BNL3279, BNL3279 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL3279
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL3279_orig
Source Typegenomic
Repeat Motif(AG)15
PCR ConditionAnnealing temperature: 55
Primer 1BNL3279_F: CATGTCCAATGGATGTGTCA
Primer 2BNL3279_R: GGGCCACTTAAAGGCATTCT
PolymorphismP_ BNL3279
CommentPrimer data obtained in 2000
Alignments
The following features are aligned
Aligned FeatureFeature TypeAlignment Location
D11chromosomeD11:65886069..65886194 +
A11chromosomeA11:108314673..108314788 -
CM018212.1chromosomeCM018212.1:108029699..108029814 +
D5_11chromosomeD5_11:4540840..4540955 +
Chr11_CRI-A2_v1.0.a1chromosomeChr11_CRI-A2_v1.0.a1:6308843..6308958 -
D10_11chromosomeD10_11:63147213..63147338 -
CM016624.1chromosomeCM016624.1:137112226..137112345 -
At_chr1chromosomeAt_chr1:2512654..2512769 +
D11chromosomeD11:59769332..59769457 +
A11chromosomeA11:87135966..87136081 -
Ghir_D11chromosomeGhir_D11:66713683..66713808 -
Ghir_A11chromosomeGhir_A11:117226814..117226929 -
D11chromosomeD11:65561459..65561584 -
A11chromosomeA11:115530746..115530861 -
A11chromosomeA11:113358759..113358874 -
D11chromosomeD11:63457177..63457302 -
A11chromosomeA11:110140876..110140991 -
Dt11chromosomeDt11:62334215..62334322 +
scaffold6985supercontigscaffold6985:50787..50902 +
scaffold31745supercontigscaffold31745:7000..7107 +
Gbar_D11chromosomeGbar_D11:63498657..63498764 -
Gbar_A11chromosomeGbar_A11:107352588..107352703 -
A11chromosomeA11:110252298..110252413 -
CM017620.1chromosomeCM017620.1:112483977..112484092 +
CM017633.1chromosomeCM017633.1:65643649..65643770 -
CM017659.1chromosomeCM017659.1:67627498..67627619 -
CM017646.1chromosomeCM017646.1:120573712..120573827 -
CM017698.1chromosomeCM017698.1:108102268..108102383 +
A11chromosomeA11:116712870..116712985 +
D11chromosomeD11:66608838..66608963 -
Chr11chromosomeChr11:125138928..125139043 -
Chr11chromosomeChr11:124422484..124422599 -
Chr11chromosomeChr11:5548903..5549018 -
B_11chromosomeB_11:95567141..95567262 -
Chr07chromosomeChr07:64392304..64392423 -
chr07chromosomechr07:46120226..46120349 -
Chr_07chromosomeChr_07:44518696..44518815 -
Chr07chromosomeChr07:65784777..65784896 -
Chr07chromosomeChr07:40793804..40793929 -
Chr07chromosomeChr07:34267132..34267247 -
Chr07chromosomeChr07:42927318..42927431 -
E11chromosomeE11:108380667..108380778 -
F11chromosomeF11:93833176..93833293 -
Chr11chromosomeChr11:4350233..4350348 +
Chr07chromosomeBNL3279:1..619 .
Chr07:56142481..56143089 -
Chr7chromosomeBNL3279:1..619 .
Chr7:5702866..5703474 +
Germplasm
Stock NameType
Deltapine 90accession
Relationships

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

Feature NameUnique NameSpeciesType
BNL3279_origBNL3279_origGossypium hirsutumsequence_feature


Image
File NameLegend
CRS-49-1151_F3_poly.jpgPolymorphisms of BNL1066 and BNL3279 on a reniform nematode resistance trait-association panel. [Image from Dighe et al., 2009, CRS-49-1151]
CRS-49-1151_F5_poly.jpgPolymorphisms of BNL1066 and BNL3279 on a reniform nematode resistance DNA panel. [Image from Dighe et al., 2009, CRS-49-1151]
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Acala-44 x Pima S-7, F2 (2004)AD_ch20_Dt.10N/A22.9BNL3279View
2CCRI-36 x Hai-7124, F2 (2007)AD_ch09_At.09N/A193.6BNL3279View
3Emian-22 x 3-79, BC1 (2011)AD_ch21_Dt.11N/A214.26BNL3279View
4Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch21_Dt.11N/A35.3BNL3279View
5Guazuncho-2 x VH8-4602, consensus (2009)AD_ch21_Dt.11N/A32.93BNL3279View
6Guazuncho-2 x VH8-4602, RIL (2009)AD_ch21_Dt.11N/A17.3BNL3279View
7Hai-7124 x Junmian-1, BC1 (2008) partAD_ch21_Dt.11N/A29.9BNL3279View
8AD-genome wide Reference Map (2009)AD_ch09_At.09N/A15BNL3279View
9Xinluzao-1 x Hai-7124, F2 (2008)AD_chUN/A198BNL3279View
10Yumian-1 x T586, F2:3 (2005)AD_ch05_At.05N/A2.8BNL3279View
11Yumian-1 x T586, F2:7 (2008)AD_ch21_Dt.11N/A4.5BNL3279View
12AD-genome wide Reference Map (2009)AD_ch21_Dt.11N/A32BNL3279View
13Yumian-1 x T586, RIL (2006)AD_ch21_Dt.11N/A10.2BNL3279View
14Yumian-1 x T586, F2:3 (2005.v0)AD_ch05_At.05N/A2.8BNL3279View
15NemX x SJ-2, RIL (2005)AD_ch11_At.11N/A158.6BNL3279View
16Yumian-1 x T586, RIL (2015)AD_ch21_Dt.11N/A155.6BNL3279View
17W10 x TM-1, F2:3 (2015)AD_ch21_Dt.11N/A21.2BNL3279View
18CCRI 12-4 x (AD)5-7, F2 (2015)AD_ch11_At.11N/A141BNL3279View
19Monsanto SSR Bin Map, (2009)AD_ch21_Dt.11N/A121BNL3279View
20TM-1 x Hai-7124, BC1 (2007)AD_ch21_Dt.11N/A39.5BNL3279-120View
21TM-1 x Hai-7124, BC1 (2008)AD_ch21_Dt.11N/A31.8BNL3279-120View
22Vsg x (TM-1 x Hai-7124), DH (2005)AD_ch21_Dt.11N/A37.8BNL3279-120View
23TM-1 x Hai-7124, BC1 (2012)AD_ch21_Dt.11N/A145.3BNL3279-120View
24Yumian-1 x T586, RIL (2009)AD_ch21_Dt.11N/A4.3BNL3279/120y(C21)View
25GB713 x Nem-X, F2 (2011)AD_ch21_Dt.11N/A184.5BNL3279_106View
26TM-1 x (TX-0256 + TX-1046), CSIL (2016)AD_ch03_At.03N/A33.3BNL3279aView
27TM-1 x (TX-0256 + TX-1046), CSIL (2016)AD_ch21_Dt.11N/A143.4BNL3279bView
28Emian-22 x 3-79, BC1 (2015)AD_ch21_Dt.11N/A203.2BNL3278View
Sequence
>BNL3279 ID=BNL3279; Name=BNL3279; organism=Gossypium hirsutum; type=genetic_marker; length=126bp
CATGTCCAATGGATGTGTCATTAGAGAGAGAGAGAGAGAGAGAGAGAGAG
AGTACCTCGAATCACCAACAAAATCATTAGAGACAACATCTTCTTCTGTG
TATCCAAGAATGCCTTTAAGTGGCCC