BNL3452, BNL3452 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL3452
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL3452_orig
Source Typegenomic
Repeat Motif(CA)13
PCR ConditionAnnealing temperature: 55
Primer 1BNL3452_F: TGTAACTGAGCAGCCGTACG
Primer 2BNL3452_R: GCCAAAGCAGAGTGAGATCC
PolymorphismP_ BNL3452
CommentPrimer data obtained in 2000
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D05chromosomeD05:3937172..3937362 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018219.1chromosomeCM018219.1:3639161..3639357 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_05chromosomeD5_05:3523964..3524146 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
D10_05chromosomeD10_05:56985040..56985218 +Gossypium turneri (D10) genome NSF_v1_a2n/a
Dt_chr9chromosomeDt_chr9:65608970..65609160 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D05chromosomeD05:3777082..3777272 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D05chromosomeGhir_D05:3910939..3911127 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D05chromosomeD05:3710987..3711177 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D05chromosomeD05:3822007..3822197 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D05chromosomeD05:3682407..3682597 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
scaffold1848supercontigscaffold1848:51566..51764 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D05chromosomeGbar_D05:3810233..3810427 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D05chromosomeD05:3958740..3958936 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017627.1chromosomeCM017627.1:3779270..3779460 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017653.1chromosomeCM017653.1:3967546..3967734 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017705.1chromosomeCM017705.1:3790842..3791038 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D05chromosomeD05:3846501..3846691 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr05chromosomeChr05:3549696..3549876 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_05chromosomeB_05:81898415..81898595 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr09chromosomeChr09:3651568..3651750 -Gossypium thurberi (D1-5) genome CRI_v1n/a
chr09chromosomechr09:3437130..3437317 -Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr09chromosomeChr09:3834659..3834843 -Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr09chromosomeChr09:3444298..3444478 -Gossypium aridum (D4) genome ISU_v1n/a
Chr09chromosomeChr09:2799110..2799300 -Gossypium gossypioides (D6) genome ISU_v1n/a
Chr09chromosomeChr09:3380583..3380763 -Gossypium lobatum (D7) genome ISU_v1n/a
E05chromosomeE05:4671114..4671301 -Gossypium stocksii (E1) genome NSF_v1n/a
F05chromosomeF05:3680131..3680311 -Gossypium longicalyx (F1) genome NSF_v1n/a
Chr09chromosomeBNL3452:1..566 .
Chr09:3512741..3513296 -		n/a
Chr9chromosomeBNL3452:1..566 .
Chr9:3092204..3092759 +		n/a
Germplasm
Stock NameType
Deltapine 90accession
Relationships

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

Feature NameUnique NameSpeciesType
BNL3452_origBNL3452_origGossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1(SM3 x SM12) x (X4133 x 8891), 4WC (2008)AD_ch19_Dt.05N/A18.9BNL3452View
27235 x TM-1, RIL (2007)AD_ch10_At.10N/A18.6BNL3452View
3Emian-22 x 3-79, BC1 (2011)AD_ch19_Dt.05N/A207.59BNL3452View
4Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch19_Dt.05N/A31.5BNL3452View
5Guazuncho-2 x VH8-4602, BC2 (2005)AD_ch19_Dt.05N/A13.1BNL3452View
6Guazuncho-2 x VH8-4602, consensus (2009)AD_ch19_Dt.05N/A25.73BNL3452View
7Guazuncho-2 x VH8-4602, RIL (2009)AD_ch19_Dt.05N/A8.09BNL3452View
8Hai-7124 x Junmian-1, BC1 (2008) partAD_ch19_Dt.05N/A96.5BNL3452View
9Handan-208 x Pima-90, F2:3 (2007)AD_ch19_Dt.05N/A33BNL3452View
10Palmeri x K-101, F2 (2007)AD_ch19_Dt.05N/A26.5BNL3452View
11AD-genome wide Reference Map (2009)AD_ch19_Dt.05N/A60BNL3452View
12AD-genome wide Reference Map (2009)AD_ch05_At.05N/A16BNL3452View
13TM-1 x 3-79, RIL (2006)AD_ch19_Dt.05N/A19.6BNL3452View
14Xinluzao-1 x Hai-7124, F2 (2008)AD_ch19_Dt.05N/A320.6BNL3452View
15Zhongmiansuo-12 x 8891, RIL (2007)AD_ch05_At.05N/A3BNL3452View
16CCRI-36 x Hai-7124, F2 (2007)AD_ch19_Dt.05N/A196.4BNL3452View
177235 x TM-1, F2:3 (2005)AD_ch10_At.10N/A0BNL3452View
18Baimian 1 x TM-1 , F2:3 (2014)AD_ch19_Dt.05N/A14.7BNL3452View
19TM-1 x (TX-0256 + TX-1046), CSIL (2016)AD_ch05_At.05N/A28.6BNL3452View
20CCRI 12-4 x (AD)5-7, F2 (2015)AD_ch19_Dt.05N/A196BNL3452View
21TM-1 x 3-79, RIL (2012)AD_ch05_At.05N/A22.74BNL3452aView
22TM-1 x 3-79, RIL (2014)AD_ch05_At.05N/A180.2BNL3452aView
23Monsanto SSR Bin Map, (2009)AD_ch05_At.05N/A181BNL3452aView
24TM-1 x 3-79, RIL (2012)AD_ch19_Dt.05N/A22.59BNL3452bView
25TM-1 x 3-79, RIL (2014)AD_ch19_Dt.05N/A160.2BNL3452bView
26Monsanto SSR Bin Map, (2009)AD_ch19_Dt.05N/A221BNL3452bView
27TM-1 x Hai-7124, BC1 (2007)AD_ch05_At.05N/A29.2BNL3452-170View
28TM-1 x Hai-7124, BC1 (2008)AD_ch05_At.05N/A26.14BNL3452-170View
29TM-1 x Hai-7124, BC1 (2012)AD_ch05_At.05N/A183.6BNL3452-170View
30TM-1 x Hai-7124, BC1 (2007)AD_ch19_Dt.05N/A23.7BNL3452-180View
31TM-1 x Hai-7124, BC1 (2008)AD_ch19_Dt.05N/A23.5BNL3452-180View
32Vsg x (TM-1 x Hai-7124), DH (2005)AD_ch19_Dt.05N/A0BNL3452-180View
33TM-1 x Hai-7124, BC1 (2005.v0)AD_ch19_Dt.05N/A15.7BNL3452-180View
34TM-1 x Hai-7124, BC1 (2012)AD_ch19_Dt.05N/A166.8BNL3452-180View
35Vsg x (TM-1 x Hai-7124), DH (2005)AD_ch19_Dt.05N/A26.1BNL3452-195View
36TM-1 x 3-79, RIL (2012.v3)AD_ch05_At.05N/A180.21BNL3452aView
37TM-1 x 3-79, RIL (2012.v3)AD_ch19_Dt.05N/A160.17BNL3452bView
38MGG-293-793, MAGIC (2018)AD_ch19_Dt.05N/A214.1BNL3452View
Sequence
>BNL3452 ID=BNL3452; Name=BNL3452; organism=Gossypium hirsutum; type=genetic_marker; length=191bp
TGTAACTGAGCAGCCGTACGTTCTTCATGATAGAAATTCATTCCATGATT
TGATTTGTTCGACGATGGACACACACACACACACACACACACACATATAT
AATATAATACACTGTAACTTTTGGGAAGGTTTCCTGTGCTGGTCGACAGC
TGGAATTGAACACCGCAACAGGGATCTCACTCTGCTTTGGC