HAU0952, HAU0952 (genetic_marker) gossypium spp

Marker Overview
NameHAU0952
AliasTA22312_3635
Genbank IDN/A
TypeSSR
SpeciesGossypium spp.
Source TypeEST
Repeat Motif(AAG)6
PCR ConditionAnnealing temperature: 57.3
Primer 1HAU0952_F: CCAGCCAAATGTAGTGTCAA
Primer 2HAU0952_R: AAATTCCATCCCAAAATCCT
Product Length168
Publication[view all]
CommentPrimer data obtained in 2012
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D02chromosomeD02:4528911..4529197 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A02chromosomeA02:3281701..3281991 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018216.1chromosomeCM018216.1:3905638..3905928 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018203.1chromosomeCM018203.1:3322111..3322398 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_03chromosomeD5_03:59818303..59818593 +Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
KI_03chromosomeKI_03:2763858..2764145 -Gossypioides kirkii genome ISU_v3n/a
Chr03_CRI-A2_v1.0.a1chromosomeChr03_CRI-A2_v1.0.a1:3648380..3648673 -Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_03chromosomeD10_03:64889672..64889962 -Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016616.1chromosomeCM016616.1:148334361..148334654 +Gossypium australe (G2) genome CRI_v1.1n/a
At_chr9chromosomeAt_chr9:4029604..4029891 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
scaffold189.1supercontigscaffold189.1:539313..539599 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
scaffold112574supercontigscaffold112574:24..310 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
D02chromosomeD02:4483776..4484062 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A02chromosomeA02:3176932..3177222 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D02chromosomeGhir_D02:4317599..4317885 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A02chromosomeGhir_A02:3320489..3320779 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D02chromosomeD02:4120615..4120901 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A02chromosomeA02:3178653..3178943 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D02chromosomeD02:4337472..4337758 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A02chromosomeA02:3437898..3438185 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D02chromosomeD02:4258186..4258472 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A02chromosomeA02:3310504..3310794 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Dt02chromosomeDt02:3154456..3154746 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold9852supercontigscaffold9852:113365..113652 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold2354supercontigscaffold2354:574261..574551 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D02chromosomeGbar_D02:4409848..4410138 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A02chromosomeGbar_A02:3257081..3257368 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D02chromosomeD02:4087661..4087950 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A02chromosomeA02:3255141..3255428 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017624.1chromosomeCM017624.1:4713333..4713618 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017611.1chromosomeCM017611.1:3327805..3328101 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017650.1chromosomeCM017650.1:4937337..4937622 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017637.1chromosomeCM017637.1:3366649..3366935 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017702.1chromosomeCM017702.1:4352065..4352355 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017689.1chromosomeCM017689.1:3328600..3328887 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D02chromosomeD02:4439777..4440063 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A02chromosomeA02:3458947..3459237 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr03chromosomeChr03:128315798..128316088 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr03chromosomeChr03:127179272..127179565 +Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr03chromosomeChr03:3707243..3707533 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_03chromosomeB_03:103509564..103509847 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr05chromosomeChr05:4158488..4158784 -Gossypium thurberi (D1-5) genome CRI_v1n/a
chr05chromosomechr05:2965600..2965888 -Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr_05chromosomeChr_05:3542939..3543228 -Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr05chromosomeChr05:4291312..4291608 -Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr05chromosomeChr05:3258094..3258390 -Gossypium aridum (D4) genome ISU_v1n/a
Chr05chromosomeChr05:2547212..2547501 -Gossypium gossypioides (D6) genome ISU_v1n/a
Chr05chromosomeChr05:3561806..3562095 -Gossypium lobatum (D7) genome ISU_v1n/a
F03chromosomeF03:3295707..3295991 -Gossypium longicalyx (F1) genome NSF_v1n/a
Chr03chromosomeChr03:200991496..200991776 +Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1W10 x TM-1, F2:3 (2015)AD_ch02_At.02N/A70.5HAU952View
2CCRI 12-4 x (AD)5-7, F2 (2015)AD_ch14_Dt.02N/A31.1HAU0952View
Sequence
>HAU0952 ID=HAU0952; Name=HAU0952; organism=Gossypium spp.; type=genetic_marker; length=168bp
CCAGCCAAATGTAGTGTCAACATCCCTTACAAGATCAGCACTTCCACTAA
CTGCAAAAATGTGAAGTGAGATGGATGAAGAGAGGGTTTTGCAGCAGCTT
GCAGGAGATAAAATATATGATTAAAAAGAAGAAGAAGAAGAATGAATAAG
GATTTTGGGATGGAATTT