 3-79, RIL (2012)AD_ch23_Dt.09N/A55.03BNL1030bView
20TM-1 x 3-79, RIL (2014)AD_ch23_Dt.09N/A91.2BNL1030bView
21Monsanto SSR Bin Map, (2009)AD_ch23_Dt.09N/A41BNL1030bView
22TM-1 x 3-79, RIL (2012)AD_ch09_At.09N/A52.35BNL1030aView
23Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch23_Dt.09N/A174.4BNL1030aView
24TM-1 x 3-79, RIL (2014)AD_ch09_At.09N/A90.1BNL1030aView
25Monsanto SSR Bin Map, (2009)AD_ch09_At.09N/A41BNL1030aView
26TM-1 x Hai-7124, BC1 (2007)AD_ch09_At.09N/A96.5BNL1030-225View
27TM-1 x Hai-7124, BC1 (2008)AD_ch09_At.09N/A97.05BNL1030-225View
28Vsg x (TM-1 x Hai-7124), DH (2005)AD_ch09_At.09N/A92.4BNL1030-225View
29TM-1 x Hai-7124, BC1 (2012)AD_ch09_At.09N/A95.8BNL1030-225View
30Yumian-1 x T586, RIL (2009)AD_ch09_At.09N/A12.4BNL1030/450y(C9)View
31CCRI-35 x Yumian-1, RIL (2017)AD_ch09_At.09N/A100.93BNL1030View
32TM-1 x 3-79, RIL (2012.v3)AD_ch09_At.09N/A90.1BNL1030aView
33TM-1 x 3-79, RIL (2012.v3)AD_ch23_Dt.09N/A91.18BNL1030bView
34PD 94042 x (AD)4-08, F2 (2016)AD_ch09_At.09N/A150.1BNL1030aView
35PD 94042 x (AD)4-08, F2 (2016)AD_ch23_Dt.09N/A194.6BNL1030bView
Sequence
>BNL1030 ID=BNL1030; Name=BNL1030; organism=Gossypium hirsutum; type=genetic_marker; length=237bp
TTTGGAGCCATTTACATGCATAGACAATGGTAATAACAACAATAAGAGGA
AAAGAAGACCCGCAGGAACACCTGGTACGTATTATATATATATATGAAAG
CTTTTTACCCAATTATTCAAAATGGATATATGTGTGTGTGTGTGTGTGTG
TGTGTGTTTGTGTTCATGATTGGCTTTCTTTTTGTCTAATTGGAAAATAT
AATTGGGTGATGTTAGATCCAGATGCAGAAGTGGTTT