HAU0921, HAU0921 (genetic_marker) gossypium spp

Marker Overview
NameHAU0921
AliasTA21453_3635
Genbank IDN/A
TypeSSR
SpeciesGossypium spp.
Source TypeEST
Repeat Motif(CCA)5+(GCATCC)4
PCR ConditionAnnealing temperature: 56.8
Primer 1HAU0921_F: TCAAGCAAAATATGGGGTTT
Primer 2HAU0921_R: GGTAAACAGGTGGGTGAGTT
Product Length279
Publication[view all]
CommentPrimer data obtained in 2012
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D06chromosomeD06:47123811..47124077 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A06chromosomeA06:86918371..86918649 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018220.1chromosomeCM018220.1:42349269..42349523 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018207.1chromosomeCM018207.1:78880534..78880812 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_06chromosomeD5_06:40825834..40826094 +Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
KI_06chromosomeKI_06:57043099..57043347 -Gossypioides kirkii genome ISU_v3n/a
D10_06chromosomeD10_06:20161977..20162231 -Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016619.1chromosomeCM016619.1:48610551..48610809 -Gossypium australe (G2) genome CRI_v1.1n/a
Dt_chr10chromosomeDt_chr10:44859439..44859705 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D06chromosomeD06:43306540..43306806 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A06chromosomeA06:73031957..73032235 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D06chromosomeGhir_D06:45800311..45800577 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A06chromosomeGhir_A06:84543351..84543629 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D06chromosomeD06:45284029..45284295 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A06chromosomeA06:87443091..87443369 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D06chromosomeD06:45279599..45279865 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A06chromosomeA06:86067669..86067947 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D06chromosomeD06:42326154..42326420 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A06chromosomeA06:83340132..83340410 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
scaffold7727supercontigscaffold7727:382846..383100 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold16552supercontigscaffold16552:82381..82659 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D06chromosomeGbar_D06:42519615..42519869 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A06chromosomeGbar_A06:77764555..77764833 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D06chromosomeD06:42875155..42875409 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A06chromosomeA06:80927299..80927577 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017628.1chromosomeCM017628.1:43159533..43159799 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017615.1chromosomeCM017615.1:83809809..83810087 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017654.1chromosomeCM017654.1:45485795..45486055 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017641.1chromosomeCM017641.1:86942962..86943222 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017706.1chromosomeCM017706.1:42950029..42950283 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017693.1chromosomeCM017693.1:82064145..82064417 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D06chromosomeD06:45683792..45684058 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A06chromosomeA06:87940348..87940626 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr06chromosomeChr06:87033916..87034182 -Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr06chromosomeChr06:88951612..88951875 -Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr06chromosomeChr06:40597478..40597738 +Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_06chromosomeB_06:34877350..34877616 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr10chromosomeChr10:42814884..42815150 +Gossypium thurberi (D1-5) genome CRI_v1n/a
chr10chromosomechr10:32561860..32562176 +Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr10chromosomeChr10:44350346..44350618 -Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr10chromosomeChr10:23837176..23837500 +Gossypium gossypioides (D6) genome ISU_v1n/a
E06chromosomeE06:37612429..37612694 -Gossypium stocksii (E1) genome NSF_v1n/a
F06chromosomeF06:68670019..68670279 +Gossypium longicalyx (F1) genome NSF_v1n/a
Chr06chromosomeChr06:83988336..83988602 +Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Yumian-1 x T586, RIL (2015)AD_ch06_At.06N/A76.7HAU0921View
2DH962 X Ji Mian 5, F2 (2015)AD_ch06_At.06N/A9.59HAU0921View
3GX1135 x GX100-2, RIL (2015)AD_ch06_At.06N/A38.2HAU0921View
4GX1135 x GX100-2, RIL (2016)AD_ch06_At.06N/A84.5HAU0921View
5GX1135 x VGX100-2, RIL (2016)AD_ch06_At.06N/A66.5HAU0921View
6DH962 x Ji Mian 5, RIL (2015)AD_ch06_At.06N/A36.2HAU0921View
Sequence
>HAU0921 ID=HAU0921; Name=HAU0921; organism=Gossypium spp.; type=genetic_marker; length=279bp
TCAAGCAAAATATGGGGTTTGCAGTAGCAACTAAAGCTGCCTTGCTCCTG
CACCTTTCCCTTTTCGTACTGAGTAGCTTCACGGTGTCTTCTCAGATCTT
GCCTGAGGCTTTGCCTCCTCATTACCATGGAATTTCGCCTGTAGTGCCAC
CTGCTCACCCACCAAGCCACCACCACCACCATCACCATCCCCATCCGCAT
CCGCATCCGCATCCGCATCCGCATCCCCACCAGCCAACCCCTTCCCCTAC
TAAGCCCCCAACTCACCCACCTGTTTACC