HAU0625, HAU0625 (genetic_marker) gossypium spp

Marker Overview
NameHAU0625
Genbank IDN/A
TypeSSR
SpeciesGossypium spp.
Source TypeEST
Repeat Motif(TG)8
PCR ConditionAnnealing temperature: 57.0
Primer 1HAU0625_F: GCTTACATCCTCCTGCAAGT
Primer 2HAU0625_R: TTGCATGGAAGTAAAGCAAA
Product Length207
Publication[view all]
CommentPrimer data obtained in 2012
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D03chromosomeD03:35476087..35476278 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A03chromosomeA03:16320450..16320724 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018217.1chromosomeCM018217.1:36109536..36109733 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018204.1chromosomeCM018204.1:16056092..16056366 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_02chromosomeD5_02:30085667..30085873 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
Chr01_CRI-A2_v1.0.a1chromosomeChr01_CRI-A2_v1.0.a1:95675715..95675989 +Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_02chromosomeD10_02:34538742..34539018 -Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016615.1chromosomeCM016615.1:81445110..81445406 -Gossypium australe (G2) genome CRI_v1.1n/a
Dt_chr3chromosomeDt_chr3:16003867..16004058 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
At_chr5chromosomeAt_chr5:9510729..9511003 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D03chromosomeD03:29597504..29597695 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A03chromosomeA03:14872027..14872301 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D03chromosomeGhir_D03:35523498..35523689 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A03chromosomeGhir_A03:17169665..17169939 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D03chromosomeD03:37107877..37108068 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A03chromosomeA03:16440443..16440717 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D03chromosomeD03:36462578..36462769 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A03chromosomeA03:16997860..16998134 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D03chromosomeD03:35888304..35888495 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A03chromosomeA03:16266920..16267194 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Dt03chromosomeDt03:31561278..31561475 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold3841supercontigscaffold3841:185462..185736 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold3035supercontigscaffold3035:194590..194787 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D03chromosomeGbar_D03:34523630..34523827 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A03chromosomeGbar_A03:16018801..16019075 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D03chromosomeD03:37103098..37103295 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A03chromosomeA03:16011448..16011722 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017625.1chromosomeCM017625.1:35510556..35510747 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017612.1chromosomeCM017612.1:16405448..16405722 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017651.1chromosomeCM017651.1:39360532..39360723 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017638.1chromosomeCM017638.1:16754360..16754634 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017703.1chromosomeCM017703.1:37061821..37062012 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017690.1chromosomeCM017690.1:16215585..16215859 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D03chromosomeD03:37536542..37536733 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A03chromosomeA03:17324950..17325224 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr02chromosomeChr02:16268209..16268483 -Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr01chromosomeChr01:101563956..101564230 +Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr02chromosomeChr02:32171093..32171299 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_04chromosomeB_04:20637295..20637556 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr03chromosomeChr03:33647609..33647809 -Gossypium thurberi (D1-5) genome CRI_v1n/a
chr03chromosomechr03:21248227..21248502 -Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr03_4591881chromosomeChr03_4591881:3333..3609 -Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr03chromosomeChr03:35457998..35458189 -Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr03chromosomeChr03:18530821..18531096 -Gossypium aridum (D4) genome ISU_v1n/a
Chr03chromosomeChr03:15788687..15788968 -Gossypium gossypioides (D6) genome ISU_v1n/a
Chr03chromosomeChr03:19765942..19766217 -Gossypium lobatum (D7) genome ISU_v1n/a
E02chromosomeE02:63348679..63348953 -Gossypium stocksii (E1) genome NSF_v1n/a
F02chromosomeF02:57314226..57314500 -Gossypium longicalyx (F1) genome NSF_v1n/a
Chr02chromosomeChr02:39763501..39763775 +Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Emian-22 x 3-79, BC1 (2011)AD_ch17_Dt.03N/A77.62HAU0625View
2TM-1 x Hai-7124, BC1 (2012)AD_ch17_Dt.03N/A62.6HAU0625-200View
Sequence
>HAU0625 ID=HAU0625; Name=HAU0625; organism=Gossypium spp.; type=genetic_marker; length=207bp
GCTTACATCCTCCTGCAAGTTTGTCTAATTTTGGTTTCCCTGTTGAAGAT
CATCCTTTCTGGTCTTGGACTTATTAAGTTATATATCTACAATGCAATCC
ATATGTGTGTATGTGTGTATATGTATATGTATATATATAAATTGAGAGAT
CAATCAATGGCACCCCAATCAATGGCACCCTCAATGGTTTGCTTTACTTC
CATGCAA