HAU3236, HAU3236 (genetic_marker) gossypium spp

Marker Overview
NameHAU3236
Genbank IDGR716890
TypeSSR
SpeciesGossypium spp.
Source SequenceGR709056.1
Source TypeEST
Repeat Motif(TCT)11
PCR ConditionAnnealing temperature: 55.8
Primer 1HAU3236_F: GCCGTCTGTTGGTGTTCTTGG
Primer 2HAU3236_R: ACACGTCACACCCTTCACCT
Product Length236
Publication[view all]
CommentPrimer data obtained in 2012
Cross References
External references for this genetic_marker
DatabaseAccession
DB:genbankGR716890
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D02chromosomeD02:4757485..4757735 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A02chromosomeA02:3528618..3528835 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018216.1chromosomeCM018216.1:4163831..4164069 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018203.1chromosomeCM018203.1:3566017..3566234 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_03chromosomeD5_03:59583284..59583513 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
KI_03chromosomeKI_03:2968630..2968856 +Gossypioides kirkii genome ISU_v3n/a
Chr03_CRI-A2_v1.0.a1chromosomeChr03_CRI-A2_v1.0.a1:3902423..3902640 +Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_03chromosomeD10_03:60927472..60927701 -Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016616.1chromosomeCM016616.1:148039927..148040150 -Gossypium australe (G2) genome CRI_v1.1n/a
scaffold189.1supercontigscaffold189.1:768027..768277 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
scaffold4267.1supercontigscaffold4267.1:31880..32097 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D02chromosomeD02:4721761..4722011 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A02chromosomeA02:3420091..3420308 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D02chromosomeGhir_D02:4547247..4547497 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A02chromosomeGhir_A02:3566996..3567213 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D02chromosomeD02:4346619..4346869 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A02chromosomeA02:3418445..3418662 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D02chromosomeD02:4566022..4566272 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A02chromosomeA02:3682195..3682412 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D02chromosomeD02:4486770..4487020 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A02chromosomeA02:3557425..3557642 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
scaffold8917supercontigscaffold8917:111733..111968 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold8917supercontigscaffold8917:105579..105796 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold8917supercontigscaffold8917:102630..102847 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold10579supercontigscaffold10579:113316..113533 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D02chromosomeGbar_D02:4667939..4668171 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A02chromosomeGbar_A02:3492425..3492642 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D02chromosomeD02:4303316..4303548 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A02chromosomeA02:3488805..3489022 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017624.1chromosomeCM017624.1:4939044..4939279 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017611.1chromosomeCM017611.1:3566665..3566882 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017650.1chromosomeCM017650.1:5203871..5204106 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017637.1chromosomeCM017637.1:3615320..3615537 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017702.1chromosomeCM017702.1:4594891..4595129 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017689.1chromosomeCM017689.1:3559475..3559692 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D02chromosomeD02:4668354..4668604 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A02chromosomeA02:3705868..3706085 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr03chromosomeChr03:128040556..128040773 -Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr03chromosomeChr03:3941917..3942146 +Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_03chromosomeB_03:103198379..103198602 -Gossypium anomalum (B1) genome NSF_v1n/a
Chr05chromosomeChr05:4376903..4377123 +Gossypium thurberi (D1-5) genome CRI_v1n/a
chr05chromosomechr05:3189564..3190653 +Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr_05chromosomeChr_05:3790865..3791085 +Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr05chromosomeChr05:4516075..4516304 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr05chromosomeChr05:3559453..3559673 +Gossypium aridum (D4) genome ISU_v1n/a
Chr05chromosomeChr05:2724855..2725081 +Gossypium gossypioides (D6) genome ISU_v1n/a
Chr05chromosomeChr05:3789824..3790053 +Gossypium lobatum (D7) genome ISU_v1n/a
E03chromosomeE03:5464828..5465054 +Gossypium stocksii (E1) genome NSF_v1n/a
F03chromosomeF03:3587978..3588201 +Gossypium longicalyx (F1) genome NSF_v1n/a
Chr03chromosomeChr03:200652816..200653033 -Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Chr05chromosomeHAU3236:1..877 .
Chr05:3929306..3930178 +		n/a
Chr5chromosomeHAU3236:1..877 .
Chr5:1265941..1266813 -		n/a
Relationships

The following sequence_feature feature(s) derives from this genetic_marker:

Feature NameUnique NameSpeciesType
GR709056.1GR709056.1Gossypium spp.sequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Emian-22 x 3-79, BC1 (2011)AD_ch14_Dt.02N/A84.73HAU3236View
2TM-1 x (TX-0256 + TX-1046), CSIL (2016)AD_ch14_Dt.02N/A9.9HAU3236View
3CCRI-35 x Yumian-1, RIL (2015)AD_ch03_At.03N/A38.1HAU3236View
4CCRI-35 x Yumian-1, RIL (2017)AD_ch03_At.03N/A34.25HAU3236View
5TM-1 x Hai-7124, BC1 (2012)AD_ch14_Dt.02N/A16.9HAU3236-230View
Sequence
>HAU3236 ID=HAU3236; Name=HAU3236; organism=Gossypium spp.; type=genetic_marker; length=236bp
GCCGTCTGTTGGTGTTCTTGGCTTCTTTCTTGCTGCTGTTTGTGTGATTT
GTTGTTTCTTTTACTTGGATTATAGAGCTGTGGTTAAAGGGTACAGGGTT
CCAACTCAGTCAGATAGATTCATGTGGCTTAAACTAGATGGGTCTTCTTC
TTCTTCTTCTTCTTCTTCTTCTTCTTCAAGTGATATTGTCAAAAGAGTTG
ATTTCTTGAGTTTTGAAGGTGAAGGGTGTGACGTGT