HAU0916, HAU0916 (genetic_marker) gossypium spp

Marker Overview
NameHAU0916
AliasTA21336_3635
Genbank IDN/A
TypeSSR
SpeciesGossypium spp.
Source TypeEST
Repeat Motif(AAG)6
PCR ConditionAnnealing temperature: 57.1
Primer 1HAU0916_F: CACCAATGGCAAATACAAGA
Primer 2HAU0916_R: TGTTACAATGGGAGCAGTTG
Product Length274
Publication[view all]
CommentPrimer data obtained in 2012
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
A07chromosomeA07:13303510..13303783 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A07chromosomeA07:13285688..13285953 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018221.1chromosomeCM018221.1:10841653..10841929 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018208.1chromosomeCM018208.1:13795212..13795485 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018208.1chromosomeCM018208.1:13765447..13765712 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
KI_07chromosomeKI_07:30259785..30260050 -Gossypioides kirkii genome ISU_v3n/a
KI_07chromosomeKI_07:30267494..30267763 -Gossypioides kirkii genome ISU_v3n/a
tig00004541_CRI-A2_v1.0.a1chromosometig00004541_CRI-A2_v1.0.a1:56522..56986 -Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
tig00004541_CRI-A2_v1.0.a1chromosometig00004541_CRI-A2_v1.0.a1:86492..86757 -Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
CM016620.1chromosomeCM016620.1:97181297..97181570 -Gossypium australe (G2) genome CRI_v1.1n/a
At_chr9chromosomeAt_chr9:16567062..16567335 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
A07chromosomeA07:12791518..12791791 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A07chromosomeA07:12773694..12773959 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_A07chromosomeGhir_A07:13854134..13854407 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A07chromosomeGhir_A07:13836328..13836593 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
A07chromosomeA07:13211950..13212223 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A07chromosomeA07:13195752..13196017 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A07chromosomeA07:13807800..13808073 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A07chromosomeA07:13789978..13790243 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A07chromosomeA07:13744066..13744339 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A07chromosomeA07:13726244..13726509 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
scaffold2179supercontigscaffold2179:52128..52401 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold2179supercontigscaffold2179:75459..75727 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D07chromosomeGbar_D07:11246145..11246421 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A07chromosomeGbar_A07:13863415..13863688 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A07chromosomeGbar_A07:13840601..13840866 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D07chromosomeD07:10982981..10983263 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A07chromosomeA07:13614648..13614921 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A07chromosomeA07:13592798..13593063 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017616.1chromosomeCM017616.1:13529773..13530046 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017616.1chromosomeCM017616.1:13511928..13512193 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017642.1chromosomeCM017642.1:13577626..13577899 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017642.1chromosomeCM017642.1:13559826..13560091 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017694.1chromosomeCM017694.1:13780336..13780609 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017694.1chromosomeCM017694.1:13757520..13757785 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
A07chromosomeA07:13959228..13959501 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A07chromosomeA07:13941406..13941671 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr07chromosomeChr07:14543673..14544138 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr07chromosomeChr07:14514649..14514914 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr07chromosomeChr07:14736172..14736636 +Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr07chromosomeChr07:14706348..14706613 +Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
B_07chromosomeB_07:13996039..13996312 +Gossypium anomalum (B1) genome NSF_v1n/a
B_07chromosomeB_07:14030584..14030857 +Gossypium anomalum (B1) genome NSF_v1n/a
B_07chromosomeB_07:14011355..14011627 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr01chromosomeChr01:11085165..11085441 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr01_3437362chromosomeChr01_3437362:1308..1579 -Gossypium gossypioides (D6) genome ISU_v1n/a
E07chromosomeE07:77297992..77298461 -Gossypium stocksii (E1) genome NSF_v1n/a
E07chromosomeE07:77316550..77316815 -Gossypium stocksii (E1) genome NSF_v1n/a
F07chromosomeF07:12901789..12902254 +Gossypium longicalyx (F1) genome NSF_v1n/a
F07chromosomeF07:12881265..12881530 +Gossypium longicalyx (F1) genome NSF_v1n/a
Chr07chromosomeChr07:22593919..22594192 +Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
10-153 x sGK9708, RIL (2015)AD_ch25_Dt.06N/A60.85HAU916View
20-153 x sGK9708, RIL (2016)AD_ch16_Dt.07N/A63.7HAU916aView
30-153 x sGK9708, RIL (2016)AD_ch25_Dt.06N/A117HAU916bView
Sequence
>HAU0916 ID=HAU0916; Name=HAU0916; organism=Gossypium spp.; type=genetic_marker; length=274bp
CACCAATGGCAAATACAAGAGCGTGGAGCACAGGGTGATTGCCCAAACCG
ACGGGGCTCGCATGTCGATAGCTTCGTTCTATAACCCCGGCAGCGACGCC
ATTATCTACCCGGCGCCGGCCCTGGTGGAGAAAGAAGAAGAAGAGAAGAA
AGGATTGTACCCAAAATTTGTGTTCGAAGATTACATGAAGCTTTACGCAG
TGCTTAAACTCCAGGCCAAGGAGCCCAGGTTTGAAGCCATGAAAGCCAGG
GAAGCAACTGCTCCCATTGTAACA