MUCS0425, MUCS0425 (genetic_marker) Gossypium arboreum

Marker Overview
NameMUCS0425
AliasMUCS425
Genbank IDN/A
TypeSSR
SpeciesGossypium arboreum
GermplasmAKA 8401
Source TypeEST
Repeat MotifAGGAA(2)CCT(2)
PCR ConditionAnnealing temperature: 55
Primer 1MUCS425_F: CCATCTCTTTCGCTATCTGC
Primer 2MUCS425_R: ACGGCTCTCCTCTTTCTGC
Product Length298
ContactUlloa, Mauricio
CommentPrimer data obtained in 2007-11
Contact
NameDetails
Ulloa, Mauricio
Description:Breeding, genetics, and Genomics
First name:Mauricio
Last name:Ulloa
Title:Research Geneticist
Institution:USDA-ARS, W.I.C.S., Res. Unit
Address:17053 N. Shafter Ave., Shafter, California 93263
Country:United States
Email:mauricio.ulloa@usda.gov
Phone:661-746-8009
Fax:746-746-1619
Keywords:Breeding and Genomics
Last update:27-Apr-2010
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D05chromosomeD05:20945527..20945824 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A05chromosomeA05:22739318..22739615 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018219.1chromosomeCM018219.1:19781428..19781725 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018206.1chromosomeCM018206.1:21802759..21803056 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_05chromosomeD5_05:18547171..18547468 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
KI_05chromosomeKI_05:16698595..16698892 -Gossypioides kirkii genome ISU_v3n/a
Chr05_CRI-A2_v1.0.a1chromosomeChr05_CRI-A2_v1.0.a1:22306552..22306849 -Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_05chromosomeD10_05:41772733..41773030 +Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016618.1chromosomeCM016618.1:90128455..90128752 +Gossypium australe (G2) genome CRI_v1.1n/a
At_chr9chromosomeAt_chr9:38893979..38894276 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
Dt_chr9chromosomeDt_chr9:48020277..48020574 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
scaffold72077supercontigscaffold72077:85..382 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
D05chromosomeD05:20162036..20162333 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A05chromosomeA05:20126792..20127089 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A05chromosomeA05:20121217..20121514 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D05chromosomeGhir_D05:20261995..20262291 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A05chromosomeGhir_A05:22334382..22334679 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D05chromosomeD05:19796569..19796866 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A05chromosomeA05:21686063..21686360 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D05chromosomeD05:20111889..20112186 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A05chromosomeA05:22367164..22367461 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D05chromosomeD05:19988455..19988752 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A05chromosomeA05:22532089..22532386 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
At05chromosomeAt05:17269734..17270031 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
At05chromosomeAt05:17261695..17261992 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold9514supercontigscaffold9514:108347..108644 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold1798supercontigscaffold1798:191578..191875 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold1798supercontigscaffold1798:183539..183836 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D05chromosomeGbar_D05:20144264..20144561 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A05chromosomeGbar_A05:21471571..21471868 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D05chromosomeD05:20150845..20151142 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A05chromosomeA05:22162761..22163058 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017627.1chromosomeCM017627.1:19970691..19970988 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017614.1chromosomeCM017614.1:21960485..21960782 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017653.1chromosomeCM017653.1:20418720..20419017 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017640.1chromosomeCM017640.1:22309111..22309408 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017705.1chromosomeCM017705.1:20090077..20090374 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017692.1chromosomeCM017692.1:21694720..21695017 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D05chromosomeD05:20572770..20573067 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A05chromosomeA05:22706986..22707283 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr05chromosomeChr05:23816221..23816517 -Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr05chromosomeChr05:22219003..22219300 -Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr05chromosomeChr05:18625530..18625827 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_05chromosomeB_05:64146522..64146819 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr09chromosomeChr09:19256531..19256827 -Gossypium thurberi (D1-5) genome CRI_v1n/a
chr09chromosomechr09:17211357..17212027 -Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr_09chromosomeChr_09:16011542..16011839 -Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr09chromosomeChr09:19900591..19900891 -Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr09chromosomeChr09:16288787..16289084 -Gossypium aridum (D4) genome ISU_v1n/a
Chr09chromosomeChr09:14286584..14286884 -Gossypium gossypioides (D6) genome ISU_v1n/a
Chr09chromosomeChr09:16585800..16586097 -Gossypium lobatum (D7) genome ISU_v1n/a
E05chromosomeE05:24159434..24159734 -Gossypium stocksii (E1) genome NSF_v1n/a
F05chromosomeF05:19132705..19133002 -Gossypium longicalyx (F1) genome NSF_v1n/a
Chr05chromosomeChr05:108516685..108516982 +Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Chr09chromosomeMUCS0425:14..605 .
Chr09:18508830..18509421 -		n/a
Chr9chromosomeMUCS0425:14..605 .
Chr9:25313774..25314365 +		n/a
Germplasm
Stock NameType
AKA 8401accession
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1JLZM x ZJXSLS, F2 (2008)A_JZ_A01N/A15.7MUCS425View
Sequence
>MUCS0425 ID=MUCS0425; Name=MUCS0425; organism=Gossypium arboreum; type=genetic_marker; length=298bp
CCATCTCTTTCGCTATCTGCCTTTTCCCTTTCTCTCTATCTGATTCCTAT
CGACAATGGCCGCCGCCGCCACTTCTTCACCCCGCGAGGAAAATGTCTAC
ATGGCGAAACTCGCCGAGCAAGCCGAACGCTACGAGGAAATGGTTGAGTT
CATGGAGAAAGTCTCTGCCTCCGCCGACAACGAGGAGCTCACCGTCGAGG
AAAGGAACCTCCTCTCCGTCGCTTACAAGAATGTTATCGGCGCTCGCCGT
GCTTCCTGGCGCATCATTTCCTCCATTGAGCAGAAAGAGGAGAGCCGT