CSIRO_D5chr07_54556289 (genetic_marker) Gossypium hirsutum

Marker Overview
NameCSIRO_D5chr07_54556289
AliasChr07_54556289
dbSNP IDN/A
TypeSNP
SNP AllelesC/G
5' Flanking SequenceGCAGCACCAGCACCAGTCAACCCACTACCTACACCAGCACCACTCAACCTACCATATCGA GTTGAACCTGGTCCACCATATGGACCACCAAGTCCAGAAC
3' Flanking SequenceATGCCCACCAGCACCCCCTACATTGCCACCCAAAACACCCACCCCAACTCCTGATGAATT CAAATGATGAGGGTGATTCATTTATAGGAATATTATTTTG
SpeciesGossypium hirsutum
GermplasmSiokra 1-4
MCU-5 (PI 694627)
Source Typerestriction-site associated DNA
RNA-seq and restriction-site associated DNA
Restriction EnzymeEcoRI; ApekI; SbfI
Publication[view all]
ContactZhu, Qian-Hao
Wilson, Iain
CommentData obtained 2014. SNP location is based on D5 JGI 221 position
Contact
NameDetails
Zhu, Qian-Hao
First name:Qian-Hao
Last name:Zhu
Title:Research Scientist
Institution:CSIRO
Address:CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601,
Country:Australia
Email:Qianhao.Zhu@csiro.au
Phone:61 2 62464903
Last update:24-Aug-2014
Wilson, Iain
Description:SNPs; Disease resistance
First name:Iain
Last name:Wilson
Title:Senior Scientist
Institution:CSIRO
Address:Black Mountain Laboratories Clunies Ross Street, Black Mountain, ACT 2601
Country:Australia
Email:iain.wilson@csiro.au
Phone:+61 (0)2 62465211
Last update:28-Feb-2010
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D5_11chromosomeD5_11:6184062..6184261 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
Chr11_CRI-A2_v1.0.a1chromosomeChr11_CRI-A2_v1.0.a1:8173984..8174184 -Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
At_chr1chromosomeAt_chr1:980142..980342 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D11chromosomeD11:60419282..60419483 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A11chromosomeA11:86491101..86491301 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D11chromosomeGhir_D11:65677546..65677747 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A11chromosomeGhir_A11:116113969..116114169 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D11chromosomeD11:64656100..64656301 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A11chromosomeA11:114533678..114533878 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A11chromosomeA11:112250590..112250790 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D11chromosomeD11:62275505..62275706 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A11chromosomeA11:109043807..109044007 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A11chromosomeA11:108519373..108519575 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017620.1chromosomeCM017620.1:114025952..114026152 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017646.1chromosomeCM017646.1:118786325..118786525 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017711.1chromosomeCM017711.1:62056912..62057113 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017698.1chromosomeCM017698.1:107604472..107604672 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D11chromosomeD11:65445001..65445202 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A11chromosomeA11:117819251..117819451 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr11chromosomeChr11:123660846..123661046 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr11chromosomeChr11:121419585..121419785 +Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr11chromosomeChr11:4119449..4119649 +Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
Chr07chromosomeChr07:39460711..39460911 +Gossypium aridum (D4) genome ISU_v1n/a
Chr07chromosomeChr07:42063710..42063910 +Gossypium lobatum (D7) genome ISU_v1n/a
Germplasm
Stock NameType
Siokra 1-4accession
MCU-5 (PI 694627)accession
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1MCU-5 x Siokra 1-4, RIL (2015 SNP)AD_ch11_At.11N/A51.44Chr07_54556289View
Sequence
>CSIRO_D5chr07_54556289 ID=CSIRO_D5chr07_54556289; Name=CSIRO_D5chr07_54556289; organism=Gossypium hirsutum; type=genetic_marker; length=205bp
GCAGCACCAGCACCAGTCAACCCACTACCTACACCAGCACCACTCAACCT
ACCATATCGAGTTGAACCTGGTCCACCATATGGACCACCAAGTCCAGAAC
[C/G]ATGCCCACCAGCACCCCCTACATTGCCACCCAAAACACCCACCCC
AACTCCTGATGAATTCAAATGATGAGGGTGATTCATTTATAGGAATATTA
TTTTG