COT043, COT043 (genetic_marker) Gossypium hirsutum

Marker Overview
NameCOT043
Genbank IDGQ393132
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 20
Source SequenceMONCS1406
Source Typegenomic
Primer 1COT043_F: GAAACAATAATCATAGACACA
Primer 2COT043_R: GACATTGTAAGTTAAGTTGGT
Publication[view all]
ContactMonsanto
CommentPrimer data obtained in 2009-05
Contact
NameDetails
Monsanto
Country:United States
Cross References
External references for this genetic_marker
DatabaseAccession
DB:genbankGQ393132
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
A13chromosomeA13:46904163..46904399 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A02chromosomeA02:42672911..42673155 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018214.1chromosomeCM018214.1:47872880..47873126 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018203.1chromosomeCM018203.1:41185485..41185711 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
Chr01_CRI-A2_v1.0.a1chromosomeChr01_CRI-A2_v1.0.a1:85246027..85246258 +Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
At_chr3chromosomeAt_chr3:23931776..23932020 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
At_chr13chromosomeAt_chr13:49760737..49760973 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
scaffold3576_A13supercontigscaffold3576_A13:297236..297472 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A02chromosomeA02:39963485..39963729 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_A13chromosomeGhir_A13:47783589..47783825 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A10chromosomeGhir_A10:54857936..54858138 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A05chromosomeGhir_A05:78817420..78817622 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A05chromosomeGhir_A05:84127656..84127860 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A03chromosomeGhir_A03:42244651..42244855 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A02chromosomeGhir_A02:43886392..43886632 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
A13chromosomeA13:50305946..50306182 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A04chromosomeA04:69526250..69526538 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A02chromosomeA02:42114155..42114399 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A13chromosomeA13:48550371..48550607 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A04chromosomeA04:66494011..66494295 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A02chromosomeA02:42388672..42388914 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A13chromosomeA13:47316972..47317206 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A04chromosomeA04:62076208..62076496 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A02chromosomeA02:41847752..41847990 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Dt10chromosomeDt10:33048559..33048763 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
At05chromosomeAt05:74374635..74374839 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold7743supercontigscaffold7743:155040..155266 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold6628supercontigscaffold6628:80565..80767 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold4108supercontigscaffold4108:137184..137430 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold3950supercontigscaffold3950:43685..43876 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold3876supercontigscaffold3876:449098..449302 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold3193supercontigscaffold3193:19404..19609 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold3125supercontigscaffold3125:58184..58390 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold3013supercontigscaffold3013:185492..185694 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold24053supercontigscaffold24053:33833..34037 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold10543supercontigscaffold10543:125277..125481 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_A13chromosomeGbar_A13:48407844..48408090 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A08chromosomeGbar_A08:76606481..76606677 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A05chromosomeGbar_A05:73828010..73828214 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A05chromosomeGbar_A05:79206016..79206220 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A03chromosomeGbar_A03:38393091..38393295 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A02chromosomeGbar_A02:41733108..41733334 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
A13chromosomeA13:50981933..50982177 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A02chromosomeA02:42140955..42141181 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017622.1chromosomeCM017622.1:50172564..50172798 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017611.1chromosomeCM017611.1:41404076..41404306 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017700.1chromosomeCM017700.1:49622945..49623189 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017689.1chromosomeCM017689.1:41937196..41937420 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
A13chromosomeA13:50209322..50209558 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A02chromosomeA02:43265485..43265729 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr13chromosomeChr13:68961835..68962091 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr02chromosomeChr02:26865721..26865947 -Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr01chromosomeChr01:91160565..91160798 +Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Germplasm
Stock NameType
Deltapine 20accession
Relationships

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

Feature NameUnique NameSpeciesType
MONCS1406MONCS1406Gossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1TM-1 x 3-79, RIL (2014)AD_ch02_At.02N/A62.8COT043View
2GX1135 x GX100-2, F2 (2013)AD_ch02_At.02N/A72.9COT043View
3CCRI 12-4 x (AD)5-7, F2 (2015)AD_ch02_At.02N/A92.9COT043View
4Monsanto SSR Bin Map, (2009)AD_ch02_At.02N/A61COT043View
5LMY22 x LY343, RIL (2016)chr.2N/A47.4COT043View
6TM-1 x 3-79, RIL (2012.v3)AD_ch02_At.02N/A62.84COT043View
7TM-1 x Hai-7124, BC1 (2012)AD_ch02_At.02N/A49cot043-230View
Sequence
>COT043 ID=COT043; Name=COT043; organism=Gossypium hirsutum; type=genetic_marker; length=241bp
GAAACAATAATCATAGACACACACACACACACACACACACACACACACAC
ACACACATATATATATATAAACATTAGTAACATAGCATAGATTTACTTAT
GTGTTATTCTAAACTCATAGATATAACTCAAATTTGTAAGCATAACTTAC
ACATTTTCAATTTTACCAAAATTTCATCACATATTGAGATCATACATGAG
AGTTTATCGTACATACCTATACCAACTTAACTTACAATGTC