CSIRO_D5s15_43693, CSIRO_D5s15_43693 (genetic_marker) Gossypium hirsutum

Marker Overview


Name	CSIRO_D5s15_43693
Alias	scaffold_15_43693
dbSNP ID	N/A
Type	SNP
SNP Alleles	A/G
5' Flanking Sequence	GTTTCTTCTTGGGGAGCAAAAAGAAATGAAGAAGGCTTCCGTTTTAAGCTTGGAGTAAGC CTGAGCTCTACGCTGTTGAATTTCAAGGAATTTGCGAAGT
3' Flanking Sequence	AATTGAGAATTTCATTGCTTTTACTGCAATTGCTGTTTTCTTGTTCAATCTCCATTGAGT CTTTTATTGAAACCTTCTTCTCAAAATCTTCCATTCCTTT
Species	Gossypium hirsutum
Germplasm	Namcala Sicala 40 Sicot 81 Sicala V-2 Sicot 71 Sicala 3-2 Lu Mian 14 Deltapine 90 Coker 315 Tamcot SP37 Delta Opal Sicot 70 Sicot 189 Siokra 1-4 Riverina Paplar Deltapine 16 MCU-5 (PI 694627)
Source Type	RNA-seq
Publication	[view all]
Contact	Zhu, Qian-Hao Wilson, Iain
Comment	SNP location is based on D5 JGI 221 position. was missed in 2014 dataset and added in May 2016.

Contact

Name

Details

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


Aligned Feature	Feature Type	Alignment Location
CM018220.1	chromosome	CM018220.1:58097397..58097597 -
D5_06	chromosome	D5_06:56309079..56309279 -
D10_06	chromosome	D10_06:4840377..4840577 +
D06	chromosome	D06:59201595..59201795 -
Ghir_D06	chromosome	Ghir_D06:61740718..61740918 -
D06	chromosome	D06:60660759..60660959 -
D06	chromosome	D06:61010479..61010679 -
D06	chromosome	D06:58202854..58203054 -
Gbar_D06	chromosome	Gbar_D06:58219560..58219760 -
D06	chromosome	D06:58226140..58226340 -
CM017628.1	chromosome	CM017628.1:58705125..58705325 -
CM017654.1	chromosome	CM017654.1:61659210..61659410 -
CM017706.1	chromosome	CM017706.1:58746318..58746518 -
D06	chromosome	D06:61749536..61749736 -
Chr06	chromosome	Chr06:55942715..55942915 -
scaffold_15	chromosome	scaffold_15:8303..8503 +
scaffold_15	chromosome	scaffold_15:12177..12377 +
scaffold_15	chromosome	scaffold_15:11669..11869 +

Publications


Year	Publication
2014	Zhu QH, Spriggs A, Taylor JM, Llewellyn D, Wilson I. Transcriptome and Complexity-Reduced-DNA Based Identification of Intraspecies Single Nucleotide Polymorphisms in the Polyploid Gossypium hirsutum L. G3 (Bethesda, Md.). 2014 Aug 7.

Germplasm


Stock Name	Type
Namcala	accession
Sicala 40	accession
Sicot 81	accession
Sicala V-2	accession
Sicot 71	accession
Sicala 3-2	accession
Lu Mian 14	accession
Deltapine 90	accession
Coker 315	accession
Tamcot SP37	accession
Delta Opal	accession
Sicot 70	accession
Sicot 189	accession
Siokra 1-4	accession
Riverina Paplar	accession
Deltapine 16	accession
MCU-5 (PI 694627)	accession

Map Positions


#	Map Name	Linkage Group	Bin	Position	Locus	MapViewer
1	MCU-5 x Siokra 1-4, RIL (2015 SNP)	AD_ch06_At.06	N/A	83.38	scaffold_15_43693	View

Sequence

>CSIRO_D5s15_43693 ID=CSIRO_D5s15_43693; Name=CSIRO_D5s15_43693; organism=Gossypium hirsutum; type=genetic_marker; length=205bp
GTTTCTTCTTGGGGAGCAAAAAGAAATGAAGAAGGCTTCCGTTTTAAGCT
TGGAGTAAGCCTGAGCTCTACGCTGTTGAATTTCAAGGAATTTGCGAAGT
[A/G]AATTGAGAATTTCATTGCTTTTACTGCAATTGCTGTTTTCTTGTT
CAATCTCCATTGAGTCTTTTATTGAAACCTTCTTCTCAAAATCTTCCATT
CCTTT

Search form

CSIRO_D5s15_43693, CSIRO_D5s15_43693 (genetic_marker) Gossypium hirsutum